Add MGnify amplicon pipeline #343

RZ9082 · 2024-02-25T22:28:01Z

WIP!

github-actions · 2024-02-25T22:57:39Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	3
Passed	0
Error	3
Failure	0
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: clan info file:
- step_state: scheduled

Step 11: SSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 12: LSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 13: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "2122be51d42f11eeb07c4bb58c2faeb8"
      
      input {"values": [{"id": 12, "src": "hdca"}]}
Step 14: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "2122be51d42f11eeb07c4bb58c2faeb8"
      
      input {"values": [{"id": 13, "src": "hdca"}]}

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpuviwuegg/job_working_directory/000/27/configs/tmp1in469vx' '/tmp/tmpuviwuegg/job_working_directory/000/27/outputs/dataset_f5bdcc75-b973-43ad-8b5e-1b457ece22f7.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 15, "src": "hdca"}]}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpuviwuegg/job_working_directory/000/28/configs/tmpqqj9unma' '/tmp/tmpuviwuegg/job_working_directory/000/28/outputs/dataset_35ea5c9b-4cff-4ebb-beda-141c963e31bc.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 16, "src": "hdca"}]}`

Step 18: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "2122be51d42f11eeb07c4bb58c2faeb8"
      
      input {"values": [{"id": 14, "src": "hdca"}]}

Step 19: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 31, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 20: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 32, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: covariance models:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpuviwuegg/job_working_directory/000/30/configs/tmpe2gn5y20' '/tmp/tmpuviwuegg/job_working_directory/000/30/outputs/dataset_5e908376-b96b-4ced-aefe-9e833ee58330.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: Unlabelled step:
- step_state: scheduled
Step 23: Unlabelled step:
- step_state: scheduled

Step 24: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 33, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 25: Unlabelled step:
- step_state: scheduled
Step 26: Unlabelled step:
- step_state: scheduled
Step 27: Unlabelled step:
- step_state: scheduled
Step 28: HDF5 SSU SILVA:
- step_state: scheduled
Step 29: JSON SSU SILVA:
- step_state: scheduled

Step 30: Krona SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1708901776_9530842_23393.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1708901776_9062724_87886.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 27, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpuviwuegg/files/5/8/d/dataset_58dd43f2-7546-458a-afca-174e5420f4d4.dat '/tmp/tmpuviwuegg/files/5/5/b/dataset_55b4fb86-6e00-4951-9b84-08aea0dd2b85.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpuviwuegg/job_working_directory/000/5/outputs/dataset_4b5aa769-fa80-42c0-93aa-0fa148315242.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpuviwuegg/files/5/8/d/dataset_58dd43f2-7546-458a-afca-174e5420f4d4.dat '/tmp/tmpuviwuegg/files/8/5/0/dataset_850bb749-f7f3-46c2-b5b2-01e5e80ae672.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpuviwuegg/job_working_directory/000/6/outputs/dataset_9784152c-cc1a-4fa2-b700-f75850778686.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 31: HDF5 LSU SILVA:
- step_state: scheduled
Step 32: JSON LSU SILVA:
- step_state: scheduled

Step 33: Krona LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1708901777_0252702_55152.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1708901776_9062724_87886.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 31, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 34: Unlabelled step:
- step_state: scheduled
Step 35: Unlabelled step:
- step_state: scheduled
Step 36: HDF5 ITSonedb:
- step_state: scheduled
Step 37: JSON ITSonedb:
- step_state: scheduled

Step 38: Krona ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1708901779_0853024_86165.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1708901776_9062724_87886.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 39: HDF5 ITS UNITE:
- step_state: scheduled
Step 40: JSON ITS UNITE:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpuviwuegg/files/3/7/1/dataset_37177514-50f4-41da-ac12-5bb53d9b0625.dat' clan_info && ln -s '/tmp/tmpuviwuegg/files/4/b/5/dataset_4b5aa769-fa80-42c0-93aa-0fa148315242.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpuviwuegg/job_working_directory/000/7/outputs/dataset_7722b91a-daab-4fbb-8921-e041678fa03f.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpuviwuegg/files/3/7/1/dataset_37177514-50f4-41da-ac12-5bb53d9b0625.dat' clan_info && ln -s '/tmp/tmpuviwuegg/files/9/7/8/dataset_9784152c-cc1a-4fa2-b700-f75850778686.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpuviwuegg/job_working_directory/000/8/outputs/dataset_5e64d0e6-3e2f-4828-a256-fc845354f75f.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 41: Krona ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1708901779_1666958_45872.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpuviwuegg/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1708901776_9062724_87886.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 46, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmpuviwuegg/job_working_directory/000/9/configs/tmp1wolok23' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpuviwuegg/job_working_directory/000/9/configs/tmphsv91ug3' -Q '/tmp/tmpuviwuegg/job_working_directory/000/9/configs/tmp1wolok23'   --no_header   -o '/tmp/tmpuviwuegg/job_working_directory/000/9/outputs/dataset_30fe24cf-a09a-4ff5-834e-97b976c6e2b1.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpuviwuegg/files/7/7/2/dataset_7722b91a-daab-4fbb-8921-e041678fa03f.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': '', 'result_file': 'results1.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": ""}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}]}`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is error

Command Line:

cat '/tmp/tmpuviwuegg/job_working_directory/000/10/configs/tmpaz6j4vuz' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpuviwuegg/job_working_directory/000/10/configs/tmpp85x76re' -Q '/tmp/tmpuviwuegg/job_working_directory/000/10/configs/tmpaz6j4vuz'   --no_header   -o '/tmp/tmpuviwuegg/job_working_directory/000/10/outputs/dataset_096e5126-2b48-433a-bdab-1e783dce9c7c.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpuviwuegg/files/5/e/6/dataset_5e64d0e6-3e2f-4828-a256-fc845354f75f.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': '', 'result_file': 'results1.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": ""}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}]}`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Step 7: SSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 8: SSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Step 9: LSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 10: LSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2122be51d42f11eeb07c4bb58c2faeb8"`
chromInfo	`"/tmp/tmpuviwuegg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - dc6df82647936543
- history_state
  - error
- invocation_id
  - dc6df82647936543
- invocation_state
  - scheduled
- workflow_id
  - dc6df82647936543

❌ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  mkdir -p ~/.ncbi && cp '/tmp/tmpe170i9hz/job_working_directory/000/1/configs/tmp0nq9cdvc' ~/.ncbi/user-settings.mkfg &&   export SRA_PREFETCH_RETRIES=3 && export SRA_PREFETCH_ATTEMPT=1 &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&  while [ $SRA_PREFETCH_ATTEMPT -le $SRA_PREFETCH_RETRIES ] ; do fasterq-dump "$acc" -e ${GALAXY_SLOTS:-1} --seq-defline '@$sn[_$rn]-$ri' --qual-defline '+' --split-3 --skip-technical 2>&1 | tee -a '/tmp/tmpe170i9hz/job_working_directory/000/1/outputs/dataset_7be390de-1e54-4970-a7ae-69001df5f380.dat'; if [ $? == 0 ] && [ $(ls *.fastq | wc -l) -ge 1 ]; then break ; else echo "Prefetch attempt $SRA_PREFETCH_ATTEMPT of $SRA_PREFETCH_RETRIES exited with code $?" ; SRA_PREFETCH_ATTEMPT=`expr $SRA_PREFETCH_ATTEMPT + 1` ; sleep 1 ; fi ; done && mkdir -p output && mkdir -p outputOther && count="$(ls *.fastq | wc -l)" && echo "There are $count fastq files" && data=($(ls *.fastq)) && if [ "$count" -eq 1 ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${data[0]}" > output/"${acc}"__single.fastqsanger.gz && rm "${data[0]}"; elif [ "--split-3" = "--split-3" ]; then if [ -e "${acc}".fastq ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${acc}".fastq > outputOther/"${acc}"__single.fastqsanger.gz; fi && pigz -cqp ${GALAXY_SLOTS:-1} "${acc}"_1.fastq > output/"${acc}"_forward.fastqsanger.gz && pigz -cqp ${GALAXY_SLOTS:-1} "${acc}"_2.fastq > output/"${acc}"_reverse.fastqsanger.gz && rm "${acc}"*.fastq; elif [ "$count" -eq 2 ]; then pigz -cqp ${GALAXY_SLOTS:-1} "${data[0]}" > output/"${acc}"_forward.fastqsanger.gz && pigz -cqp ${GALAXY_SLOTS:-1} "${data[1]}" > output/"${acc}"_reverse.fastqsanger.gz && rm "${data[0]}" && rm "${data[1]}"; else for file in ${data[*]}; do pigz -cqp ${GALAXY_SLOTS:-1} "$file" > outputOther/"$file"sanger.gz && rm "$file"; done; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Output:

Downloading accession: DRR218540...
spots read      : 67,485
reads read      : 134,970
reads written   : 134,970
There are 2 fastq files
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
adv	`{"minlen": null, "seq_defline": "@$sn[_$rn]-$ri", "skip_technical": true, "split": "--split-3"}`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "fb6ff3b4d42e11ee8a08df3b9fc2b9ae"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpe170i9hz/files/9/f/3/dataset_9f32579a-d8b2-490b-86bc-872dd57b7fbc.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmpe170i9hz/files/b/e/a/dataset_beadee15-af27-4748-8747-88c4a3047c63.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmpe170i9hz/job_working_directory/000/3/outputs/dataset_42e07f1d-5b1b-4e33-8f3f-0bd57f50e216.dat' && mv second.fastq.gz '/tmp/tmpe170i9hz/job_working_directory/000/3/outputs/dataset_cd604854-5592-48ea-8007-503dbb8e64a9.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 24 seconds

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmpe170i9hz/files/4/2/e/dataset_42e07f1d-5b1b-4e33-8f3f-0bd57f50e216.dat' -r '/tmp/tmpe170i9hz/files/c/d/6/dataset_cd604854-5592-48ea-8007-503dbb8e64a9.dat' -1 '/tmp/tmpe170i9hz/job_working_directory/000/6/outputs/dataset_9e0b3508-1826-426a-979e-29a88d8cceda.dat' -2 '/tmp/tmpe170i9hz/job_working_directory/000/6/outputs/dataset_10578acc-f431-435b-848d-78eddaf4ffee.dat'  -s '/tmp/tmpe170i9hz/job_working_directory/000/6/outputs/dataset_b62863f9-80c7-4925-8135-f14c7eedb60c.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020508

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpe170i9hz/files/b/6/2/dataset_b62863f9-80c7-4925-8135-f14c7eedb60c.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpe170i9hz/job_working_directory/000/7/outputs/dataset_7b717872-8676-4b63-a958-3166c01058ba.dat'

Exit Code:

```
1
```

Standard Error:

readlink: missing operand
Try 'readlink --help' for more information.
dirname: missing operand
Try 'dirname --help' for more information.
readlink: missing operand
Try 'readlink --help' for more information.
dirname: missing operand
Try 'dirname --help' for more information.
Trimmomatic did not finish successfully

Standard Output:

Error: Unable to access jarfile /trimmomatic.jar

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": false}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpe170i9hz/files/b/6/2/dataset_b62863f9-80c7-4925-8135-f14c7eedb60c.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpe170i9hz/job_working_directory/000/8/outputs/dataset_415e4120-cf99-4f45-a159-55af16fde83c_files' && fastqc --outdir '/tmp/tmpe170i9hz/job_working_directory/000/8/outputs/dataset_415e4120-cf99-4f45-a159-55af16fde83c_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpe170i9hz/job_working_directory/000/8/outputs/dataset_415e4120-cf99-4f45-a159-55af16fde83c_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpe170i9hz/job_working_directory/000/8/outputs/dataset_415e4120-cf99-4f45-a159-55af16fde83c_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
adapters	`None`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
adapters	`None`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpe170i9hz/job_working_directory/000/11/outputs/dataset_511e4b62-dcc6-4dce-bb2c-eac612d244c8.dat' -g    -r '^Filename\t+(\S+)$' 'Filename\t$1_intial_reads' '/tmp/tmpe170i9hz/files/0/8/0/dataset_080964ec-34d3-45cb-ad17-f3a8d3bca720.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "^Filename\\t+(\\S+)$", "global": true, "is_regex": true, "replace_pattern": "Filename\\t$1_intial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
adapters	`None`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "^Filename\\t+(\\S+)$", "global": true, "is_regex": true, "replace_pattern": "Filename\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "^Filename\\t+(\\S+)$", "global": true, "is_regex": true, "replace_pattern": "Filename\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
adapters	`None`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "^Filename\\t+(\\S+)$", "global": true, "is_regex": true, "replace_pattern": "Filename\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fb6ff3b4d42e11ee8a08df3b9fc2b9ae"`
chromInfo	`"/tmp/tmpe170i9hz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 19, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 25, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 30, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - acbf97e4e1becfdd
- history_state
  - error
- invocation_id
  - acbf97e4e1becfdd
- invocation_state
  - scheduled
- workflow_id
  - acbf97e4e1becfdd

❌ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled

Step 11: Trimming:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpagernrf3/files/0/8/e/dataset_08ea5236-905a-4883-a0c6-26802379d909.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpagernrf3/job_working_directory/000/2/outputs/dataset_076bd2e9-9581-4059-9578-cba386a9297b.dat'

Exit Code:

```
1
```

Standard Error:

readlink: missing operand
Try 'readlink --help' for more information.
dirname: missing operand
Try 'dirname --help' for more information.
readlink: missing operand
Try 'readlink --help' for more information.
dirname: missing operand
Try 'dirname --help' for more information.
Trimmomatic did not finish successfully

Standard Output:

Error: Unable to access jarfile /trimmomatic.jar

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": false}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 1, "src": "dce"}]}, "single_or_paired": "se"}`

Job 2:

Job state is error

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpagernrf3/files/9/b/8/dataset_9b803377-f1a8-401a-92d7-43ae4669d23a.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpagernrf3/job_working_directory/000/3/outputs/dataset_4e3cfbb0-45aa-41d4-a55f-d372df3029ed.dat'

Exit Code:

```
1
```

Standard Error:

readlink: missing operand
Try 'readlink --help' for more information.
dirname: missing operand
Try 'dirname --help' for more information.
readlink: missing operand
Try 'readlink --help' for more information.
dirname: missing operand
Try 'dirname --help' for more information.
Trimmomatic did not finish successfully

Standard Output:

Error: Unable to access jarfile /trimmomatic.jar

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": false}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 2, "src": "dce"}]}, "single_or_paired": "se"}`

Step 12: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpagernrf3/files/0/8/e/dataset_08ea5236-905a-4883-a0c6-26802379d909.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpagernrf3/job_working_directory/000/4/outputs/dataset_982cd942-6e17-4255-ac17-3ffe01acb86f_files' && fastqc --outdir '/tmp/tmpagernrf3/job_working_directory/000/4/outputs/dataset_982cd942-6e17-4255-ac17-3ffe01acb86f_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpagernrf3/job_working_directory/000/4/outputs/dataset_982cd942-6e17-4255-ac17-3ffe01acb86f_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpagernrf3/job_working_directory/000/4/outputs/dataset_982cd942-6e17-4255-ac17-3ffe01acb86f_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adapters	`None`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpagernrf3/files/9/b/8/dataset_9b803377-f1a8-401a-92d7-43ae4669d23a.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpagernrf3/job_working_directory/000/5/outputs/dataset_2b0873d4-c2c7-4182-addd-38a9513633a0_files' && fastqc --outdir '/tmp/tmpagernrf3/job_working_directory/000/5/outputs/dataset_2b0873d4-c2c7-4182-addd-38a9513633a0_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpagernrf3/job_working_directory/000/5/outputs/dataset_2b0873d4-c2c7-4182-addd-38a9513633a0_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpagernrf3/job_working_directory/000/5/outputs/dataset_2b0873d4-c2c7-4182-addd-38a9513633a0_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adapters	`None`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 13: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adapters	`None`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adapters	`None`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpagernrf3/job_working_directory/000/10/outputs/dataset_89d19ec6-4fab-4f0a-9e3d-608cc8f0f76b.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpagernrf3/files/6/3/b/dataset_63b9fa53-50a4-40a1-95f4-c632ec43e723.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpagernrf3/job_working_directory/000/11/outputs/dataset_f19cbe0e-18d0-45d8-ae91-5fb536b3842e.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpagernrf3/files/f/5/1/dataset_f512cdd6-5499-4209-9a15-86c3a98f2d30.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 16: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 9, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 10, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adapters	`None`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adapters	`None`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
descr_columns	`"1"`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
descr_columns	`"1"`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adapters	`None`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adapters	`None`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 3: Trimmomatic - LEADING:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 22: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment_char	`true`
dbkey	`"?"`
linefilters	`[{"__index__": 0, "filter": {"__current_case__": 5, "filter_type": "append_dataset_name"}}, {"__index__": 1, "filter": {"__current_case__": 7, "column_text": ".", "filter_type": "append_text"}}, {"__index__": 2, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 3, "filter": {"__current_case__": 7, "column_text": "-", "filter_type": "append_text"}}, {"__index__": 4, "filter": {"__current_case__": 9, "columns": "5,6,1,7,2,3,4", "filter_type": "select_columns"}}]`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment_char	`true`
dbkey	`"?"`
linefilters	`[{"__index__": 0, "filter": {"__current_case__": 5, "filter_type": "append_dataset_name"}}, {"__index__": 1, "filter": {"__current_case__": 7, "column_text": ".", "filter_type": "append_text"}}, {"__index__": 2, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 3, "filter": {"__current_case__": 7, "column_text": "-", "filter_type": "append_text"}}, {"__index__": 4, "filter": {"__current_case__": 9, "columns": "5,6,1,7,2,3,4", "filter_type": "select_columns"}}]`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 24: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
col1	`"1"`
col2	`"2"`
columns	`[{"__index__": 0, "datacol": "3"}, {"__index__": 1, "datacol": "4"}, {"__index__": 2, "datacol": "5"}]`
dbkey	`"?"`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
col1	`"1"`
col2	`"2"`
columns	`[{"__index__": 0, "datacol": "3"}, {"__index__": 1, "datacol": "4"}, {"__index__": 2, "datacol": "5"}]`
dbkey	`"?"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment_char	`true`
dbkey	`"?"`
linefilters	`[{"__index__": 0, "filter": {"__current_case__": 9, "columns": "8,6,7", "filter_type": "select_columns"}}]`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment_char	`true`
dbkey	`"?"`
linefilters	`[{"__index__": 0, "filter": {"__current_case__": 9, "columns": "8,6,7", "filter_type": "select_columns"}}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
seq_col	`"2"`
title_col	`"1"`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
seq_col	`"2"`
title_col	`"1"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
identifier	`"1"`
quality	`"3"`
sequence	`"2"`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
identifier	`"1"`
quality	`"3"`
sequence	`"2"`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.3.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
all	`false`
basename	`false`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
skip_err	`false`
tabular	`true`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
all	`false`
basename	`false`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
skip_err	`false`
tabular	`true`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/fastq_info/fastq_info/0.25.1+Galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"__current_case__": 0, "fastq_1": {"values": [{"id": 45, "src": "dce"}]}, "input_type": "single"}`
q	`true`
r	`false`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"__current_case__": 0, "fastq_1": {"values": [{"id": 46, "src": "dce"}]}, "input_type": "single"}`
q	`true`
r	`false`

Step 32: toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.3.1+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
all	`false`
basename	`false`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
skip_err	`false`
tabular	`true`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
all	`false`
basename	`false`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
skip_err	`false`
tabular	`true`

Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpagernrf3/job_working_directory/000/1/configs/tmptm30omum' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$sn[_$rn]-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-02-25T22:43:36 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-02-25T22:43:36 prefetch.3.0.8: 1) Downloading 'DRR011051'...
2024-02-25T22:43:36 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-02-25T22:43:36 prefetch.3.0.8:  Downloading via HTTPS...
2024-02-25T22:43:36 prefetch.3.0.8:  HTTPS download succeed
2024-02-25T22:43:36 prefetch.3.0.8:  'DRR011051' is valid
2024-02-25T22:43:36 prefetch.3.0.8: 1) 'DRR011051' was downloaded successfully
2024-02-25T22:43:37 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-02-25T22:43:37 prefetch.3.0.8: 1) Downloading 'DRR010705'...
2024-02-25T22:43:37 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-02-25T22:43:37 prefetch.3.0.8:  Downloading via HTTPS...
2024-02-25T22:43:38 prefetch.3.0.8:  HTTPS download succeed
2024-02-25T22:43:38 prefetch.3.0.8:  'DRR010705' is valid
2024-02-25T22:43:38 prefetch.3.0.8: 1) 'DRR010705' was downloaded successfully

Standard Output:

Downloading accession: DRR011051...

Rejected 270 READS because of filtering out non-biological READS
Read 90 spots for DRR011051
Written 90 spots for DRR011051
Downloading accession: DRR010705...

Rejected 588 READS because of filtering out non-biological READS
Read 196 spots for DRR010705
Written 196 spots for DRR010705
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23c8af4ad42f11eeaffc7f7c014b5d89"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$sn[_$rn]-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpagernrf3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 6013b668be782172
- history_state
  - error
- invocation_id
  - 6013b668be782172
- invocation_state
  - scheduled
- workflow_id
  - 6013b668be782172

github-actions · 2024-02-28T10:51:29Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	3
Passed	0
Error	3
Failure	0
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: clan info file:
- step_state: scheduled

Step 11: SSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 12: LSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 13: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "fe2b3c4bd62411ee98e1b7cd55aab005"
      
      input {"values": [{"id": 12, "src": "hdca"}]}
Step 14: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "fe2b3c4bd62411ee98e1b7cd55aab005"
      
      input {"values": [{"id": 13, "src": "hdca"}]}

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp_lhrj5bo/job_working_directory/000/27/configs/tmp3ulc1q7_' '/tmp/tmp_lhrj5bo/job_working_directory/000/27/outputs/dataset_33229cf0-8b2e-4526-aa56-0766ea671486.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 15, "src": "hdca"}]}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp_lhrj5bo/job_working_directory/000/28/configs/tmpige0p4t8' '/tmp/tmp_lhrj5bo/job_working_directory/000/28/outputs/dataset_2cca93c5-0dc0-4999-9562-07856dc8f836.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 16, "src": "hdca"}]}`

Step 18: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "fe2b3c4bd62411ee98e1b7cd55aab005"
      
      input {"values": [{"id": 14, "src": "hdca"}]}

Step 19: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 31, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 20: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 32, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: covariance models:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp_lhrj5bo/job_working_directory/000/30/configs/tmpbl3f649s' '/tmp/tmp_lhrj5bo/job_working_directory/000/30/outputs/dataset_c218d644-4345-43a3-9386-570e06188320.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: Unlabelled step:
- step_state: scheduled
Step 23: Unlabelled step:
- step_state: scheduled

Step 24: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 33, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 25: Unlabelled step:
- step_state: scheduled
Step 26: Unlabelled step:
- step_state: scheduled
Step 27: Unlabelled step:
- step_state: scheduled
Step 28: HDF5 SSU SILVA:
- step_state: scheduled
Step 29: JSON SSU SILVA:
- step_state: scheduled

Step 30: Krona SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709117322_3340697_72954.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709117321_258564_33191.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 35, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmp_lhrj5bo/files/3/5/b/dataset_35b06b18-f566-4ae4-b2fb-35b503652bd8.dat '/tmp/tmp_lhrj5bo/files/d/a/0/dataset_da0e413d-013e-41ab-a945-6442188c8250.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmp_lhrj5bo/job_working_directory/000/5/outputs/dataset_a6e82b24-259e-422b-8b28-fbc13a706fd8.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmp_lhrj5bo/files/3/5/b/dataset_35b06b18-f566-4ae4-b2fb-35b503652bd8.dat '/tmp/tmp_lhrj5bo/files/e/1/9/dataset_e195e2d8-9673-4f53-8bd7-a8fd18244640.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmp_lhrj5bo/job_working_directory/000/6/outputs/dataset_7d5b2a58-ce83-4b84-8d36-e2bb3da9abdf.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 31: HDF5 LSU SILVA:
- step_state: scheduled
Step 32: JSON LSU SILVA:
- step_state: scheduled

Step 33: Krona LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709117321_2921498_88206.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709117321_258564_33191.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 34: Unlabelled step:
- step_state: scheduled
Step 35: Unlabelled step:
- step_state: scheduled
Step 36: HDF5 ITSonedb:
- step_state: scheduled
Step 37: JSON ITSonedb:
- step_state: scheduled

Step 38: Krona ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709117322_4239507_87759.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709117321_258564_33191.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 39: HDF5 ITS UNITE:
- step_state: scheduled
Step 40: JSON ITS UNITE:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp_lhrj5bo/files/4/f/1/dataset_4f14eaa5-b5b9-4f40-8558-957784923791.dat' clan_info && ln -s '/tmp/tmp_lhrj5bo/files/a/6/e/dataset_a6e82b24-259e-422b-8b28-fbc13a706fd8.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmp_lhrj5bo/job_working_directory/000/7/outputs/dataset_8c9ede7e-a316-4160-b981-58d0eb80f7c9.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp_lhrj5bo/files/4/f/1/dataset_4f14eaa5-b5b9-4f40-8558-957784923791.dat' clan_info && ln -s '/tmp/tmp_lhrj5bo/files/7/d/5/dataset_7d5b2a58-ce83-4b84-8d36-e2bb3da9abdf.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmp_lhrj5bo/job_working_directory/000/8/outputs/dataset_c8b9d56a-6d85-4a5f-973b-5eddddf86fce.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 41: Krona ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709117322_5070434_28925.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp_lhrj5bo/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709117321_258564_33191.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 46, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmp_lhrj5bo/job_working_directory/000/9/configs/tmp_yd_sccg' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmp_lhrj5bo/job_working_directory/000/9/configs/tmpfsjwzem3' -Q '/tmp/tmp_lhrj5bo/job_working_directory/000/9/configs/tmp_yd_sccg'   --no_header   -o '/tmp/tmp_lhrj5bo/job_working_directory/000/9/outputs/dataset_4d2140c1-b21f-456e-b767-31c0b66877b2.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmp_lhrj5bo/files/8/c/9/dataset_8c9ede7e-a316-4160-b981-58d0eb80f7c9.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': '', 'result_file': 'results1.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": ""}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}]}`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is error

Command Line:

cat '/tmp/tmp_lhrj5bo/job_working_directory/000/10/configs/tmpx7yx7n9x' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmp_lhrj5bo/job_working_directory/000/10/configs/tmpgohjf8m0' -Q '/tmp/tmp_lhrj5bo/job_working_directory/000/10/configs/tmpx7yx7n9x'   --no_header   -o '/tmp/tmp_lhrj5bo/job_working_directory/000/10/outputs/dataset_0105fa85-109a-4a14-9a25-875a3f905801.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmp_lhrj5bo/files/c/8/b/dataset_c8b9d56a-6d85-4a5f-973b-5eddddf86fce.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': '', 'result_file': 'results1.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": ""}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}]}`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Step 7: SSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 8: SSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Step 9: LSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 10: LSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fe2b3c4bd62411ee98e1b7cd55aab005"`
chromInfo	`"/tmp/tmp_lhrj5bo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 429c11dcd39950e4
- history_state
  - error
- invocation_id
  - 429c11dcd39950e4
- invocation_state
  - scheduled
- workflow_id
  - 429c11dcd39950e4

❌ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg": "Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2 (version 0.39+galaxy2)", "err_code": 0, "traceback": "Traceback (most recent call last):\n  File \"/tmp/tmp_10yhkdm/galaxy-dev/lib/galaxy/web/framework/decorators.py\", line 337, in decorator\n    rval = func(self, trans, *args, **kwargs)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/tmp/tmp_10yhkdm/galaxy-dev/lib/galaxy/webapps/galaxy/api/workflows.py\", line 757, in invoke\n    raise exceptions.MessageException(missing_tools_message)\ngalaxy.exceptions.MessageException: Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2 (version 0.39+galaxy2)\n"}

❌ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg": "Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2 (version 0.39+galaxy2)", "err_code": 0, "traceback": "Traceback (most recent call last):\n  File \"/tmp/tmprybus1_n/galaxy-dev/lib/galaxy/web/framework/decorators.py\", line 337, in decorator\n    rval = func(self, trans, *args, **kwargs)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/tmp/tmprybus1_n/galaxy-dev/lib/galaxy/webapps/galaxy/api/workflows.py\", line 757, in invoke\n    raise exceptions.MessageException(missing_tools_message)\ngalaxy.exceptions.MessageException: Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2 (version 0.39+galaxy2)\n"}

github-actions · 2024-02-29T16:23:50Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	3
Passed	0
Error	1
Failure	2
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: clan info file:
- step_state: scheduled

Step 11: SSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 12: LSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 13: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "e5186b59d71c11ee928bb3290092d493"
      
      input {"values": [{"id": 12, "src": "hdca"}]}
Step 14: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "e5186b59d71c11ee928bb3290092d493"
      
      input {"values": [{"id": 13, "src": "hdca"}]}

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp25xshxbe/job_working_directory/000/27/configs/tmpekmgj9kk' '/tmp/tmp25xshxbe/job_working_directory/000/27/outputs/dataset_5406effc-ef2d-454a-8ba9-906fa731c6d9.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 15, "src": "hdca"}]}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp25xshxbe/job_working_directory/000/28/configs/tmppx_x1t99' '/tmp/tmp25xshxbe/job_working_directory/000/28/outputs/dataset_99e46e68-16ae-43e0-9501-5c45001d3294.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 16, "src": "hdca"}]}`

Step 18: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "e5186b59d71c11ee928bb3290092d493"
      
      input {"values": [{"id": 14, "src": "hdca"}]}

Step 19: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 31, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 20: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 32, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: covariance models:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp25xshxbe/job_working_directory/000/30/configs/tmpa6g0ja67' '/tmp/tmp25xshxbe/job_working_directory/000/30/outputs/dataset_8a93c384-583a-4e41-a86e-9a6c4d51868d.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: Unlabelled step:
- step_state: scheduled
Step 23: Unlabelled step:
- step_state: scheduled

Step 24: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 33, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 25: Unlabelled step:
- step_state: scheduled
Step 26: Unlabelled step:
- step_state: scheduled
Step 27: Unlabelled step:
- step_state: scheduled
Step 28: HDF5 SSU SILVA:
- step_state: scheduled
Step 29: JSON SSU SILVA:
- step_state: scheduled

Step 30: Krona SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709223762_6017244_15279.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709223762_4514966_44802.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmp25xshxbe/files/b/c/9/dataset_bc95d7a6-d848-4985-acd9-e60479de0f9c.dat '/tmp/tmp25xshxbe/files/d/9/4/dataset_d94866ad-e965-48e4-a864-67b6cd44e84e.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmp25xshxbe/job_working_directory/000/5/outputs/dataset_be86189c-0813-464d-b520-9021a378da6b.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmp25xshxbe/files/b/c/9/dataset_bc95d7a6-d848-4985-acd9-e60479de0f9c.dat '/tmp/tmp25xshxbe/files/6/7/8/dataset_678cf1f8-6131-494b-b769-20a9f7e84b5e.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmp25xshxbe/job_working_directory/000/6/outputs/dataset_0f77a225-bc3b-490e-8424-e0bd1b48d091.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 31: HDF5 LSU SILVA:
- step_state: scheduled
Step 32: JSON LSU SILVA:
- step_state: scheduled

Step 33: Krona LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709223762_6865308_31844.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709223762_4514966_44802.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 33, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 34: Unlabelled step:
- step_state: scheduled
Step 35: Unlabelled step:
- step_state: scheduled
Step 36: HDF5 ITSonedb:
- step_state: scheduled
Step 37: JSON ITSonedb:
- step_state: scheduled

Step 38: Krona ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709223762_4883075_62976.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709223762_4514966_44802.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 39: HDF5 ITS UNITE:
- step_state: scheduled
Step 40: JSON ITS UNITE:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp25xshxbe/files/6/e/5/dataset_6e5f4646-2c26-48cb-b066-c4229b1c07b6.dat' clan_info && ln -s '/tmp/tmp25xshxbe/files/b/e/8/dataset_be86189c-0813-464d-b520-9021a378da6b.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmp25xshxbe/job_working_directory/000/7/outputs/dataset_a123e48b-9b03-41ec-90d1-828c6073de96.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp25xshxbe/files/6/e/5/dataset_6e5f4646-2c26-48cb-b066-c4229b1c07b6.dat' clan_info && ln -s '/tmp/tmp25xshxbe/files/0/f/7/dataset_0f77a225-bc3b-490e-8424-e0bd1b48d091.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmp25xshxbe/job_working_directory/000/8/outputs/dataset_16bf448d-039d-4ff6-8705-cccfc5649835.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 41: Krona ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709223763_7392247_15102.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp25xshxbe/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709223762_4514966_44802.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 46, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmp25xshxbe/job_working_directory/000/9/configs/tmp3okwsz_c' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmp25xshxbe/job_working_directory/000/9/configs/tmp1hcd4a65' -Q '/tmp/tmp25xshxbe/job_working_directory/000/9/configs/tmp3okwsz_c'   --no_header   -o '/tmp/tmp25xshxbe/job_working_directory/000/9/outputs/dataset_717e4f71-e24d-4c52-99eb-ae6ea9554e18.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmp25xshxbe/files/a/1/2/dataset_a123e48b-9b03-41ec-90d1-828c6073de96.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is error

Command Line:

cat '/tmp/tmp25xshxbe/job_working_directory/000/10/configs/tmpo_9x10qr' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmp25xshxbe/job_working_directory/000/10/configs/tmpn6fa20yh' -Q '/tmp/tmp25xshxbe/job_working_directory/000/10/configs/tmpo_9x10qr'   --no_header   -o '/tmp/tmp25xshxbe/job_working_directory/000/10/outputs/dataset_bd67f268-7403-4687-bc7d-7f2d147a52cf.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmp25xshxbe/files/1/6/b/dataset_16bf448d-039d-4ff6-8705-cccfc5649835.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Step 7: SSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 8: SSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Step 9: LSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 10: LSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"e5186b59d71c11ee928bb3290092d493"`
chromInfo	`"/tmp/tmp25xshxbe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - e0a245e2d438b07b
- history_state
  - error
- invocation_id
  - e0a245e2d438b07b
- invocation_state
  - scheduled
- workflow_id
  - e0a245e2d438b07b

Failed Tests

❌ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Problems:

Output with path /tmp/tmp6fqzktny/MultiQC_report__af43240d-84d8-4ebc-a8bc-d34933afebbc different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-quality-control-paired-end/test-data/MultiQC_report/MultiQC_report.html v. /tmp/tmpaa014dspMultiQC_report.html )
--- local_file
+++ history_data
@@ -1,54 +1,40 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
-<!--
-  __  __       _ _   _  ___   ____
- |  \/  |_   _| | |_(_)/ _ \ / ___|
- | |\/| | | | | | __| | | | | |
- | |  | | |_| | | |_| | |_| | |___
- |_|  |_|\__,_|_|\__|_|\__\_\\____|
-
-Abandon hope all ye who enter here..
-http://multiqc.info
--->
+
+
+
+
 
   
 
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
********
*SNIP *
********
           <div class="col-sm-6 regex_example_demo">
-            <input type="text" class="form-control" />
-<pre>
-<span>samp_1</span>
+            <input type="text" class="form-control">
+<pre><span>samp_1</span>
 <span>samp_1_edited</span>
 <span>samp_2</span>
 <span>samp_2_edited</span>
@@ -7017,11 +6749,12 @@
         </div>
       </div>
       <div class="modal-footer">
-        <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+        <button type="button" class="btn btn-default">Close</button>
       </div>
     </div>
   </div>
 </div>
 
-</body>
-</html>
+
+
+</div></div></div>

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmprf2andrx/job_working_directory/000/1/configs/tmpp4ow9wfm' ~/.ncbi/user-settings.mkfg &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-02-29T16:08:47 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-02-29T16:08:47 prefetch.3.0.8: 1) Downloading 'DRR218540'...
2024-02-29T16:08:47 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-02-29T16:08:47 prefetch.3.0.8:  Downloading via HTTPS...
2024-02-29T16:08:49 prefetch.3.0.8:  HTTPS download succeed
2024-02-29T16:08:49 prefetch.3.0.8:  'DRR218540' is valid
2024-02-29T16:08:49 prefetch.3.0.8: 1) 'DRR218540' was downloaded successfully
2024-02-29T16:08:49 prefetch.3.0.8: 'DRR218540' has 0 unresolved dependencies

Standard Output:

Downloading accession: DRR218540...

Read 67485 spots for DRR218540
Written 67485 spots for DRR218540
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "c4b186c6d71c11eea51f09780c1861d9"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprf2andrx/files/7/f/a/dataset_7fa6beb7-d57a-4048-a257-aed8469f9f8d.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmprf2andrx/files/2/f/e/dataset_2fea12b2-6ee8-48f2-967d-b80db252f0e4.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmprf2andrx/job_working_directory/000/3/outputs/dataset_f5083620-1ea4-46a9-92be-f03ad534a209.dat' && mv second.fastq.gz '/tmp/tmprf2andrx/job_working_directory/000/3/outputs/dataset_0e03ff03-2dc5-435f-8cba-31b7874e0e33.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 27 seconds

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmprf2andrx/files/f/5/0/dataset_f5083620-1ea4-46a9-92be-f03ad534a209.dat' -r '/tmp/tmprf2andrx/files/0/e/0/dataset_0e03ff03-2dc5-435f-8cba-31b7874e0e33.dat' -1 '/tmp/tmprf2andrx/job_working_directory/000/6/outputs/dataset_d80ae950-5662-4c72-acc0-6f41986807f9.dat' -2 '/tmp/tmprf2andrx/job_working_directory/000/6/outputs/dataset_dfcdcb48-6e13-4480-9fb2-4bf6e12708f0.dat'  -s '/tmp/tmprf2andrx/job_working_directory/000/6/outputs/dataset_317a1c3c-295a-417e-a4e9-f9c1af56a3a8.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020947

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmprf2andrx/files/3/1/7/dataset_317a1c3c-295a-417e-a4e9-f9c1af56a3a8.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmprf2andrx/job_working_directory/000/7/outputs/dataset_414d0a74-bf68-4c9a-892e-a575cea706df.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 6434 Surviving: 6432 (99.97%) Dropped: 2 (0.03%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprf2andrx/files/3/1/7/dataset_317a1c3c-295a-417e-a4e9-f9c1af56a3a8.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmprf2andrx/job_working_directory/000/8/outputs/dataset_05dc1ad3-f38e-4a9c-90a8-e1a10bc34548_files' && fastqc --outdir '/tmp/tmprf2andrx/job_working_directory/000/8/outputs/dataset_05dc1ad3-f38e-4a9c-90a8-e1a10bc34548_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmprf2andrx/job_working_directory/000/8/outputs/dataset_05dc1ad3-f38e-4a9c-90a8-e1a10bc34548_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprf2andrx/job_working_directory/000/8/outputs/dataset_05dc1ad3-f38e-4a9c-90a8-e1a10bc34548_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
adapters	`None`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmprf2andrx/files/4/1/4/dataset_414d0a74-bf68-4c9a-892e-a575cea706df.dat' '/tmp/tmprf2andrx/job_working_directory/000/9/configs/tmpm9ofkhwz' '/tmp/tmprf2andrx/job_working_directory/000/9/outputs/dataset_c6c21a5b-b375-4005-9a7d-827bb093588f.dat' '/tmp/tmprf2andrx/job_working_directory/000/9/outputs/dataset_c6c21a5b-b375-4005-9a7d-827bb093588f_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 6432 of 6432 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprf2andrx/files/4/1/4/dataset_414d0a74-bf68-4c9a-892e-a575cea706df.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmprf2andrx/job_working_directory/000/10/outputs/dataset_9442e205-09f1-46d7-93b4-94c920b53960_files' && fastqc --outdir '/tmp/tmprf2andrx/job_working_directory/000/10/outputs/dataset_9442e205-09f1-46d7-93b4-94c920b53960_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmprf2andrx/job_working_directory/000/10/outputs/dataset_9442e205-09f1-46d7-93b4-94c920b53960_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprf2andrx/job_working_directory/000/10/outputs/dataset_9442e205-09f1-46d7-93b4-94c920b53960_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
adapters	`None`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprf2andrx/job_working_directory/000/11/outputs/dataset_9af4fe97-25e8-4f91-83ee-c93611051115.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmprf2andrx/files/0/0/e/dataset_00e73f7f-36e4-4e8e-ac79-bc128360176f.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprf2andrx/files/c/6/c/dataset_c6c21a5b-b375-4005-9a7d-827bb093588f.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmprf2andrx/job_working_directory/000/12/outputs/dataset_2bf1dee0-ad9d-488e-8d0a-a553bcf54cc9_files' && fastqc --outdir '/tmp/tmprf2andrx/job_working_directory/000/12/outputs/dataset_2bf1dee0-ad9d-488e-8d0a-a553bcf54cc9_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmprf2andrx/job_working_directory/000/12/outputs/dataset_2bf1dee0-ad9d-488e-8d0a-a553bcf54cc9_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprf2andrx/job_working_directory/000/12/outputs/dataset_2bf1dee0-ad9d-488e-8d0a-a553bcf54cc9_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
adapters	`None`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmprf2andrx/files/c/6/c/dataset_c6c21a5b-b375-4005-9a7d-827bb093588f.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 6,432
	Input bases: 2,151,394
	Input mean length: 334.48
	Good sequences: 6,432 (100.00%)
	Good bases: 2,151,394
	Good mean length: 334.48
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprf2andrx/job_working_directory/000/14/outputs/dataset_16bd095c-c5b8-461e-94dc-919fa4f4e7d4.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmprf2andrx/files/8/e/8/dataset_8e81843b-809d-4e1a-93be-41aa23f6077a.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprf2andrx/job_working_directory/000/15/outputs/dataset_4e300407-3548-4e98-be62-f02fe8781d7b.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmprf2andrx/files/b/9/2/dataset_b92996e0-dbfc-417f-8653-b268bdd6ac36.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmprf2andrx/files/7/8/8/dataset_7882bcc1-f546-485a-a605-957558e1f2f4.dat' '/tmp/tmprf2andrx/job_working_directory/000/16/outputs/dataset_a9abce41-2011-47b9-b7c6-fe0aefd4403b.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

6432 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprf2andrx/files/7/8/8/dataset_7882bcc1-f546-485a-a605-957558e1f2f4.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmprf2andrx/job_working_directory/000/17/outputs/dataset_8c9febda-2acc-4a38-a0d2-fce424e512a4_files' && fastqc --outdir '/tmp/tmprf2andrx/job_working_directory/000/17/outputs/dataset_8c9febda-2acc-4a38-a0d2-fce424e512a4_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmprf2andrx/job_working_directory/000/17/outputs/dataset_8c9febda-2acc-4a38-a0d2-fce424e512a4_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprf2andrx/job_working_directory/000/17/outputs/dataset_8c9febda-2acc-4a38-a0d2-fce424e512a4_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
adapters	`None`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmprf2andrx/files/a/9/a/dataset_a9abce41-2011-47b9-b7c6-fe0aefd4403b.dat' | fasta_formatter -w 0 -o '/tmp/tmprf2andrx/job_working_directory/000/18/outputs/dataset_e97d27cf-e748-4993-a058-0053d4893423.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprf2andrx/job_working_directory/000/19/outputs/dataset_3a0ca645-51d4-43c8-9a71-62057930013b.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmprf2andrx/files/e/e/b/dataset_eeb95f7e-bdb4-4f43-8c24-29c6c9a417fd.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmprf2andrx/files/9/a/f/dataset_9af4fe97-25e8-4f91-83ee-c93611051115.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmprf2andrx/files/1/6/b/dataset_16bd095c-c5b8-461e-94dc-919fa4f4e7d4.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmprf2andrx/files/4/e/3/dataset_4e300407-3548-4e98-be62-f02fe8781d7b.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmprf2andrx/files/3/a/0/dataset_3a0ca645-51d4-43c8-9a71-62057930013b.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmprf2andrx/job_working_directory/000/20/working/multiqc_WDir
|            fastqc | Found 4 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c4b186c6d71c11eea51f09780c1861d9"`
chromInfo	`"/tmp/tmprf2andrx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 23, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- history_id
  - 0c6723c21d1153dc
- history_state
  - ok
- invocation_id
  - 0c6723c21d1153dc
- invocation_state
  - scheduled
- workflow_id
  - 0c6723c21d1153dc

❌ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Problems:

Output with path /tmp/tmpltyii1l2/MultiQC_report__bb4ae559-df9b-4d8c-9584-23b5691cc9ff different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-quality-control-single-end/test-data/MultiQC_report/MultiQC_report.html v. /tmp/tmph_p1g6brMultiQC_report.html )
--- local_file
+++ history_data
@@ -1,54 +1,40 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
-<!--
-  __  __       _ _   _  ___   ____
- |  \/  |_   _| | |_(_)/ _ \ / ___|
- | |\/| | | | | | __| | | | | |
- | |  | | |_| | | |_| | |_| | |___
- |_|  |_|\__,_|_|\__|_|\__\_\\____|
-
-Abandon hope all ye who enter here..
-http://multiqc.info
--->
+
+
+
+
 
   
 
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
********
*SNIP *
********
           <div class="col-sm-6 regex_example_demo">
-            <input type="text" class="form-control" />
-<pre>
-<span>samp_1</span>
+            <input type="text" class="form-control">
+<pre><span>samp_1</span>
 <span>samp_1_edited</span>
 <span>samp_2</span>
 <span>samp_2_edited</span>
@@ -7017,11 +6749,12 @@
         </div>
       </div>
       <div class="modal-footer">
-        <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+        <button type="button" class="btn btn-default">Close</button>
       </div>
     </div>
   </div>
 </div>
 
-</body>
-</html>
+
+
+</div></div></div>

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled

Step 11: Trimming:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpz8n3rric/files/8/6/6/dataset_8665274e-2fd7-495b-a35b-c2bc01be7efb.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpz8n3rric/job_working_directory/000/2/outputs/dataset_af0375f6-96f1-4ffb-9cd8-7f3a64cfcd0a.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 196 Surviving: 184 (93.88%) Dropped: 12 (6.12%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 1, "src": "dce"}]}, "single_or_paired": "se"}`

Job 2:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpz8n3rric/files/2/a/b/dataset_2ab08c68-5823-4f12-9818-50e164088054.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpz8n3rric/job_working_directory/000/3/outputs/dataset_c752ae3b-e634-4348-b17b-21050f70d05b.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 90 Surviving: 90 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 2, "src": "dce"}]}, "single_or_paired": "se"}`

Step 12: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpz8n3rric/files/8/6/6/dataset_8665274e-2fd7-495b-a35b-c2bc01be7efb.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpz8n3rric/job_working_directory/000/4/outputs/dataset_aa9854d5-e1ea-4dc0-bb98-ccfd35aaf50c_files' && fastqc --outdir '/tmp/tmpz8n3rric/job_working_directory/000/4/outputs/dataset_aa9854d5-e1ea-4dc0-bb98-ccfd35aaf50c_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpz8n3rric/job_working_directory/000/4/outputs/dataset_aa9854d5-e1ea-4dc0-bb98-ccfd35aaf50c_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpz8n3rric/job_working_directory/000/4/outputs/dataset_aa9854d5-e1ea-4dc0-bb98-ccfd35aaf50c_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adapters	`None`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpz8n3rric/files/2/a/b/dataset_2ab08c68-5823-4f12-9818-50e164088054.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpz8n3rric/job_working_directory/000/5/outputs/dataset_1e53247e-6100-4217-a859-ce3ee593290b_files' && fastqc --outdir '/tmp/tmpz8n3rric/job_working_directory/000/5/outputs/dataset_1e53247e-6100-4217-a859-ce3ee593290b_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpz8n3rric/job_working_directory/000/5/outputs/dataset_1e53247e-6100-4217-a859-ce3ee593290b_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpz8n3rric/job_working_directory/000/5/outputs/dataset_1e53247e-6100-4217-a859-ce3ee593290b_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adapters	`None`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 13: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpz8n3rric/files/a/f/0/dataset_af0375f6-96f1-4ffb-9cd8-7f3a64cfcd0a.dat' '/tmp/tmpz8n3rric/job_working_directory/000/6/configs/tmpcvp5761x' '/tmp/tmpz8n3rric/job_working_directory/000/6/outputs/dataset_8375327a-36a7-45de-a227-2e64857f890c.dat' '/tmp/tmpz8n3rric/job_working_directory/000/6/outputs/dataset_8375327a-36a7-45de-a227-2e64857f890c_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 184 of 184 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Job 2:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpz8n3rric/files/c/7/5/dataset_c752ae3b-e634-4348-b17b-21050f70d05b.dat' '/tmp/tmpz8n3rric/job_working_directory/000/7/configs/tmp8yyxegnr' '/tmp/tmpz8n3rric/job_working_directory/000/7/outputs/dataset_d6520251-1b4c-481c-bb53-192c52f5f06e.dat' '/tmp/tmpz8n3rric/job_working_directory/000/7/outputs/dataset_d6520251-1b4c-481c-bb53-192c52f5f06e_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 90 of 90 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpz8n3rric/files/a/f/0/dataset_af0375f6-96f1-4ffb-9cd8-7f3a64cfcd0a.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpz8n3rric/job_working_directory/000/8/outputs/dataset_a4a48b87-e551-4b84-9b19-6738a6a2023c_files' && fastqc --outdir '/tmp/tmpz8n3rric/job_working_directory/000/8/outputs/dataset_a4a48b87-e551-4b84-9b19-6738a6a2023c_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpz8n3rric/job_working_directory/000/8/outputs/dataset_a4a48b87-e551-4b84-9b19-6738a6a2023c_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpz8n3rric/job_working_directory/000/8/outputs/dataset_a4a48b87-e551-4b84-9b19-6738a6a2023c_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adapters	`None`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpz8n3rric/files/c/7/5/dataset_c752ae3b-e634-4348-b17b-21050f70d05b.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpz8n3rric/job_working_directory/000/9/outputs/dataset_b9de363f-0afc-420c-9361-2ed9ef5bf13b_files' && fastqc --outdir '/tmp/tmpz8n3rric/job_working_directory/000/9/outputs/dataset_b9de363f-0afc-420c-9361-2ed9ef5bf13b_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpz8n3rric/job_working_directory/000/9/outputs/dataset_b9de363f-0afc-420c-9361-2ed9ef5bf13b_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpz8n3rric/job_working_directory/000/9/outputs/dataset_b9de363f-0afc-420c-9361-2ed9ef5bf13b_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adapters	`None`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpz8n3rric/job_working_directory/000/10/outputs/dataset_3ad5f206-f5bb-4b3f-afc1-f7f51adca308.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpz8n3rric/files/0/3/9/dataset_039e503a-1e56-4327-9111-3167823802cc.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpz8n3rric/job_working_directory/000/11/outputs/dataset_ea6593cd-9c60-4e9a-8147-bef23c68b9d7.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpz8n3rric/files/e/6/7/dataset_e6751a86-1c16-4b34-b88b-96a1fbe22ef5.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 16: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpz8n3rric/files/8/3/7/dataset_8375327a-36a7-45de-a227-2e64857f890c.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 184
	Input bases: 46,942
	Input mean length: 255.12
	Good sequences: 184 (100.00%)
	Good bases: 46,942
	Good mean length: 255.12
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 9, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Job 2:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpz8n3rric/files/d/6/5/dataset_d6520251-1b4c-481c-bb53-192c52f5f06e.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 90
	Input bases: 31,735
	Input mean length: 352.61
	Good sequences: 90 (100.00%)
	Good bases: 31,735
	Good mean length: 352.61
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 10, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpz8n3rric/files/8/3/7/dataset_8375327a-36a7-45de-a227-2e64857f890c.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpz8n3rric/job_working_directory/000/14/outputs/dataset_55f0fd4e-697f-42c4-b798-b14450402a3b_files' && fastqc --outdir '/tmp/tmpz8n3rric/job_working_directory/000/14/outputs/dataset_55f0fd4e-697f-42c4-b798-b14450402a3b_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpz8n3rric/job_working_directory/000/14/outputs/dataset_55f0fd4e-697f-42c4-b798-b14450402a3b_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpz8n3rric/job_working_directory/000/14/outputs/dataset_55f0fd4e-697f-42c4-b798-b14450402a3b_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adapters	`None`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpz8n3rric/files/d/6/5/dataset_d6520251-1b4c-481c-bb53-192c52f5f06e.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpz8n3rric/job_working_directory/000/15/outputs/dataset_ab87b2f3-f0a2-456a-9d55-d6c19dac9e24_files' && fastqc --outdir '/tmp/tmpz8n3rric/job_working_directory/000/15/outputs/dataset_ab87b2f3-f0a2-456a-9d55-d6c19dac9e24_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpz8n3rric/job_working_directory/000/15/outputs/dataset_ab87b2f3-f0a2-456a-9d55-d6c19dac9e24_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpz8n3rric/job_working_directory/000/15/outputs/dataset_ab87b2f3-f0a2-456a-9d55-d6c19dac9e24_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adapters	`None`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpz8n3rric/job_working_directory/000/16/outputs/dataset_07a32db7-b0f6-44b2-8fc7-94b4255b0a22.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpz8n3rric/files/f/f/2/dataset_ff20da79-3421-4f67-adf3-1078f4300446.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpz8n3rric/job_working_directory/000/17/outputs/dataset_32bc3016-ce7b-449c-949c-4074875647c9.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpz8n3rric/files/2/e/1/dataset_2e13910c-524c-4e2c-97f4-468b98c7c917.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpz8n3rric/files/7/d/e/dataset_7deb5832-412a-4877-b539-93575c1c9d1a.dat' '/tmp/tmpz8n3rric/job_working_directory/000/18/outputs/dataset_650516c0-6e70-448e-8866-866198e2e241.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

184 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpz8n3rric/files/5/c/f/dataset_5cfbc873-4a60-4502-b4ce-ddfdd8c3614c.dat' '/tmp/tmpz8n3rric/job_working_directory/000/19/outputs/dataset_85ebfeb2-4097-4852-bd71-ff7e21f5fcc4.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

90 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpz8n3rric/files/7/d/e/dataset_7deb5832-412a-4877-b539-93575c1c9d1a.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpz8n3rric/job_working_directory/000/20/outputs/dataset_ff561282-f064-466b-95cf-6905fbf94f3d_files' && fastqc --outdir '/tmp/tmpz8n3rric/job_working_directory/000/20/outputs/dataset_ff561282-f064-466b-95cf-6905fbf94f3d_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpz8n3rric/job_working_directory/000/20/outputs/dataset_ff561282-f064-466b-95cf-6905fbf94f3d_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpz8n3rric/job_working_directory/000/20/outputs/dataset_ff561282-f064-466b-95cf-6905fbf94f3d_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adapters	`None`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpz8n3rric/files/5/c/f/dataset_5cfbc873-4a60-4502-b4ce-ddfdd8c3614c.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpz8n3rric/job_working_directory/000/21/outputs/dataset_8d7fe093-b7d9-40e9-9085-382700528298_files' && fastqc --outdir '/tmp/tmpz8n3rric/job_working_directory/000/21/outputs/dataset_8d7fe093-b7d9-40e9-9085-382700528298_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpz8n3rric/job_working_directory/000/21/outputs/dataset_8d7fe093-b7d9-40e9-9085-382700528298_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpz8n3rric/job_working_directory/000/21/outputs/dataset_8d7fe093-b7d9-40e9-9085-382700528298_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adapters	`None`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 3: Trimmomatic - LEADING:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpz8n3rric/job_working_directory/000/22/outputs/dataset_1404e828-fcd5-4ea5-8623-6b1e1425ad10.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpz8n3rric/files/a/a/5/dataset_aa5778fb-73c5-4bfe-83ec-35ac6eefa7c0.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpz8n3rric/job_working_directory/000/23/outputs/dataset_5da8cbb6-a10a-43e5-9e7a-5637a352f32b.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpz8n3rric/files/b/8/c/dataset_b8c2bd91-2456-4f94-b10e-2c66186c9542.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpz8n3rric/files/6/5/0/dataset_650516c0-6e70-448e-8866-866198e2e241.dat' | fasta_formatter -w 60 -o '/tmp/tmpz8n3rric/job_working_directory/000/24/outputs/dataset_abb0d3b7-08bd-42f6-932f-da86c8dc9c0b.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Job 2:

Job state is ok

Command Line:

cat '/tmp/tmpz8n3rric/files/8/5/e/dataset_85ebfeb2-4097-4852-bd71-ff7e21f5fcc4.dat' | fasta_formatter -w 60 -o '/tmp/tmpz8n3rric/job_working_directory/000/25/outputs/dataset_83be642d-64a7-4645-b706-49ab4cecd6d4.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpz8n3rric/job_working_directory/000/26/outputs/dataset_299ae8cb-d887-447e-9014-0c89c95d651d.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpz8n3rric/files/4/5/b/dataset_45be952c-765e-4de7-b3f5-5db2208706d9.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpz8n3rric/job_working_directory/000/27/outputs/dataset_60361f9a-1d0f-4688-8306-896c153f858d.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpz8n3rric/files/2/8/c/dataset_28c72e21-ba51-4c4f-8ac9-536a3a9be055.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmpz8n3rric/files/3/a/d/dataset_3ad5f206-f5bb-4b3f-afc1-f7f51adca308.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/tmp/tmpz8n3rric/files/e/a/6/dataset_ea6593cd-9c60-4e9a-8147-bef23c68b9d7.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmpz8n3rric/files/0/7/a/dataset_07a32db7-b0f6-44b2-8fc7-94b4255b0a22.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_1/file_1' && ln -s '/tmp/tmpz8n3rric/files/3/2/b/dataset_32bc3016-ce7b-449c-949c-4074875647c9.dat' 'multiqc_WDir/fastqc_0/data_1/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmpz8n3rric/files/1/4/0/dataset_1404e828-fcd5-4ea5-8623-6b1e1425ad10.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_2/file_1' && ln -s '/tmp/tmpz8n3rric/files/5/d/a/dataset_5da8cbb6-a10a-43e5-9e7a-5637a352f32b.dat' 'multiqc_WDir/fastqc_0/data_2/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmpz8n3rric/files/2/9/9/dataset_299ae8cb-d887-447e-9014-0c89c95d651d.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_3/file_1' && ln -s '/tmp/tmpz8n3rric/files/6/0/3/dataset_60361f9a-1d0f-4688-8306-896c153f858d.dat' 'multiqc_WDir/fastqc_0/data_3/file_1/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpz8n3rric/job_working_directory/000/28/working/multiqc_WDir
|            fastqc | Found 8 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 8/8

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled
Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpz8n3rric/job_working_directory/000/1/configs/tmpqsbrhzp3' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-02-29T16:08:42 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-02-29T16:08:42 prefetch.3.0.8: 1) Downloading 'DRR011051'...
2024-02-29T16:08:42 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-02-29T16:08:42 prefetch.3.0.8:  Downloading via HTTPS...
2024-02-29T16:08:42 prefetch.3.0.8:  HTTPS download succeed
2024-02-29T16:08:42 prefetch.3.0.8:  'DRR011051' is valid
2024-02-29T16:08:42 prefetch.3.0.8: 1) 'DRR011051' was downloaded successfully
2024-02-29T16:08:42 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-02-29T16:08:42 prefetch.3.0.8: 1) Downloading 'DRR010705'...
2024-02-29T16:08:42 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-02-29T16:08:42 prefetch.3.0.8:  Downloading via HTTPS...
2024-02-29T16:08:43 prefetch.3.0.8:  HTTPS download succeed
2024-02-29T16:08:43 prefetch.3.0.8:  'DRR010705' is valid
2024-02-29T16:08:43 prefetch.3.0.8: 1) 'DRR010705' was downloaded successfully

Standard Output:

Downloading accession: DRR011051...

Rejected 270 READS because of filtering out non-biological READS
Read 90 spots for DRR011051
Written 90 spots for DRR011051
Downloading accession: DRR010705...

Rejected 588 READS because of filtering out non-biological READS
Read 196 spots for DRR010705
Written 196 spots for DRR010705
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c142b226d71c11ee8e6c4be50c92e681"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpz8n3rric/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- history_id
  - 518e25b602048f81
- history_state
  - ok
- invocation_id
  - 518e25b602048f81
- invocation_state
  - scheduled
- workflow_id
  - 518e25b602048f81

github-actions · 2024-03-01T11:50:02Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	3
Passed	2
Error	1
Failure	0
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: clan info file:
- step_state: scheduled

Step 11: SSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 12: LSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 13: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cb23f25bd7bf11ee93495f711304291f"
      
      input {"values": [{"id": 12, "src": "hdca"}]}
Step 14: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cb23f25bd7bf11ee93495f711304291f"
      
      input {"values": [{"id": 13, "src": "hdca"}]}

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp8kb8sehn/job_working_directory/000/27/configs/tmp5tlwjsxn' '/tmp/tmp8kb8sehn/job_working_directory/000/27/outputs/dataset_8d67802b-5d91-44fb-96c2-bb5e51a0477b.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 15, "src": "hdca"}]}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp8kb8sehn/job_working_directory/000/28/configs/tmpgzvjsx29' '/tmp/tmp8kb8sehn/job_working_directory/000/28/outputs/dataset_d4bc3a4e-2d2e-4945-b5d5-4b6348d489c2.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 16, "src": "hdca"}]}`

Step 18: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cb23f25bd7bf11ee93495f711304291f"
      
      input {"values": [{"id": 14, "src": "hdca"}]}

Step 19: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 31, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 20: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 32, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: covariance models:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp8kb8sehn/job_working_directory/000/30/configs/tmpxzlwo5zr' '/tmp/tmp8kb8sehn/job_working_directory/000/30/outputs/dataset_ff733cf3-095d-45a7-a87b-2da7c1ce79fa.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: Unlabelled step:
- step_state: scheduled
Step 23: Unlabelled step:
- step_state: scheduled

Step 24: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 33, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 25: Unlabelled step:
- step_state: scheduled
Step 26: Unlabelled step:
- step_state: scheduled
Step 27: Unlabelled step:
- step_state: scheduled
Step 28: HDF5 SSU SILVA:
- step_state: scheduled
Step 29: JSON SSU SILVA:
- step_state: scheduled

Step 30: Krona SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709293731_178722_55220.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709293731_141015_42662.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmp8kb8sehn/files/b/8/3/dataset_b831f7f5-19c7-4a7f-a679-0ca42b5bb304.dat '/tmp/tmp8kb8sehn/files/8/2/d/dataset_82d134e4-08e3-4486-b208-8fbbe6b718fd.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmp8kb8sehn/job_working_directory/000/5/outputs/dataset_aaf81623-18f6-4516-8edc-da3e0265d007.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmp8kb8sehn/files/b/8/3/dataset_b831f7f5-19c7-4a7f-a679-0ca42b5bb304.dat '/tmp/tmp8kb8sehn/files/8/6/5/dataset_865eea09-63e8-4b75-a175-4bd1851b087d.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmp8kb8sehn/job_working_directory/000/6/outputs/dataset_6432f9ec-c6fa-4555-b7ae-aa428c18a272.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 31: HDF5 LSU SILVA:
- step_state: scheduled
Step 32: JSON LSU SILVA:
- step_state: scheduled

Step 33: Krona LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709293731_386192_59465.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709293731_141015_42662.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 33, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 34: Unlabelled step:
- step_state: scheduled
Step 35: Unlabelled step:
- step_state: scheduled
Step 36: HDF5 ITSonedb:
- step_state: scheduled
Step 37: JSON ITSonedb:
- step_state: scheduled

Step 38: Krona ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709293731_2741215_94501.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709293731_141015_42662.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 39: HDF5 ITS UNITE:
- step_state: scheduled
Step 40: JSON ITS UNITE:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp8kb8sehn/files/4/7/9/dataset_4798cf29-5f67-442e-9632-128bf42fe22b.dat' clan_info && ln -s '/tmp/tmp8kb8sehn/files/a/a/f/dataset_aaf81623-18f6-4516-8edc-da3e0265d007.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmp8kb8sehn/job_working_directory/000/7/outputs/dataset_8f1e2cf7-44d6-44ae-b567-e9bc07083ce4.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp8kb8sehn/files/4/7/9/dataset_4798cf29-5f67-442e-9632-128bf42fe22b.dat' clan_info && ln -s '/tmp/tmp8kb8sehn/files/6/4/3/dataset_6432f9ec-c6fa-4555-b7ae-aa428c18a272.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmp8kb8sehn/job_working_directory/000/8/outputs/dataset_340acd27-396a-4671-af60-40d9129640b2.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 41: Krona ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709293731_456031_70078.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8kb8sehn/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709293731_141015_42662.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 46, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmp8kb8sehn/job_working_directory/000/9/configs/tmpahzowcz6' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmp8kb8sehn/job_working_directory/000/9/configs/tmpums9eyr7' -Q '/tmp/tmp8kb8sehn/job_working_directory/000/9/configs/tmpahzowcz6'   --no_header   -o '/tmp/tmp8kb8sehn/job_working_directory/000/9/outputs/dataset_4029a05f-2093-4ac3-81b1-7a0e6665bea7.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmp8kb8sehn/files/8/f/1/dataset_8f1e2cf7-44d6-44ae-b567-e9bc07083ce4.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is error

Command Line:

cat '/tmp/tmp8kb8sehn/job_working_directory/000/10/configs/tmpqhjds3yb' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmp8kb8sehn/job_working_directory/000/10/configs/tmpj1_bpwls' -Q '/tmp/tmp8kb8sehn/job_working_directory/000/10/configs/tmpqhjds3yb'   --no_header   -o '/tmp/tmp8kb8sehn/job_working_directory/000/10/outputs/dataset_7f3abd3e-8837-41d5-b3ea-eb0a0f44ca20.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmp8kb8sehn/files/3/4/0/dataset_340acd27-396a-4671-af60-40d9129640b2.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Step 7: SSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 8: SSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Step 9: LSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 10: LSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"cb23f25bd7bf11ee93495f711304291f"`
chromInfo	`"/tmp/tmp8kb8sehn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 243af191ffc6dc20
- history_state
  - error
- invocation_id
  - 243af191ffc6dc20
- invocation_state
  - scheduled
- workflow_id
  - 243af191ffc6dc20

Passed Tests

✅ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpix2oug0e/job_working_directory/000/1/configs/tmpdvkamrvd' ~/.ncbi/user-settings.mkfg &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-01T11:35:22 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-01T11:35:22 prefetch.3.0.8: 1) Downloading 'DRR218540'...
2024-03-01T11:35:22 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-01T11:35:22 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-01T11:35:23 prefetch.3.0.8:  HTTPS download succeed
2024-03-01T11:35:23 prefetch.3.0.8:  'DRR218540' is valid
2024-03-01T11:35:23 prefetch.3.0.8: 1) 'DRR218540' was downloaded successfully
2024-03-01T11:35:23 prefetch.3.0.8: 'DRR218540' has 0 unresolved dependencies

Standard Output:

Downloading accession: DRR218540...

Read 67485 spots for DRR218540
Written 67485 spots for DRR218540
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "bd815518d7bf11eebdf3c5ab8c76cc22"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpix2oug0e/files/1/5/c/dataset_15caa508-4dbf-45ac-90c6-70e4c727c13f.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmpix2oug0e/files/4/2/f/dataset_42f26d52-4936-4c07-b6f4-0c3afd17ee43.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmpix2oug0e/job_working_directory/000/3/outputs/dataset_bca68e8a-8269-41b8-add8-ec08167d0121.dat' && mv second.fastq.gz '/tmp/tmpix2oug0e/job_working_directory/000/3/outputs/dataset_71547785-70aa-4c29-99b5-2b3823b82446.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 25 seconds

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmpix2oug0e/files/b/c/a/dataset_bca68e8a-8269-41b8-add8-ec08167d0121.dat' -r '/tmp/tmpix2oug0e/files/7/1/5/dataset_71547785-70aa-4c29-99b5-2b3823b82446.dat' -1 '/tmp/tmpix2oug0e/job_working_directory/000/6/outputs/dataset_7d4e0af4-b6ed-4a32-bc26-0be88bcafac4.dat' -2 '/tmp/tmpix2oug0e/job_working_directory/000/6/outputs/dataset_cdf435de-9356-4cb6-a137-4cfbf1df48bc.dat'  -s '/tmp/tmpix2oug0e/job_working_directory/000/6/outputs/dataset_444782ba-b70d-4523-87bb-2c1f970edd97.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020856

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpix2oug0e/files/4/4/4/dataset_444782ba-b70d-4523-87bb-2c1f970edd97.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpix2oug0e/job_working_directory/000/7/outputs/dataset_d215b974-39bb-4bfd-921e-4c0845b72e3a.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 6434 Surviving: 6432 (99.97%) Dropped: 2 (0.03%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpix2oug0e/files/4/4/4/dataset_444782ba-b70d-4523-87bb-2c1f970edd97.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpix2oug0e/job_working_directory/000/8/outputs/dataset_b7eb9b11-347b-4c9a-bab0-10cb4306332a_files' && fastqc --outdir '/tmp/tmpix2oug0e/job_working_directory/000/8/outputs/dataset_b7eb9b11-347b-4c9a-bab0-10cb4306332a_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpix2oug0e/job_working_directory/000/8/outputs/dataset_b7eb9b11-347b-4c9a-bab0-10cb4306332a_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpix2oug0e/job_working_directory/000/8/outputs/dataset_b7eb9b11-347b-4c9a-bab0-10cb4306332a_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
adapters	`None`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpix2oug0e/files/d/2/1/dataset_d215b974-39bb-4bfd-921e-4c0845b72e3a.dat' '/tmp/tmpix2oug0e/job_working_directory/000/9/configs/tmppdnxcxyv' '/tmp/tmpix2oug0e/job_working_directory/000/9/outputs/dataset_e366dde9-432e-4b4e-b3db-8895da3bb58f.dat' '/tmp/tmpix2oug0e/job_working_directory/000/9/outputs/dataset_e366dde9-432e-4b4e-b3db-8895da3bb58f_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 6432 of 6432 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpix2oug0e/files/d/2/1/dataset_d215b974-39bb-4bfd-921e-4c0845b72e3a.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpix2oug0e/job_working_directory/000/10/outputs/dataset_caf4c93b-27f6-40ae-9033-7b5b2b298987_files' && fastqc --outdir '/tmp/tmpix2oug0e/job_working_directory/000/10/outputs/dataset_caf4c93b-27f6-40ae-9033-7b5b2b298987_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpix2oug0e/job_working_directory/000/10/outputs/dataset_caf4c93b-27f6-40ae-9033-7b5b2b298987_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpix2oug0e/job_working_directory/000/10/outputs/dataset_caf4c93b-27f6-40ae-9033-7b5b2b298987_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
adapters	`None`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpix2oug0e/job_working_directory/000/11/outputs/dataset_6e5b5c03-bcc7-4eed-89a6-8ecbf15c0f27.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpix2oug0e/files/c/1/0/dataset_c10bdbd3-8049-4fc1-9af9-cc7a8dfc06e4.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpix2oug0e/files/e/3/6/dataset_e366dde9-432e-4b4e-b3db-8895da3bb58f.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpix2oug0e/job_working_directory/000/12/outputs/dataset_45a7f9b2-cf68-4ef9-a1cb-5c16f4c1e8e4_files' && fastqc --outdir '/tmp/tmpix2oug0e/job_working_directory/000/12/outputs/dataset_45a7f9b2-cf68-4ef9-a1cb-5c16f4c1e8e4_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpix2oug0e/job_working_directory/000/12/outputs/dataset_45a7f9b2-cf68-4ef9-a1cb-5c16f4c1e8e4_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpix2oug0e/job_working_directory/000/12/outputs/dataset_45a7f9b2-cf68-4ef9-a1cb-5c16f4c1e8e4_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
adapters	`None`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpix2oug0e/files/e/3/6/dataset_e366dde9-432e-4b4e-b3db-8895da3bb58f.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 6,432
	Input bases: 2,151,394
	Input mean length: 334.48
	Good sequences: 6,432 (100.00%)
	Good bases: 2,151,394
	Good mean length: 334.48
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpix2oug0e/job_working_directory/000/14/outputs/dataset_db3cc797-081b-4110-accd-f89d6085d73f.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpix2oug0e/files/7/9/1/dataset_7910d35f-d7a2-4843-8c0b-a3bb4d91dd6e.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpix2oug0e/job_working_directory/000/15/outputs/dataset_7253b3bd-c1f2-494e-9d2c-41576306c616.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpix2oug0e/files/5/5/a/dataset_55a29681-58d6-4e4e-9a8b-ecb12233707d.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpix2oug0e/files/9/c/0/dataset_9c0c35f4-12dc-43b3-b0c5-8ccfb87fae74.dat' '/tmp/tmpix2oug0e/job_working_directory/000/16/outputs/dataset_3e2ceef9-907a-49ab-b31a-d31032a89280.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

6432 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpix2oug0e/files/9/c/0/dataset_9c0c35f4-12dc-43b3-b0c5-8ccfb87fae74.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpix2oug0e/job_working_directory/000/17/outputs/dataset_c443c180-6744-4d87-88d2-47627fef38a6_files' && fastqc --outdir '/tmp/tmpix2oug0e/job_working_directory/000/17/outputs/dataset_c443c180-6744-4d87-88d2-47627fef38a6_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpix2oug0e/job_working_directory/000/17/outputs/dataset_c443c180-6744-4d87-88d2-47627fef38a6_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpix2oug0e/job_working_directory/000/17/outputs/dataset_c443c180-6744-4d87-88d2-47627fef38a6_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
adapters	`None`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpix2oug0e/files/3/e/2/dataset_3e2ceef9-907a-49ab-b31a-d31032a89280.dat' | fasta_formatter -w 0 -o '/tmp/tmpix2oug0e/job_working_directory/000/18/outputs/dataset_f99cd360-e245-484d-83bb-2f058d30fb7d.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpix2oug0e/job_working_directory/000/19/outputs/dataset_4e2994ae-fc08-4487-831c-f789b885f491.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpix2oug0e/files/0/d/1/dataset_0d18130e-08c0-45cd-83b6-52cffa8465c1.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmpix2oug0e/files/6/e/5/dataset_6e5b5c03-bcc7-4eed-89a6-8ecbf15c0f27.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmpix2oug0e/files/d/b/3/dataset_db3cc797-081b-4110-accd-f89d6085d73f.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmpix2oug0e/files/7/2/5/dataset_7253b3bd-c1f2-494e-9d2c-41576306c616.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmpix2oug0e/files/4/e/2/dataset_4e2994ae-fc08-4487-831c-f789b885f491.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpix2oug0e/job_working_directory/000/20/working/multiqc_WDir
|            fastqc | Found 4 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bd815518d7bf11eebdf3c5ab8c76cc22"`
chromInfo	`"/tmp/tmpix2oug0e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 23, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- history_id
  - 08956bebf1fe41b7
- history_state
  - ok
- invocation_id
  - 08956bebf1fe41b7
- invocation_state
  - scheduled
- workflow_id
  - 08956bebf1fe41b7

✅ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled

Step 11: Trimming:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmp_8cqju6z/files/0/c/c/dataset_0cce528e-fd46-4665-8963-94bc946ce86a.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmp_8cqju6z/job_working_directory/000/2/outputs/dataset_f8676c6a-9932-4a7b-bd68-9370f9774855.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 196 Surviving: 184 (93.88%) Dropped: 12 (6.12%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 1, "src": "dce"}]}, "single_or_paired": "se"}`

Job 2:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmp_8cqju6z/files/0/a/3/dataset_0a39214e-38f2-4830-b821-9d529b144f7b.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmp_8cqju6z/job_working_directory/000/3/outputs/dataset_4cb59fe2-9f92-4382-9d17-f5ae80f4f391.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 90 Surviving: 90 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 2, "src": "dce"}]}, "single_or_paired": "se"}`

Step 12: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp_8cqju6z/files/0/c/c/dataset_0cce528e-fd46-4665-8963-94bc946ce86a.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmp_8cqju6z/job_working_directory/000/4/outputs/dataset_09859d16-b725-47d0-b894-c10adcca7910_files' && fastqc --outdir '/tmp/tmp_8cqju6z/job_working_directory/000/4/outputs/dataset_09859d16-b725-47d0-b894-c10adcca7910_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmp_8cqju6z/job_working_directory/000/4/outputs/dataset_09859d16-b725-47d0-b894-c10adcca7910_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp_8cqju6z/job_working_directory/000/4/outputs/dataset_09859d16-b725-47d0-b894-c10adcca7910_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adapters	`None`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp_8cqju6z/files/0/a/3/dataset_0a39214e-38f2-4830-b821-9d529b144f7b.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmp_8cqju6z/job_working_directory/000/5/outputs/dataset_5c9f42bc-c2f8-45f8-8319-bdf6332b8eb0_files' && fastqc --outdir '/tmp/tmp_8cqju6z/job_working_directory/000/5/outputs/dataset_5c9f42bc-c2f8-45f8-8319-bdf6332b8eb0_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmp_8cqju6z/job_working_directory/000/5/outputs/dataset_5c9f42bc-c2f8-45f8-8319-bdf6332b8eb0_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp_8cqju6z/job_working_directory/000/5/outputs/dataset_5c9f42bc-c2f8-45f8-8319-bdf6332b8eb0_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adapters	`None`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 13: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmp_8cqju6z/files/f/8/6/dataset_f8676c6a-9932-4a7b-bd68-9370f9774855.dat' '/tmp/tmp_8cqju6z/job_working_directory/000/6/configs/tmp6sh4hffr' '/tmp/tmp_8cqju6z/job_working_directory/000/6/outputs/dataset_95c6f729-83a1-43fc-8cd0-a3c815cf1ece.dat' '/tmp/tmp_8cqju6z/job_working_directory/000/6/outputs/dataset_95c6f729-83a1-43fc-8cd0-a3c815cf1ece_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 184 of 184 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Job 2:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmp_8cqju6z/files/4/c/b/dataset_4cb59fe2-9f92-4382-9d17-f5ae80f4f391.dat' '/tmp/tmp_8cqju6z/job_working_directory/000/7/configs/tmpci9miqmh' '/tmp/tmp_8cqju6z/job_working_directory/000/7/outputs/dataset_7d3947d6-c000-40db-bb2c-bf14b0703be7.dat' '/tmp/tmp_8cqju6z/job_working_directory/000/7/outputs/dataset_7d3947d6-c000-40db-bb2c-bf14b0703be7_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 90 of 90 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp_8cqju6z/files/f/8/6/dataset_f8676c6a-9932-4a7b-bd68-9370f9774855.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmp_8cqju6z/job_working_directory/000/8/outputs/dataset_fd5149b7-4c80-416a-88c5-83e188799376_files' && fastqc --outdir '/tmp/tmp_8cqju6z/job_working_directory/000/8/outputs/dataset_fd5149b7-4c80-416a-88c5-83e188799376_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmp_8cqju6z/job_working_directory/000/8/outputs/dataset_fd5149b7-4c80-416a-88c5-83e188799376_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp_8cqju6z/job_working_directory/000/8/outputs/dataset_fd5149b7-4c80-416a-88c5-83e188799376_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adapters	`None`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp_8cqju6z/files/4/c/b/dataset_4cb59fe2-9f92-4382-9d17-f5ae80f4f391.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmp_8cqju6z/job_working_directory/000/9/outputs/dataset_6275053b-ff0d-4f07-9082-70fcdf436180_files' && fastqc --outdir '/tmp/tmp_8cqju6z/job_working_directory/000/9/outputs/dataset_6275053b-ff0d-4f07-9082-70fcdf436180_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmp_8cqju6z/job_working_directory/000/9/outputs/dataset_6275053b-ff0d-4f07-9082-70fcdf436180_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp_8cqju6z/job_working_directory/000/9/outputs/dataset_6275053b-ff0d-4f07-9082-70fcdf436180_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adapters	`None`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp_8cqju6z/job_working_directory/000/10/outputs/dataset_6e078ad7-2b58-4224-916b-d9dbb0be163e.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmp_8cqju6z/files/c/1/8/dataset_c180df9a-1b99-4350-b642-84890f735211.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp_8cqju6z/job_working_directory/000/11/outputs/dataset_f4f56db3-e3ef-4965-b838-6f3156b06108.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmp_8cqju6z/files/f/9/7/dataset_f9723bc8-c2fd-45a4-ac6e-8d23dcd63686.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 16: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmp_8cqju6z/files/9/5/c/dataset_95c6f729-83a1-43fc-8cd0-a3c815cf1ece.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 184
	Input bases: 46,942
	Input mean length: 255.12
	Good sequences: 184 (100.00%)
	Good bases: 46,942
	Good mean length: 255.12
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 9, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Job 2:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmp_8cqju6z/files/7/d/3/dataset_7d3947d6-c000-40db-bb2c-bf14b0703be7.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 90
	Input bases: 31,735
	Input mean length: 352.61
	Good sequences: 90 (100.00%)
	Good bases: 31,735
	Good mean length: 352.61
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 10, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp_8cqju6z/files/9/5/c/dataset_95c6f729-83a1-43fc-8cd0-a3c815cf1ece.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmp_8cqju6z/job_working_directory/000/14/outputs/dataset_afd5bb47-3e66-4b7e-9c07-78bf69c8b65f_files' && fastqc --outdir '/tmp/tmp_8cqju6z/job_working_directory/000/14/outputs/dataset_afd5bb47-3e66-4b7e-9c07-78bf69c8b65f_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmp_8cqju6z/job_working_directory/000/14/outputs/dataset_afd5bb47-3e66-4b7e-9c07-78bf69c8b65f_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp_8cqju6z/job_working_directory/000/14/outputs/dataset_afd5bb47-3e66-4b7e-9c07-78bf69c8b65f_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adapters	`None`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp_8cqju6z/files/7/d/3/dataset_7d3947d6-c000-40db-bb2c-bf14b0703be7.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmp_8cqju6z/job_working_directory/000/15/outputs/dataset_b6d8b882-d511-4520-b7dd-2378ba7cd387_files' && fastqc --outdir '/tmp/tmp_8cqju6z/job_working_directory/000/15/outputs/dataset_b6d8b882-d511-4520-b7dd-2378ba7cd387_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmp_8cqju6z/job_working_directory/000/15/outputs/dataset_b6d8b882-d511-4520-b7dd-2378ba7cd387_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp_8cqju6z/job_working_directory/000/15/outputs/dataset_b6d8b882-d511-4520-b7dd-2378ba7cd387_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adapters	`None`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp_8cqju6z/job_working_directory/000/16/outputs/dataset_a3112f5e-d921-4712-83f4-9ce1b80082b7.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmp_8cqju6z/files/7/7/2/dataset_77243647-b021-48f6-9c85-17e52557c6fa.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp_8cqju6z/job_working_directory/000/17/outputs/dataset_8446a62e-daa1-4f15-be93-075eccb3f8b9.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmp_8cqju6z/files/7/a/7/dataset_7a7a978b-51a9-4c36-81ee-83512b2629e4.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmp_8cqju6z/files/3/7/2/dataset_372005dc-5b0e-41db-b737-02e579e29101.dat' '/tmp/tmp_8cqju6z/job_working_directory/000/18/outputs/dataset_d90c793b-4a89-4fa2-a540-7a2afed67a76.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

184 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmp_8cqju6z/files/4/8/8/dataset_4883f914-b095-4c33-8823-0b2d8167821a.dat' '/tmp/tmp_8cqju6z/job_working_directory/000/19/outputs/dataset_fb5623f2-e634-4c0e-908d-e4f154747428.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

90 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp_8cqju6z/files/3/7/2/dataset_372005dc-5b0e-41db-b737-02e579e29101.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmp_8cqju6z/job_working_directory/000/20/outputs/dataset_c8183bcd-0719-47a8-939d-2b7d13751022_files' && fastqc --outdir '/tmp/tmp_8cqju6z/job_working_directory/000/20/outputs/dataset_c8183bcd-0719-47a8-939d-2b7d13751022_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmp_8cqju6z/job_working_directory/000/20/outputs/dataset_c8183bcd-0719-47a8-939d-2b7d13751022_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp_8cqju6z/job_working_directory/000/20/outputs/dataset_c8183bcd-0719-47a8-939d-2b7d13751022_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adapters	`None`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp_8cqju6z/files/4/8/8/dataset_4883f914-b095-4c33-8823-0b2d8167821a.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmp_8cqju6z/job_working_directory/000/21/outputs/dataset_a2686583-c198-4a6e-9b64-8bb3ca6b1ae1_files' && fastqc --outdir '/tmp/tmp_8cqju6z/job_working_directory/000/21/outputs/dataset_a2686583-c198-4a6e-9b64-8bb3ca6b1ae1_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmp_8cqju6z/job_working_directory/000/21/outputs/dataset_a2686583-c198-4a6e-9b64-8bb3ca6b1ae1_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp_8cqju6z/job_working_directory/000/21/outputs/dataset_a2686583-c198-4a6e-9b64-8bb3ca6b1ae1_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adapters	`None`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 3: Trimmomatic - LEADING:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp_8cqju6z/job_working_directory/000/22/outputs/dataset_ababdbab-62bc-4e64-a859-48d46af0ea14.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmp_8cqju6z/files/4/9/3/dataset_49356f2f-1733-4e35-899e-8951317c1ad5.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp_8cqju6z/job_working_directory/000/23/outputs/dataset_c95e806b-2c4d-43a6-945a-d3edf7957c0f.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmp_8cqju6z/files/a/6/9/dataset_a6906099-0ea3-404f-99db-f704758cc498.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp_8cqju6z/files/d/9/0/dataset_d90c793b-4a89-4fa2-a540-7a2afed67a76.dat' | fasta_formatter -w 60 -o '/tmp/tmp_8cqju6z/job_working_directory/000/24/outputs/dataset_355d2f83-41b2-44fe-af71-e4c10a83da87.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Job 2:

Job state is ok

Command Line:

cat '/tmp/tmp_8cqju6z/files/f/b/5/dataset_fb5623f2-e634-4c0e-908d-e4f154747428.dat' | fasta_formatter -w 60 -o '/tmp/tmp_8cqju6z/job_working_directory/000/25/outputs/dataset_50a19477-5f12-4b93-b550-15beefaf68e5.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp_8cqju6z/job_working_directory/000/26/outputs/dataset_e96f074f-edbd-4ca4-959e-7bbae4b97282.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmp_8cqju6z/files/9/4/a/dataset_94a78b1e-fa5f-43ef-9d6b-3c07d31e29e2.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp_8cqju6z/job_working_directory/000/27/outputs/dataset_049701aa-2d50-47a0-b77f-8cf4a44a806e.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmp_8cqju6z/files/a/9/6/dataset_a965af55-a523-46a1-aae7-7751d5e49862.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmp_8cqju6z/files/6/e/0/dataset_6e078ad7-2b58-4224-916b-d9dbb0be163e.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/tmp/tmp_8cqju6z/files/f/4/f/dataset_f4f56db3-e3ef-4965-b838-6f3156b06108.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmp_8cqju6z/files/a/3/1/dataset_a3112f5e-d921-4712-83f4-9ce1b80082b7.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_1/file_1' && ln -s '/tmp/tmp_8cqju6z/files/8/4/4/dataset_8446a62e-daa1-4f15-be93-075eccb3f8b9.dat' 'multiqc_WDir/fastqc_0/data_1/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmp_8cqju6z/files/a/b/a/dataset_ababdbab-62bc-4e64-a859-48d46af0ea14.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_2/file_1' && ln -s '/tmp/tmp_8cqju6z/files/c/9/5/dataset_c95e806b-2c4d-43a6-945a-d3edf7957c0f.dat' 'multiqc_WDir/fastqc_0/data_2/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmp_8cqju6z/files/e/9/6/dataset_e96f074f-edbd-4ca4-959e-7bbae4b97282.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_3/file_1' && ln -s '/tmp/tmp_8cqju6z/files/0/4/9/dataset_049701aa-2d50-47a0-b77f-8cf4a44a806e.dat' 'multiqc_WDir/fastqc_0/data_3/file_1/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmp_8cqju6z/job_working_directory/000/28/working/multiqc_WDir
|            fastqc | Found 8 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 8/8

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled
Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmp_8cqju6z/job_working_directory/000/1/configs/tmp9m_d2zht' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-01T11:36:52 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-01T11:36:52 prefetch.3.0.8: 1) Downloading 'DRR011051'...
2024-03-01T11:36:52 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-01T11:36:52 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-01T11:36:53 prefetch.3.0.8:  HTTPS download succeed
2024-03-01T11:36:53 prefetch.3.0.8:  'DRR011051' is valid
2024-03-01T11:36:53 prefetch.3.0.8: 1) 'DRR011051' was downloaded successfully
2024-03-01T11:36:53 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-01T11:36:54 prefetch.3.0.8: 1) Downloading 'DRR010705'...
2024-03-01T11:36:54 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-01T11:36:54 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-01T11:36:54 prefetch.3.0.8:  HTTPS download succeed
2024-03-01T11:36:54 prefetch.3.0.8:  'DRR010705' is valid
2024-03-01T11:36:54 prefetch.3.0.8: 1) 'DRR010705' was downloaded successfully

Standard Output:

Downloading accession: DRR011051...

Rejected 270 READS because of filtering out non-biological READS
Read 90 spots for DRR011051
Written 90 spots for DRR011051
Downloading accession: DRR010705...

Rejected 588 READS because of filtering out non-biological READS
Read 196 spots for DRR010705
Written 196 spots for DRR010705
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d9f69a0ad7bf11eea0d55f87c7f8f61e"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmp_8cqju6z/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- history_id
  - 684c51be72d853f8
- history_state
  - ok
- invocation_id
  - 684c51be72d853f8
- invocation_state
  - scheduled
- workflow_id
  - 684c51be72d853f8

github-actions · 2024-03-01T16:04:01Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	4
Passed	2
Error	2
Failure	0
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: clan info file:
- step_state: scheduled

Step 11: SSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 12: LSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 13: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "882e2d8bd7e211ee8d6e61ae14d6ad6a"
      
      input {"values": [{"id": 12, "src": "hdca"}]}
Step 14: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "882e2d8bd7e211ee8d6e61ae14d6ad6a"
      
      input {"values": [{"id": 13, "src": "hdca"}]}

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpagfnirzq/job_working_directory/000/27/configs/tmpv09brgmz' '/tmp/tmpagfnirzq/job_working_directory/000/27/outputs/dataset_c600449a-ff32-4be4-b472-7f5f1c759fae.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 15, "src": "hdca"}]}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpagfnirzq/job_working_directory/000/28/configs/tmpra7gv30e' '/tmp/tmpagfnirzq/job_working_directory/000/28/outputs/dataset_b1ee3535-e90d-4904-bd58-78f9598b80fb.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 16, "src": "hdca"}]}`

Step 18: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "882e2d8bd7e211ee8d6e61ae14d6ad6a"
      
      input {"values": [{"id": 14, "src": "hdca"}]}

Step 19: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 31, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 20: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 32, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: covariance models:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpagfnirzq/job_working_directory/000/30/configs/tmpkltvdjkn' '/tmp/tmpagfnirzq/job_working_directory/000/30/outputs/dataset_877cfece-be32-4d9a-b352-d14b3e7094a2.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: Unlabelled step:
- step_state: scheduled
Step 23: Unlabelled step:
- step_state: scheduled

Step 24: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 33, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 25: Unlabelled step:
- step_state: scheduled
Step 26: Unlabelled step:
- step_state: scheduled
Step 27: Unlabelled step:
- step_state: scheduled
Step 28: HDF5 SSU SILVA:
- step_state: scheduled
Step 29: JSON SSU SILVA:
- step_state: scheduled

Step 30: Krona SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709308678_1299715_82646.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709308678_0227113_10749.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 27, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpagfnirzq/files/e/a/6/dataset_ea6fe317-f275-4746-9d83-2ea3bfd62338.dat '/tmp/tmpagfnirzq/files/0/f/a/dataset_0fa1333e-ae56-4ad2-a8e1-59cea35391b2.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpagfnirzq/job_working_directory/000/5/outputs/dataset_9660a0f8-c932-4bcb-9913-358c088cb8d1.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpagfnirzq/files/e/a/6/dataset_ea6fe317-f275-4746-9d83-2ea3bfd62338.dat '/tmp/tmpagfnirzq/files/d/c/b/dataset_dcb2a028-a03a-4761-ba94-f1f77c74f116.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpagfnirzq/job_working_directory/000/6/outputs/dataset_156735be-984d-41da-8fdf-4dd283e008d6.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 31: HDF5 LSU SILVA:
- step_state: scheduled
Step 32: JSON LSU SILVA:
- step_state: scheduled

Step 33: Krona LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709308678_0589333_98196.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709308678_0227113_10749.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 31, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 34: Unlabelled step:
- step_state: scheduled
Step 35: Unlabelled step:
- step_state: scheduled
Step 36: HDF5 ITSonedb:
- step_state: scheduled
Step 37: JSON ITSonedb:
- step_state: scheduled

Step 38: Krona ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709308680_334089_76491.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709308678_0227113_10749.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 39: HDF5 ITS UNITE:
- step_state: scheduled
Step 40: JSON ITS UNITE:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpagfnirzq/files/5/c/f/dataset_5cf557bd-b5c8-449f-a884-f4ea400a3fa9.dat' clan_info && ln -s '/tmp/tmpagfnirzq/files/9/6/6/dataset_9660a0f8-c932-4bcb-9913-358c088cb8d1.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpagfnirzq/job_working_directory/000/7/outputs/dataset_a58c31db-b82a-42ba-8c17-18220525a94d.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpagfnirzq/files/5/c/f/dataset_5cf557bd-b5c8-449f-a884-f4ea400a3fa9.dat' clan_info && ln -s '/tmp/tmpagfnirzq/files/1/5/6/dataset_156735be-984d-41da-8fdf-4dd283e008d6.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpagfnirzq/job_working_directory/000/8/outputs/dataset_acacbc3f-9036-44e9-99bf-7d794a2d6d2a.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 41: Krona ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709308680_243598_51479.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpagfnirzq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709308678_0227113_10749.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 46, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmpagfnirzq/job_working_directory/000/9/configs/tmp_m1uea93' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpagfnirzq/job_working_directory/000/9/configs/tmpci4ezj2v' -Q '/tmp/tmpagfnirzq/job_working_directory/000/9/configs/tmp_m1uea93'   --no_header   -o '/tmp/tmpagfnirzq/job_working_directory/000/9/outputs/dataset_5e2a79e2-d3e4-4eec-8da1-ba4199771d9d.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpagfnirzq/files/a/5/8/dataset_a58c31db-b82a-42ba-8c17-18220525a94d.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is error

Command Line:

cat '/tmp/tmpagfnirzq/job_working_directory/000/10/configs/tmpny5l0v6a' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpagfnirzq/job_working_directory/000/10/configs/tmpbs6zeszd' -Q '/tmp/tmpagfnirzq/job_working_directory/000/10/configs/tmpny5l0v6a'   --no_header   -o '/tmp/tmpagfnirzq/job_working_directory/000/10/outputs/dataset_d5635a62-d3d3-4747-903e-71e2ea906e08.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpagfnirzq/files/a/c/a/dataset_acacbc3f-9036-44e9-99bf-7d794a2d6d2a.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Step 7: SSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 8: SSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Step 9: LSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 10: LSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"882e2d8bd7e211ee8d6e61ae14d6ad6a"`
chromInfo	`"/tmp/tmpagfnirzq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 0d21d3895bfd9520
- history_state
  - error
- invocation_id
  - 0d21d3895bfd9520
- invocation_state
  - scheduled
- workflow_id
  - 0d21d3895bfd9520

❌ testing_query_tabular.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: covariance models:
- step_state: scheduled
Step 3: clan info file:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpqtc1udji/files/3/d/c/dataset_3dc0bc48-932b-4882-aa91-233551dedc0a.dat '/tmp/tmpqtc1udji/files/0/9/a/dataset_09ad046c-f520-4d84-992c-6067238b1e3f.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpqtc1udji/job_working_directory/000/5/outputs/dataset_ab195767-5030-4a0d-b84d-e76082312f9e.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"5540180dd7e211ee8fbe83277ed0cc97"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpqtc1udji/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is running

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpqtc1udji/files/3/d/c/dataset_3dc0bc48-932b-4882-aa91-233551dedc0a.dat '/tmp/tmpqtc1udji/files/2/f/b/dataset_2fb8903e-b6dd-4b79-ac48-0a9f2de2bddc.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpqtc1udji/job_working_directory/000/6/outputs/dataset_53c04763-636e-4e5e-b402-734041f128f0.dat'

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"5540180dd7e211ee8fbe83277ed0cc97"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpqtc1udji/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpqtc1udji/files/9/c/4/dataset_9c4bf298-cf74-49c3-8c60-a6af94b51525.dat' clan_info && ln -s '/tmp/tmpqtc1udji/files/a/b/1/dataset_ab195767-5030-4a0d-b84d-e76082312f9e.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpqtc1udji/job_working_directory/000/7/outputs/dataset_d717d430-4233-4f43-a80b-e0e7612a1e39.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5540180dd7e211ee8fbe83277ed0cc97"`
chromInfo	`"/tmp/tmpqtc1udji/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5540180dd7e211ee8fbe83277ed0cc97"`
chromInfo	`"/tmp/tmpqtc1udji/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmpqtc1udji/job_working_directory/000/9/configs/tmpz7hfgnqe' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpqtc1udji/job_working_directory/000/9/configs/tmpin47yu78' -Q '/tmp/tmpqtc1udji/job_working_directory/000/9/configs/tmpz7hfgnqe'   --no_header   -o '/tmp/tmpqtc1udji/job_working_directory/000/9/outputs/dataset_cc872ce2-7d8d-4a0f-a30b-cf46321dd804.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpqtc1udji/files/d/7/1/dataset_d717d430-4233-4f43-a80b-e0e7612a1e39.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5540180dd7e211ee8fbe83277ed0cc97"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmpqtc1udji/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"5540180dd7e211ee8fbe83277ed0cc97"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmpqtc1udji/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - e0b1cbb866acbca0
- history_state
  - error
- invocation_id
  - e0b1cbb866acbca0
- invocation_state
  - scheduled
- workflow_id
  - e0b1cbb866acbca0

Passed Tests

✅ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmplp9p2rbh/job_working_directory/000/1/configs/tmp1q8ygfv4' ~/.ncbi/user-settings.mkfg &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-01T15:44:28 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-01T15:44:28 prefetch.3.0.8: 1) Downloading 'DRR218540'...
2024-03-01T15:44:28 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-01T15:44:28 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-01T15:44:29 prefetch.3.0.8:  HTTPS download succeed
2024-03-01T15:44:29 prefetch.3.0.8:  'DRR218540' is valid
2024-03-01T15:44:29 prefetch.3.0.8: 1) 'DRR218540' was downloaded successfully
2024-03-01T15:44:29 prefetch.3.0.8: 'DRR218540' has 0 unresolved dependencies

Standard Output:

Downloading accession: DRR218540...

Read 67485 spots for DRR218540
Written 67485 spots for DRR218540
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "7852e632d7e211ee9362614cfa555fe8"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmplp9p2rbh/files/d/5/1/dataset_d5105685-4105-47bc-9a89-2e031b56830c.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmplp9p2rbh/files/b/2/1/dataset_b215751f-4989-46bd-8980-0aa8f28245de.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmplp9p2rbh/job_working_directory/000/3/outputs/dataset_debdc61b-b77d-4ffd-96a4-554923fd3688.dat' && mv second.fastq.gz '/tmp/tmplp9p2rbh/job_working_directory/000/3/outputs/dataset_00c23411-de66-4a59-a464-ef49f1f13e4d.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 25 seconds

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmplp9p2rbh/files/d/e/b/dataset_debdc61b-b77d-4ffd-96a4-554923fd3688.dat' -r '/tmp/tmplp9p2rbh/files/0/0/c/dataset_00c23411-de66-4a59-a464-ef49f1f13e4d.dat' -1 '/tmp/tmplp9p2rbh/job_working_directory/000/6/outputs/dataset_c60bc381-26f7-4dfa-be0c-2dbb4fbea4bd.dat' -2 '/tmp/tmplp9p2rbh/job_working_directory/000/6/outputs/dataset_3a8f5854-cf60-4e08-b8c2-10a2234615c3.dat'  -s '/tmp/tmplp9p2rbh/job_working_directory/000/6/outputs/dataset_03f6acb1-aca5-4027-8c4a-7eb6f1dd7746.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020722

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmplp9p2rbh/files/0/3/f/dataset_03f6acb1-aca5-4027-8c4a-7eb6f1dd7746.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmplp9p2rbh/job_working_directory/000/7/outputs/dataset_4c9f5aa8-5595-4d49-a9ac-1666212254b1.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 6434 Surviving: 6432 (99.97%) Dropped: 2 (0.03%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmplp9p2rbh/files/0/3/f/dataset_03f6acb1-aca5-4027-8c4a-7eb6f1dd7746.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmplp9p2rbh/job_working_directory/000/8/outputs/dataset_96d1cfba-6db2-491d-84f7-5fe418b03eb1_files' && fastqc --outdir '/tmp/tmplp9p2rbh/job_working_directory/000/8/outputs/dataset_96d1cfba-6db2-491d-84f7-5fe418b03eb1_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmplp9p2rbh/job_working_directory/000/8/outputs/dataset_96d1cfba-6db2-491d-84f7-5fe418b03eb1_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmplp9p2rbh/job_working_directory/000/8/outputs/dataset_96d1cfba-6db2-491d-84f7-5fe418b03eb1_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
adapters	`None`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmplp9p2rbh/files/4/c/9/dataset_4c9f5aa8-5595-4d49-a9ac-1666212254b1.dat' '/tmp/tmplp9p2rbh/job_working_directory/000/9/configs/tmp2dw46bhh' '/tmp/tmplp9p2rbh/job_working_directory/000/9/outputs/dataset_48bf5f67-00ed-4afb-a553-bdb83aa0a43b.dat' '/tmp/tmplp9p2rbh/job_working_directory/000/9/outputs/dataset_48bf5f67-00ed-4afb-a553-bdb83aa0a43b_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 6432 of 6432 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmplp9p2rbh/files/4/c/9/dataset_4c9f5aa8-5595-4d49-a9ac-1666212254b1.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmplp9p2rbh/job_working_directory/000/10/outputs/dataset_23db909b-793b-45fc-b892-2657cb1bec24_files' && fastqc --outdir '/tmp/tmplp9p2rbh/job_working_directory/000/10/outputs/dataset_23db909b-793b-45fc-b892-2657cb1bec24_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmplp9p2rbh/job_working_directory/000/10/outputs/dataset_23db909b-793b-45fc-b892-2657cb1bec24_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmplp9p2rbh/job_working_directory/000/10/outputs/dataset_23db909b-793b-45fc-b892-2657cb1bec24_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
adapters	`None`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmplp9p2rbh/job_working_directory/000/11/outputs/dataset_47a26c5e-1d0a-45bf-887c-94d93705fd3e.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmplp9p2rbh/files/c/9/0/dataset_c907d9a1-7ecb-4885-a44e-48eb620155f8.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmplp9p2rbh/files/4/8/b/dataset_48bf5f67-00ed-4afb-a553-bdb83aa0a43b.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmplp9p2rbh/job_working_directory/000/12/outputs/dataset_aa40fb08-7ca9-41a7-ba66-cc4143c715b6_files' && fastqc --outdir '/tmp/tmplp9p2rbh/job_working_directory/000/12/outputs/dataset_aa40fb08-7ca9-41a7-ba66-cc4143c715b6_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmplp9p2rbh/job_working_directory/000/12/outputs/dataset_aa40fb08-7ca9-41a7-ba66-cc4143c715b6_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmplp9p2rbh/job_working_directory/000/12/outputs/dataset_aa40fb08-7ca9-41a7-ba66-cc4143c715b6_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
adapters	`None`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmplp9p2rbh/files/4/8/b/dataset_48bf5f67-00ed-4afb-a553-bdb83aa0a43b.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 6,432
	Input bases: 2,151,394
	Input mean length: 334.48
	Good sequences: 6,432 (100.00%)
	Good bases: 2,151,394
	Good mean length: 334.48
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmplp9p2rbh/job_working_directory/000/14/outputs/dataset_ef77a984-9eae-47cb-998b-09b11856960d.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmplp9p2rbh/files/d/4/7/dataset_d470a5aa-9315-4cf8-b692-6cae5021f57a.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmplp9p2rbh/job_working_directory/000/15/outputs/dataset_1989ba25-a26c-4267-9d6a-dc2d90d204f4.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmplp9p2rbh/files/7/2/f/dataset_72f43fb7-35a7-4585-b84d-57d3bb77bccc.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmplp9p2rbh/files/b/5/3/dataset_b53db854-b5ef-4545-9f98-ef092a2b99b4.dat' '/tmp/tmplp9p2rbh/job_working_directory/000/16/outputs/dataset_9d2d6bef-71f7-420a-97ca-25a9b8ecf4be.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

6432 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmplp9p2rbh/files/b/5/3/dataset_b53db854-b5ef-4545-9f98-ef092a2b99b4.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmplp9p2rbh/job_working_directory/000/17/outputs/dataset_e5d07262-cfec-4fe6-afc9-2e8f5c2f989b_files' && fastqc --outdir '/tmp/tmplp9p2rbh/job_working_directory/000/17/outputs/dataset_e5d07262-cfec-4fe6-afc9-2e8f5c2f989b_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmplp9p2rbh/job_working_directory/000/17/outputs/dataset_e5d07262-cfec-4fe6-afc9-2e8f5c2f989b_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmplp9p2rbh/job_working_directory/000/17/outputs/dataset_e5d07262-cfec-4fe6-afc9-2e8f5c2f989b_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
adapters	`None`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmplp9p2rbh/files/9/d/2/dataset_9d2d6bef-71f7-420a-97ca-25a9b8ecf4be.dat' | fasta_formatter -w 0 -o '/tmp/tmplp9p2rbh/job_working_directory/000/18/outputs/dataset_e7897f3c-2fc1-463a-8cea-8b8e879a6a0a.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmplp9p2rbh/job_working_directory/000/19/outputs/dataset_7751718d-8481-4254-bc0d-99deee70d813.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmplp9p2rbh/files/5/e/d/dataset_5edaf5fa-f9f3-4eb2-9a9c-c9e0c27a19b8.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmplp9p2rbh/files/4/7/a/dataset_47a26c5e-1d0a-45bf-887c-94d93705fd3e.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmplp9p2rbh/files/e/f/7/dataset_ef77a984-9eae-47cb-998b-09b11856960d.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmplp9p2rbh/files/1/9/8/dataset_1989ba25-a26c-4267-9d6a-dc2d90d204f4.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmplp9p2rbh/files/7/7/5/dataset_7751718d-8481-4254-bc0d-99deee70d813.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmplp9p2rbh/job_working_directory/000/20/working/multiqc_WDir
|            fastqc | Found 4 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7852e632d7e211ee9362614cfa555fe8"`
chromInfo	`"/tmp/tmplp9p2rbh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 23, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- history_id
  - e1cbd73e218d742f
- history_state
  - ok
- invocation_id
  - e1cbd73e218d742f
- invocation_state
  - scheduled
- workflow_id
  - e1cbd73e218d742f

✅ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled

Step 11: Trimming:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpq8gi4ae4/files/b/4/1/dataset_b418b167-3b22-49fd-b281-3efd0cee5705.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpq8gi4ae4/job_working_directory/000/2/outputs/dataset_3a8ace81-1477-422d-807d-814594e75e9c.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 196 Surviving: 184 (93.88%) Dropped: 12 (6.12%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 1, "src": "dce"}]}, "single_or_paired": "se"}`

Job 2:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpq8gi4ae4/files/3/5/4/dataset_35499989-b819-4503-b03b-c83093b10c4f.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpq8gi4ae4/job_working_directory/000/3/outputs/dataset_01f27b83-7482-4678-9945-145e1e305ef2.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 90 Surviving: 90 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 2, "src": "dce"}]}, "single_or_paired": "se"}`

Step 12: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpq8gi4ae4/files/b/4/1/dataset_b418b167-3b22-49fd-b281-3efd0cee5705.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpq8gi4ae4/job_working_directory/000/4/outputs/dataset_0d339f2b-b8de-4282-bbc3-e35c0c049232_files' && fastqc --outdir '/tmp/tmpq8gi4ae4/job_working_directory/000/4/outputs/dataset_0d339f2b-b8de-4282-bbc3-e35c0c049232_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/4/outputs/dataset_0d339f2b-b8de-4282-bbc3-e35c0c049232_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/4/outputs/dataset_0d339f2b-b8de-4282-bbc3-e35c0c049232_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adapters	`None`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpq8gi4ae4/files/3/5/4/dataset_35499989-b819-4503-b03b-c83093b10c4f.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpq8gi4ae4/job_working_directory/000/5/outputs/dataset_684b2403-3b91-47aa-976d-ee576e7d12cc_files' && fastqc --outdir '/tmp/tmpq8gi4ae4/job_working_directory/000/5/outputs/dataset_684b2403-3b91-47aa-976d-ee576e7d12cc_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/5/outputs/dataset_684b2403-3b91-47aa-976d-ee576e7d12cc_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/5/outputs/dataset_684b2403-3b91-47aa-976d-ee576e7d12cc_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adapters	`None`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 13: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpq8gi4ae4/files/3/a/8/dataset_3a8ace81-1477-422d-807d-814594e75e9c.dat' '/tmp/tmpq8gi4ae4/job_working_directory/000/6/configs/tmpwixs0mql' '/tmp/tmpq8gi4ae4/job_working_directory/000/6/outputs/dataset_138cea1a-a06f-4d3f-9b17-4d1077911d41.dat' '/tmp/tmpq8gi4ae4/job_working_directory/000/6/outputs/dataset_138cea1a-a06f-4d3f-9b17-4d1077911d41_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 184 of 184 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Job 2:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpq8gi4ae4/files/0/1/f/dataset_01f27b83-7482-4678-9945-145e1e305ef2.dat' '/tmp/tmpq8gi4ae4/job_working_directory/000/7/configs/tmpedpqcrk5' '/tmp/tmpq8gi4ae4/job_working_directory/000/7/outputs/dataset_cf607f58-9fb5-48c1-841b-78e1d98dc07e.dat' '/tmp/tmpq8gi4ae4/job_working_directory/000/7/outputs/dataset_cf607f58-9fb5-48c1-841b-78e1d98dc07e_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 90 of 90 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpq8gi4ae4/files/3/a/8/dataset_3a8ace81-1477-422d-807d-814594e75e9c.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpq8gi4ae4/job_working_directory/000/8/outputs/dataset_28d38b76-8996-4b4d-ba79-16b4532b7a5a_files' && fastqc --outdir '/tmp/tmpq8gi4ae4/job_working_directory/000/8/outputs/dataset_28d38b76-8996-4b4d-ba79-16b4532b7a5a_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/8/outputs/dataset_28d38b76-8996-4b4d-ba79-16b4532b7a5a_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/8/outputs/dataset_28d38b76-8996-4b4d-ba79-16b4532b7a5a_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adapters	`None`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpq8gi4ae4/files/0/1/f/dataset_01f27b83-7482-4678-9945-145e1e305ef2.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpq8gi4ae4/job_working_directory/000/9/outputs/dataset_aee8098d-2a62-43c4-bc83-c821681a67a4_files' && fastqc --outdir '/tmp/tmpq8gi4ae4/job_working_directory/000/9/outputs/dataset_aee8098d-2a62-43c4-bc83-c821681a67a4_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/9/outputs/dataset_aee8098d-2a62-43c4-bc83-c821681a67a4_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/9/outputs/dataset_aee8098d-2a62-43c4-bc83-c821681a67a4_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adapters	`None`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpq8gi4ae4/job_working_directory/000/10/outputs/dataset_367aa98d-32e9-46e4-aab0-8084ed2d3f62.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpq8gi4ae4/files/0/f/d/dataset_0fd708d8-37cf-4538-90a3-49a61c040f58.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpq8gi4ae4/job_working_directory/000/11/outputs/dataset_8cb4547a-a8e4-40cc-8f83-6bcb4f6cecd1.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpq8gi4ae4/files/1/c/a/dataset_1ca31412-ba91-48eb-995a-689299302d27.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 16: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpq8gi4ae4/files/1/3/8/dataset_138cea1a-a06f-4d3f-9b17-4d1077911d41.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 184
	Input bases: 46,942
	Input mean length: 255.12
	Good sequences: 184 (100.00%)
	Good bases: 46,942
	Good mean length: 255.12
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 9, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Job 2:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpq8gi4ae4/files/c/f/6/dataset_cf607f58-9fb5-48c1-841b-78e1d98dc07e.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 90
	Input bases: 31,735
	Input mean length: 352.61
	Good sequences: 90 (100.00%)
	Good bases: 31,735
	Good mean length: 352.61
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 10, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpq8gi4ae4/files/1/3/8/dataset_138cea1a-a06f-4d3f-9b17-4d1077911d41.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpq8gi4ae4/job_working_directory/000/14/outputs/dataset_561a88ef-ea69-4dbe-8a62-0403ee2a3e4e_files' && fastqc --outdir '/tmp/tmpq8gi4ae4/job_working_directory/000/14/outputs/dataset_561a88ef-ea69-4dbe-8a62-0403ee2a3e4e_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/14/outputs/dataset_561a88ef-ea69-4dbe-8a62-0403ee2a3e4e_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/14/outputs/dataset_561a88ef-ea69-4dbe-8a62-0403ee2a3e4e_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adapters	`None`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpq8gi4ae4/files/c/f/6/dataset_cf607f58-9fb5-48c1-841b-78e1d98dc07e.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpq8gi4ae4/job_working_directory/000/15/outputs/dataset_4a6070a5-d1a7-44ad-847b-867c5e65be5b_files' && fastqc --outdir '/tmp/tmpq8gi4ae4/job_working_directory/000/15/outputs/dataset_4a6070a5-d1a7-44ad-847b-867c5e65be5b_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/15/outputs/dataset_4a6070a5-d1a7-44ad-847b-867c5e65be5b_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/15/outputs/dataset_4a6070a5-d1a7-44ad-847b-867c5e65be5b_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adapters	`None`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpq8gi4ae4/job_working_directory/000/16/outputs/dataset_81f5141e-6d24-4648-970b-9dbd6390620e.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpq8gi4ae4/files/7/e/c/dataset_7ec1fe2b-3ba3-45e8-963f-9ce515fceb36.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpq8gi4ae4/job_working_directory/000/17/outputs/dataset_1d7251cf-7662-4db2-90c6-2fcd5d5a80b7.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpq8gi4ae4/files/4/6/a/dataset_46ac6696-2d8e-4d80-a6f8-5968e8e5f30a.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpq8gi4ae4/files/9/5/f/dataset_95ff916a-05f2-4611-accf-663e0cafe7a8.dat' '/tmp/tmpq8gi4ae4/job_working_directory/000/18/outputs/dataset_e06a8b08-e706-4e3b-83e8-e622fe8e1814.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

184 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpq8gi4ae4/files/4/a/b/dataset_4ab2524c-de77-4219-8c70-db1546528d46.dat' '/tmp/tmpq8gi4ae4/job_working_directory/000/19/outputs/dataset_50c6eb0c-406b-4033-b780-008cd0be8e58.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

90 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpq8gi4ae4/files/9/5/f/dataset_95ff916a-05f2-4611-accf-663e0cafe7a8.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpq8gi4ae4/job_working_directory/000/20/outputs/dataset_ebcf10c9-16cc-4f96-bb7b-4f5660b25573_files' && fastqc --outdir '/tmp/tmpq8gi4ae4/job_working_directory/000/20/outputs/dataset_ebcf10c9-16cc-4f96-bb7b-4f5660b25573_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/20/outputs/dataset_ebcf10c9-16cc-4f96-bb7b-4f5660b25573_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/20/outputs/dataset_ebcf10c9-16cc-4f96-bb7b-4f5660b25573_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adapters	`None`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpq8gi4ae4/files/4/a/b/dataset_4ab2524c-de77-4219-8c70-db1546528d46.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpq8gi4ae4/job_working_directory/000/21/outputs/dataset_54fa5025-ba22-4548-b2bd-804f855a0fff_files' && fastqc --outdir '/tmp/tmpq8gi4ae4/job_working_directory/000/21/outputs/dataset_54fa5025-ba22-4548-b2bd-804f855a0fff_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/21/outputs/dataset_54fa5025-ba22-4548-b2bd-804f855a0fff_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/21/outputs/dataset_54fa5025-ba22-4548-b2bd-804f855a0fff_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adapters	`None`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 3: Trimmomatic - LEADING:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpq8gi4ae4/job_working_directory/000/22/outputs/dataset_16124b22-4d97-4f08-a784-03a2a2a56752.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpq8gi4ae4/files/4/e/9/dataset_4e9be84b-0eba-4cb4-a4a3-c7ef0beb66e9.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpq8gi4ae4/job_working_directory/000/23/outputs/dataset_98bce6fd-d46b-4372-a632-7daaa750557c.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpq8gi4ae4/files/2/2/c/dataset_22cdeb17-3c1b-4b5d-839e-759fbf0a0daf.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpq8gi4ae4/files/e/0/6/dataset_e06a8b08-e706-4e3b-83e8-e622fe8e1814.dat' | fasta_formatter -w 60 -o '/tmp/tmpq8gi4ae4/job_working_directory/000/24/outputs/dataset_49b7e13f-1c4c-4b61-9698-56f6e8fb45a3.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Job 2:

Job state is ok

Command Line:

cat '/tmp/tmpq8gi4ae4/files/5/0/c/dataset_50c6eb0c-406b-4033-b780-008cd0be8e58.dat' | fasta_formatter -w 60 -o '/tmp/tmpq8gi4ae4/job_working_directory/000/25/outputs/dataset_b649efb2-2244-4321-a715-e1c59be28a01.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpq8gi4ae4/job_working_directory/000/26/outputs/dataset_f91632a7-bac6-458f-93a0-e4a7ffae9977.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpq8gi4ae4/files/1/a/4/dataset_1a4ce192-6292-4f83-996e-2498f58a889e.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpq8gi4ae4/job_working_directory/000/27/outputs/dataset_955db4d1-6601-4c84-a9c3-60ce65950d95.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpq8gi4ae4/files/2/e/0/dataset_2e00ed3a-4069-4f2a-a7ae-a37a03fbba38.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmpq8gi4ae4/files/3/6/7/dataset_367aa98d-32e9-46e4-aab0-8084ed2d3f62.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/tmp/tmpq8gi4ae4/files/8/c/b/dataset_8cb4547a-a8e4-40cc-8f83-6bcb4f6cecd1.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmpq8gi4ae4/files/8/1/f/dataset_81f5141e-6d24-4648-970b-9dbd6390620e.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_1/file_1' && ln -s '/tmp/tmpq8gi4ae4/files/1/d/7/dataset_1d7251cf-7662-4db2-90c6-2fcd5d5a80b7.dat' 'multiqc_WDir/fastqc_0/data_1/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmpq8gi4ae4/files/1/6/1/dataset_16124b22-4d97-4f08-a784-03a2a2a56752.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_2/file_1' && ln -s '/tmp/tmpq8gi4ae4/files/9/8/b/dataset_98bce6fd-d46b-4372-a632-7daaa750557c.dat' 'multiqc_WDir/fastqc_0/data_2/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmpq8gi4ae4/files/f/9/1/dataset_f91632a7-bac6-458f-93a0-e4a7ffae9977.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_3/file_1' && ln -s '/tmp/tmpq8gi4ae4/files/9/5/5/dataset_955db4d1-6601-4c84-a9c3-60ce65950d95.dat' 'multiqc_WDir/fastqc_0/data_3/file_1/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpq8gi4ae4/job_working_directory/000/28/working/multiqc_WDir
|            fastqc | Found 8 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 8/8

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled
Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpq8gi4ae4/job_working_directory/000/1/configs/tmpidrdtr7r' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-01T15:44:10 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-01T15:44:10 prefetch.3.0.8: 1) Downloading 'DRR011051'...
2024-03-01T15:44:10 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-01T15:44:10 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-01T15:44:11 prefetch.3.0.8:  HTTPS download succeed
2024-03-01T15:44:11 prefetch.3.0.8:  'DRR011051' is valid
2024-03-01T15:44:11 prefetch.3.0.8: 1) 'DRR011051' was downloaded successfully
2024-03-01T15:44:11 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-01T15:44:12 prefetch.3.0.8: 1) Downloading 'DRR010705'...
2024-03-01T15:44:12 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-01T15:44:12 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-01T15:44:12 prefetch.3.0.8:  HTTPS download succeed
2024-03-01T15:44:12 prefetch.3.0.8:  'DRR010705' is valid
2024-03-01T15:44:12 prefetch.3.0.8: 1) 'DRR010705' was downloaded successfully

Standard Output:

Downloading accession: DRR011051...

Rejected 270 READS because of filtering out non-biological READS
Read 90 spots for DRR011051
Written 90 spots for DRR011051
Downloading accession: DRR010705...

Rejected 588 READS because of filtering out non-biological READS
Read 196 spots for DRR010705
Written 196 spots for DRR010705
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6d3ca940d7e211ee9bd563e7518a111b"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpq8gi4ae4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- history_id
  - ddcb36005225608e
- history_state
  - ok
- invocation_id
  - ddcb36005225608e
- invocation_state
  - scheduled
- workflow_id
  - ddcb36005225608e

github-actions · 2024-03-05T09:11:10Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	4
Passed	2
Error	1
Failure	1
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: clan info file:
- step_state: scheduled

Step 11: SSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 12: LSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 13: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "3e5c9ae1dace11eeb10939af22ca2817"
      
      input {"values": [{"id": 12, "src": "hdca"}]}
Step 14: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "3e5c9ae1dace11eeb10939af22ca2817"
      
      input {"values": [{"id": 13, "src": "hdca"}]}

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpxik2c8yf/job_working_directory/000/27/configs/tmppi_29on3' '/tmp/tmpxik2c8yf/job_working_directory/000/27/outputs/dataset_98235950-4afc-4623-a5a4-80bf0027d38e.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 15, "src": "hdca"}]}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpxik2c8yf/job_working_directory/000/28/configs/tmp3xy94x2r' '/tmp/tmpxik2c8yf/job_working_directory/000/28/outputs/dataset_ef2ecf9d-43e9-403d-8e86-f79a055ca705.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 16, "src": "hdca"}]}`

Step 18: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "3e5c9ae1dace11eeb10939af22ca2817"
      
      input {"values": [{"id": 14, "src": "hdca"}]}

Step 19: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 31, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 20: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 32, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: covariance models:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpxik2c8yf/job_working_directory/000/30/configs/tmpsu4aesva' '/tmp/tmpxik2c8yf/job_working_directory/000/30/outputs/dataset_736c463e-5c88-40ec-acba-458d9d11fc5f.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: Unlabelled step:
- step_state: scheduled
Step 23: Unlabelled step:
- step_state: scheduled

Step 24: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 33, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 25: Unlabelled step:
- step_state: scheduled
Step 26: Unlabelled step:
- step_state: scheduled
Step 27: Unlabelled step:
- step_state: scheduled
Step 28: HDF5 SSU SILVA:
- step_state: scheduled
Step 29: JSON SSU SILVA:
- step_state: scheduled

Step 30: Krona SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709629790_3102636_41520.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709629790_27473_40952.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 27, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpxik2c8yf/files/b/d/e/dataset_bdedf5f8-4f45-42d8-889a-865b3143d37e.dat '/tmp/tmpxik2c8yf/files/a/e/3/dataset_ae3b6b64-ba53-49f7-9ee0-79fefa979711.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpxik2c8yf/job_working_directory/000/5/outputs/dataset_d73c48db-6409-40eb-b4a9-0fb8a23f2964.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpxik2c8yf/files/b/d/e/dataset_bdedf5f8-4f45-42d8-889a-865b3143d37e.dat '/tmp/tmpxik2c8yf/files/9/6/c/dataset_96c6fbac-fc31-4e68-b8b0-bb37afe04367.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpxik2c8yf/job_working_directory/000/6/outputs/dataset_7d8e0ea2-96fe-47fe-ab9e-d7cd736abc1e.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 31: HDF5 LSU SILVA:
- step_state: scheduled
Step 32: JSON LSU SILVA:
- step_state: scheduled

Step 33: Krona LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709629791_3216_90823.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709629790_27473_40952.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 31, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 34: Unlabelled step:
- step_state: scheduled
Step 35: Unlabelled step:
- step_state: scheduled
Step 36: HDF5 ITSonedb:
- step_state: scheduled
Step 37: JSON ITSonedb:
- step_state: scheduled

Step 38: Krona ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709629792_3823376_13435.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709629790_27473_40952.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 39: HDF5 ITS UNITE:
- step_state: scheduled
Step 40: JSON ITS UNITE:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpxik2c8yf/files/b/c/a/dataset_bca21e18-5e60-4794-a93d-d6a229234b6d.dat' clan_info && ln -s '/tmp/tmpxik2c8yf/files/d/7/3/dataset_d73c48db-6409-40eb-b4a9-0fb8a23f2964.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpxik2c8yf/job_working_directory/000/7/outputs/dataset_c816c704-0189-45ac-842b-4297c1bb225e.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpxik2c8yf/files/b/c/a/dataset_bca21e18-5e60-4794-a93d-d6a229234b6d.dat' clan_info && ln -s '/tmp/tmpxik2c8yf/files/7/d/8/dataset_7d8e0ea2-96fe-47fe-ab9e-d7cd736abc1e.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpxik2c8yf/job_working_directory/000/8/outputs/dataset_5f49d1f4-e380-4e2a-b126-c1281cece2c2.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 41: Krona ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709629792_4609053_87932.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpxik2c8yf/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709629790_27473_40952.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 46, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmpxik2c8yf/job_working_directory/000/9/configs/tmps6qajjh_' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpxik2c8yf/job_working_directory/000/9/configs/tmp7az9w6xf' -Q '/tmp/tmpxik2c8yf/job_working_directory/000/9/configs/tmps6qajjh_'   --no_header   -o '/tmp/tmpxik2c8yf/job_working_directory/000/9/outputs/dataset_08bb2766-6d54-412a-b39c-6988483981ed.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpxik2c8yf/files/c/8/1/dataset_c816c704-0189-45ac-842b-4297c1bb225e.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is error

Command Line:

cat '/tmp/tmpxik2c8yf/job_working_directory/000/10/configs/tmpzuh5ocks' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpxik2c8yf/job_working_directory/000/10/configs/tmpmjzljkkd' -Q '/tmp/tmpxik2c8yf/job_working_directory/000/10/configs/tmpzuh5ocks'   --no_header   -o '/tmp/tmpxik2c8yf/job_working_directory/000/10/outputs/dataset_e46caf89-1144-4e5e-a5c1-421f40268512.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpxik2c8yf/files/5/f/4/dataset_5f49d1f4-e380-4e2a-b126-c1281cece2c2.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Step 7: SSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 8: SSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Step 9: LSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 10: LSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"3e5c9ae1dace11eeb10939af22ca2817"`
chromInfo	`"/tmp/tmpxik2c8yf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 32ef81340ea6f54b
- history_state
  - error
- invocation_id
  - 32ef81340ea6f54b
- invocation_state
  - scheduled
- workflow_id
  - 32ef81340ea6f54b

Failed Tests

❌ testing_query_tabular.ga_0

Problems:

Output with path /tmp/tmpy3dbkvzy/deoverlapped_matches__05cf36e6-9925-4ab6-9af1-d15d07e57ade different than expected
Expected 18+-0 columns in output found 1

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: covariance models:
- step_state: scheduled
Step 3: clan info file:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpq1cxmtqc/files/5/8/4/dataset_5842de45-c3ae-43d7-a440-d55cb4040358.dat '/tmp/tmpq1cxmtqc/files/c/2/1/dataset_c218d770-2f8f-4b5c-8089-8b01b5aaf3e9.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpq1cxmtqc/job_working_directory/000/5/outputs/dataset_4b763fda-1b61-4243-8eb3-84abe0359ca9.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"29cc6d1ddace11ee80bc1109d3033390"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpq1cxmtqc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpq1cxmtqc/files/5/8/4/dataset_5842de45-c3ae-43d7-a440-d55cb4040358.dat '/tmp/tmpq1cxmtqc/files/3/8/8/dataset_388ea3ee-867b-42cc-8ee6-e041221f7d9c.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpq1cxmtqc/job_working_directory/000/6/outputs/dataset_36ae279a-921e-4189-93a0-0fd44743053e.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"29cc6d1ddace11ee80bc1109d3033390"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpq1cxmtqc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpq1cxmtqc/files/3/0/9/dataset_30970e1d-38fd-4662-a21e-46d800c6cbe8.dat' clan_info && ln -s '/tmp/tmpq1cxmtqc/files/4/b/7/dataset_4b763fda-1b61-4243-8eb3-84abe0359ca9.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpq1cxmtqc/job_working_directory/000/7/outputs/dataset_05cf36e6-9925-4ab6-9af1-d15d07e57ade.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"29cc6d1ddace11ee80bc1109d3033390"`
chromInfo	`"/tmp/tmpq1cxmtqc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpq1cxmtqc/files/3/0/9/dataset_30970e1d-38fd-4662-a21e-46d800c6cbe8.dat' clan_info && ln -s '/tmp/tmpq1cxmtqc/files/3/6/a/dataset_36ae279a-921e-4189-93a0-0fd44743053e.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpq1cxmtqc/job_working_directory/000/8/outputs/dataset_57202699-679a-42f4-a38a-16fe4f7e3782.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"29cc6d1ddace11ee80bc1109d3033390"`
chromInfo	`"/tmp/tmpq1cxmtqc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Other invocation details
- history_id
  - 50eb700643b7332f
- history_state
  - ok
- invocation_id
  - 50eb700643b7332f
- invocation_state
  - scheduled
- workflow_id
  - 50eb700643b7332f

Passed Tests

✅ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpiux4iihh/job_working_directory/000/1/configs/tmpeiwbwgci' ~/.ncbi/user-settings.mkfg &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-05T08:57:42 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-05T08:57:42 prefetch.3.0.8: 1) Downloading 'DRR218540'...
2024-03-05T08:57:42 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-05T08:57:42 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-05T08:57:43 prefetch.3.0.8:  HTTPS download succeed
2024-03-05T08:57:44 prefetch.3.0.8:  'DRR218540' is valid
2024-03-05T08:57:44 prefetch.3.0.8: 1) 'DRR218540' was downloaded successfully
2024-03-05T08:57:44 prefetch.3.0.8: 'DRR218540' has 0 unresolved dependencies

Standard Output:

Downloading accession: DRR218540...

Read 67485 spots for DRR218540
Written 67485 spots for DRR218540
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "596b87eedace11eead7cddf3b0d30593"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpiux4iihh/files/c/3/6/dataset_c3642035-913b-4cca-be3e-a41a8943fb2e.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmpiux4iihh/files/0/c/f/dataset_0cf4a123-b420-4889-bcf9-1edae1964dca.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmpiux4iihh/job_working_directory/000/3/outputs/dataset_8fd6ad3c-7dec-421a-8bc1-6199aca05a26.dat' && mv second.fastq.gz '/tmp/tmpiux4iihh/job_working_directory/000/3/outputs/dataset_45600478-fcb5-4469-b7b1-8a4b5b199531.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 25 seconds

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmpiux4iihh/files/8/f/d/dataset_8fd6ad3c-7dec-421a-8bc1-6199aca05a26.dat' -r '/tmp/tmpiux4iihh/files/4/5/6/dataset_45600478-fcb5-4469-b7b1-8a4b5b199531.dat' -1 '/tmp/tmpiux4iihh/job_working_directory/000/6/outputs/dataset_a5a7c33c-1474-45fa-bdb4-dbfab13e2fbf.dat' -2 '/tmp/tmpiux4iihh/job_working_directory/000/6/outputs/dataset_32705659-3285-476c-924a-ad9dbf639ff8.dat'  -s '/tmp/tmpiux4iihh/job_working_directory/000/6/outputs/dataset_f499f746-c666-42a6-a42a-86cdb30b42d3.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020961

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpiux4iihh/files/f/4/9/dataset_f499f746-c666-42a6-a42a-86cdb30b42d3.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpiux4iihh/job_working_directory/000/7/outputs/dataset_b047efbc-7eaf-4348-93a6-a7468811bb94.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 6434 Surviving: 6432 (99.97%) Dropped: 2 (0.03%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpiux4iihh/files/f/4/9/dataset_f499f746-c666-42a6-a42a-86cdb30b42d3.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpiux4iihh/job_working_directory/000/8/outputs/dataset_a0691214-9cb2-40cf-96b0-0a08f90b4a87_files' && fastqc --outdir '/tmp/tmpiux4iihh/job_working_directory/000/8/outputs/dataset_a0691214-9cb2-40cf-96b0-0a08f90b4a87_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpiux4iihh/job_working_directory/000/8/outputs/dataset_a0691214-9cb2-40cf-96b0-0a08f90b4a87_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpiux4iihh/job_working_directory/000/8/outputs/dataset_a0691214-9cb2-40cf-96b0-0a08f90b4a87_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
adapters	`None`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpiux4iihh/files/b/0/4/dataset_b047efbc-7eaf-4348-93a6-a7468811bb94.dat' '/tmp/tmpiux4iihh/job_working_directory/000/9/configs/tmpmpjk_5tg' '/tmp/tmpiux4iihh/job_working_directory/000/9/outputs/dataset_fa28e75c-a1cf-449b-a699-f9014faa2f3e.dat' '/tmp/tmpiux4iihh/job_working_directory/000/9/outputs/dataset_fa28e75c-a1cf-449b-a699-f9014faa2f3e_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 6432 of 6432 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpiux4iihh/files/b/0/4/dataset_b047efbc-7eaf-4348-93a6-a7468811bb94.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpiux4iihh/job_working_directory/000/10/outputs/dataset_61b718b6-a050-4689-8818-c58a1082bbdb_files' && fastqc --outdir '/tmp/tmpiux4iihh/job_working_directory/000/10/outputs/dataset_61b718b6-a050-4689-8818-c58a1082bbdb_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpiux4iihh/job_working_directory/000/10/outputs/dataset_61b718b6-a050-4689-8818-c58a1082bbdb_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpiux4iihh/job_working_directory/000/10/outputs/dataset_61b718b6-a050-4689-8818-c58a1082bbdb_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
adapters	`None`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpiux4iihh/job_working_directory/000/11/outputs/dataset_40210520-4af0-4625-b5f8-a6e2a68f07a3.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpiux4iihh/files/b/f/2/dataset_bf259d1d-7cd4-4042-9e3b-580daad03220.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpiux4iihh/files/f/a/2/dataset_fa28e75c-a1cf-449b-a699-f9014faa2f3e.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpiux4iihh/job_working_directory/000/12/outputs/dataset_518a2f45-3fd5-43a3-b662-bf888f62dd4d_files' && fastqc --outdir '/tmp/tmpiux4iihh/job_working_directory/000/12/outputs/dataset_518a2f45-3fd5-43a3-b662-bf888f62dd4d_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpiux4iihh/job_working_directory/000/12/outputs/dataset_518a2f45-3fd5-43a3-b662-bf888f62dd4d_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpiux4iihh/job_working_directory/000/12/outputs/dataset_518a2f45-3fd5-43a3-b662-bf888f62dd4d_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
adapters	`None`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpiux4iihh/files/f/a/2/dataset_fa28e75c-a1cf-449b-a699-f9014faa2f3e.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 6,432
	Input bases: 2,151,394
	Input mean length: 334.48
	Good sequences: 6,432 (100.00%)
	Good bases: 2,151,394
	Good mean length: 334.48
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpiux4iihh/job_working_directory/000/14/outputs/dataset_0386d4e6-74be-4569-9d0a-2f257f9cb4b1.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpiux4iihh/files/0/7/c/dataset_07c26fc1-b1b7-4f28-8198-dfb2d6ecaba5.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpiux4iihh/job_working_directory/000/15/outputs/dataset_182d6121-6a65-4fd2-b081-eb5dff11e8f5.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpiux4iihh/files/3/4/e/dataset_34ef36c2-fef5-4d88-860e-c462caec9a77.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpiux4iihh/files/f/8/b/dataset_f8b6e742-e53f-4cbb-9b47-ab034e8d8b66.dat' '/tmp/tmpiux4iihh/job_working_directory/000/16/outputs/dataset_b3749db2-766c-47d6-85c3-3be3a5ff7c00.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

6432 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpiux4iihh/files/f/8/b/dataset_f8b6e742-e53f-4cbb-9b47-ab034e8d8b66.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpiux4iihh/job_working_directory/000/17/outputs/dataset_63cf0294-9081-499e-8ad4-9a47df3fa0b0_files' && fastqc --outdir '/tmp/tmpiux4iihh/job_working_directory/000/17/outputs/dataset_63cf0294-9081-499e-8ad4-9a47df3fa0b0_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpiux4iihh/job_working_directory/000/17/outputs/dataset_63cf0294-9081-499e-8ad4-9a47df3fa0b0_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpiux4iihh/job_working_directory/000/17/outputs/dataset_63cf0294-9081-499e-8ad4-9a47df3fa0b0_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
adapters	`None`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpiux4iihh/files/b/3/7/dataset_b3749db2-766c-47d6-85c3-3be3a5ff7c00.dat' | fasta_formatter -w 0 -o '/tmp/tmpiux4iihh/job_working_directory/000/18/outputs/dataset_fa07349f-a9aa-4ad5-9a73-700b8ff6b273.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpiux4iihh/job_working_directory/000/19/outputs/dataset_2b856411-fd25-4345-9db8-c8fb99710814.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpiux4iihh/files/8/d/6/dataset_8d6b3b4b-8da4-4a61-a791-5d8f09beffd5.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmpiux4iihh/files/4/0/2/dataset_40210520-4af0-4625-b5f8-a6e2a68f07a3.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmpiux4iihh/files/0/3/8/dataset_0386d4e6-74be-4569-9d0a-2f257f9cb4b1.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmpiux4iihh/files/1/8/2/dataset_182d6121-6a65-4fd2-b081-eb5dff11e8f5.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmpiux4iihh/files/2/b/8/dataset_2b856411-fd25-4345-9db8-c8fb99710814.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpiux4iihh/job_working_directory/000/20/working/multiqc_WDir
|            fastqc | Found 4 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"596b87eedace11eead7cddf3b0d30593"`
chromInfo	`"/tmp/tmpiux4iihh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 23, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- history_id
  - bffab663a6e121ca
- history_state
  - ok
- invocation_id
  - bffab663a6e121ca
- invocation_state
  - scheduled
- workflow_id
  - bffab663a6e121ca

✅ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled

Step 11: Trimming:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpo4ssrtc6/files/7/9/6/dataset_796ff734-fd5d-4558-afd0-0ca7810d227a.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpo4ssrtc6/job_working_directory/000/2/outputs/dataset_3235ccfd-4f16-4d19-ae48-3e97ddfd7300.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 196 Surviving: 184 (93.88%) Dropped: 12 (6.12%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 1, "src": "dce"}]}, "single_or_paired": "se"}`

Job 2:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpo4ssrtc6/files/f/3/0/dataset_f30aeb22-64e4-4d7f-b421-c90589a990bc.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpo4ssrtc6/job_working_directory/000/3/outputs/dataset_ed636c05-89fc-4508-b54b-65d3c762595d.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 90 Surviving: 90 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 2, "src": "dce"}]}, "single_or_paired": "se"}`

Step 12: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpo4ssrtc6/files/7/9/6/dataset_796ff734-fd5d-4558-afd0-0ca7810d227a.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpo4ssrtc6/job_working_directory/000/4/outputs/dataset_2221d055-b654-4941-9e8a-22e17e219994_files' && fastqc --outdir '/tmp/tmpo4ssrtc6/job_working_directory/000/4/outputs/dataset_2221d055-b654-4941-9e8a-22e17e219994_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/4/outputs/dataset_2221d055-b654-4941-9e8a-22e17e219994_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/4/outputs/dataset_2221d055-b654-4941-9e8a-22e17e219994_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adapters	`None`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpo4ssrtc6/files/f/3/0/dataset_f30aeb22-64e4-4d7f-b421-c90589a990bc.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpo4ssrtc6/job_working_directory/000/5/outputs/dataset_3b1eb092-8237-4084-85c1-61a41920271b_files' && fastqc --outdir '/tmp/tmpo4ssrtc6/job_working_directory/000/5/outputs/dataset_3b1eb092-8237-4084-85c1-61a41920271b_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/5/outputs/dataset_3b1eb092-8237-4084-85c1-61a41920271b_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/5/outputs/dataset_3b1eb092-8237-4084-85c1-61a41920271b_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adapters	`None`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 13: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpo4ssrtc6/files/3/2/3/dataset_3235ccfd-4f16-4d19-ae48-3e97ddfd7300.dat' '/tmp/tmpo4ssrtc6/job_working_directory/000/6/configs/tmp5icyfaxo' '/tmp/tmpo4ssrtc6/job_working_directory/000/6/outputs/dataset_eafc3312-a3b6-4d63-a6a4-2a68b5e8cf1b.dat' '/tmp/tmpo4ssrtc6/job_working_directory/000/6/outputs/dataset_eafc3312-a3b6-4d63-a6a4-2a68b5e8cf1b_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 184 of 184 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Job 2:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpo4ssrtc6/files/e/d/6/dataset_ed636c05-89fc-4508-b54b-65d3c762595d.dat' '/tmp/tmpo4ssrtc6/job_working_directory/000/7/configs/tmpv0p_arta' '/tmp/tmpo4ssrtc6/job_working_directory/000/7/outputs/dataset_065827bd-4b65-4cb5-a45c-bebbbcf54965.dat' '/tmp/tmpo4ssrtc6/job_working_directory/000/7/outputs/dataset_065827bd-4b65-4cb5-a45c-bebbbcf54965_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 90 of 90 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpo4ssrtc6/files/3/2/3/dataset_3235ccfd-4f16-4d19-ae48-3e97ddfd7300.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpo4ssrtc6/job_working_directory/000/8/outputs/dataset_9882e557-4d8c-420c-a80d-5200f78a4bc0_files' && fastqc --outdir '/tmp/tmpo4ssrtc6/job_working_directory/000/8/outputs/dataset_9882e557-4d8c-420c-a80d-5200f78a4bc0_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/8/outputs/dataset_9882e557-4d8c-420c-a80d-5200f78a4bc0_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/8/outputs/dataset_9882e557-4d8c-420c-a80d-5200f78a4bc0_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adapters	`None`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpo4ssrtc6/files/e/d/6/dataset_ed636c05-89fc-4508-b54b-65d3c762595d.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpo4ssrtc6/job_working_directory/000/9/outputs/dataset_6c272613-f1e2-4f7f-9bc0-6a3d5cfdec47_files' && fastqc --outdir '/tmp/tmpo4ssrtc6/job_working_directory/000/9/outputs/dataset_6c272613-f1e2-4f7f-9bc0-6a3d5cfdec47_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/9/outputs/dataset_6c272613-f1e2-4f7f-9bc0-6a3d5cfdec47_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/9/outputs/dataset_6c272613-f1e2-4f7f-9bc0-6a3d5cfdec47_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adapters	`None`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpo4ssrtc6/job_working_directory/000/10/outputs/dataset_e2e8b076-3f79-4238-aefe-740ae1adf036.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpo4ssrtc6/files/5/c/d/dataset_5cdd5b73-bf5d-40d9-89c3-ebc0340f75a5.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpo4ssrtc6/job_working_directory/000/11/outputs/dataset_e1c788b0-e010-47a6-b862-c38019631342.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpo4ssrtc6/files/a/8/3/dataset_a8329fc0-3863-4932-963e-fd15e60f2544.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 16: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpo4ssrtc6/files/e/a/f/dataset_eafc3312-a3b6-4d63-a6a4-2a68b5e8cf1b.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 184
	Input bases: 46,942
	Input mean length: 255.12
	Good sequences: 184 (100.00%)
	Good bases: 46,942
	Good mean length: 255.12
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 9, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Job 2:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpo4ssrtc6/files/0/6/5/dataset_065827bd-4b65-4cb5-a45c-bebbbcf54965.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 90
	Input bases: 31,735
	Input mean length: 352.61
	Good sequences: 90 (100.00%)
	Good bases: 31,735
	Good mean length: 352.61
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 10, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpo4ssrtc6/files/e/a/f/dataset_eafc3312-a3b6-4d63-a6a4-2a68b5e8cf1b.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpo4ssrtc6/job_working_directory/000/14/outputs/dataset_541a59a9-7ca4-45f4-9251-85f65216a49b_files' && fastqc --outdir '/tmp/tmpo4ssrtc6/job_working_directory/000/14/outputs/dataset_541a59a9-7ca4-45f4-9251-85f65216a49b_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/14/outputs/dataset_541a59a9-7ca4-45f4-9251-85f65216a49b_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/14/outputs/dataset_541a59a9-7ca4-45f4-9251-85f65216a49b_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adapters	`None`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpo4ssrtc6/files/0/6/5/dataset_065827bd-4b65-4cb5-a45c-bebbbcf54965.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpo4ssrtc6/job_working_directory/000/15/outputs/dataset_e4abba3b-b302-4905-a7a3-bf40dcd107a1_files' && fastqc --outdir '/tmp/tmpo4ssrtc6/job_working_directory/000/15/outputs/dataset_e4abba3b-b302-4905-a7a3-bf40dcd107a1_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/15/outputs/dataset_e4abba3b-b302-4905-a7a3-bf40dcd107a1_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/15/outputs/dataset_e4abba3b-b302-4905-a7a3-bf40dcd107a1_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adapters	`None`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpo4ssrtc6/job_working_directory/000/16/outputs/dataset_c5fb1d48-4ee9-4cc9-a8d7-4e40d10f86f1.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpo4ssrtc6/files/3/2/4/dataset_3241ba80-8a35-4823-a4ce-1cc313ca2a52.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpo4ssrtc6/job_working_directory/000/17/outputs/dataset_0529d9da-e8a0-42fa-88ac-d7f2a5ae28f3.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpo4ssrtc6/files/d/2/6/dataset_d261c7f4-b744-4a6c-8220-beb5dc76e9ce.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpo4ssrtc6/files/1/7/0/dataset_170e0228-1f16-4929-8483-77d3050c572b.dat' '/tmp/tmpo4ssrtc6/job_working_directory/000/18/outputs/dataset_d28f5db7-85ee-4390-b27d-67a7494657e7.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

184 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpo4ssrtc6/files/1/2/3/dataset_123ea9d1-cbdd-4d5e-9d1d-d32d47fede0e.dat' '/tmp/tmpo4ssrtc6/job_working_directory/000/19/outputs/dataset_249ad3a3-c94a-485e-a751-55c5c2b69fff.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

90 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpo4ssrtc6/files/1/7/0/dataset_170e0228-1f16-4929-8483-77d3050c572b.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpo4ssrtc6/job_working_directory/000/20/outputs/dataset_4a8d2a3c-ccc6-46d7-8a1e-c9c96d2270c0_files' && fastqc --outdir '/tmp/tmpo4ssrtc6/job_working_directory/000/20/outputs/dataset_4a8d2a3c-ccc6-46d7-8a1e-c9c96d2270c0_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/20/outputs/dataset_4a8d2a3c-ccc6-46d7-8a1e-c9c96d2270c0_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/20/outputs/dataset_4a8d2a3c-ccc6-46d7-8a1e-c9c96d2270c0_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adapters	`None`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpo4ssrtc6/files/1/2/3/dataset_123ea9d1-cbdd-4d5e-9d1d-d32d47fede0e.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpo4ssrtc6/job_working_directory/000/21/outputs/dataset_8e60b61d-b045-4b2f-a70f-018afae5767a_files' && fastqc --outdir '/tmp/tmpo4ssrtc6/job_working_directory/000/21/outputs/dataset_8e60b61d-b045-4b2f-a70f-018afae5767a_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/21/outputs/dataset_8e60b61d-b045-4b2f-a70f-018afae5767a_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/21/outputs/dataset_8e60b61d-b045-4b2f-a70f-018afae5767a_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adapters	`None`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 3: Trimmomatic - LEADING:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpo4ssrtc6/job_working_directory/000/22/outputs/dataset_3ba363a1-8131-4457-bdcb-0ee759f6579a.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpo4ssrtc6/files/0/a/2/dataset_0a2f468b-7eaf-4c22-96e9-e84b70445398.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpo4ssrtc6/job_working_directory/000/23/outputs/dataset_c190bf74-f656-49c6-936f-7f404e3d7c32.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpo4ssrtc6/files/a/8/4/dataset_a84d1b4c-85d5-4dfe-a01a-02d496e3b3f9.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpo4ssrtc6/files/d/2/8/dataset_d28f5db7-85ee-4390-b27d-67a7494657e7.dat' | fasta_formatter -w 60 -o '/tmp/tmpo4ssrtc6/job_working_directory/000/24/outputs/dataset_3286de63-40f7-4068-91c0-52d3b6f334ee.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Job 2:

Job state is ok

Command Line:

cat '/tmp/tmpo4ssrtc6/files/2/4/9/dataset_249ad3a3-c94a-485e-a751-55c5c2b69fff.dat' | fasta_formatter -w 60 -o '/tmp/tmpo4ssrtc6/job_working_directory/000/25/outputs/dataset_34496f61-b9af-416f-b064-5afa97567edc.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpo4ssrtc6/job_working_directory/000/26/outputs/dataset_ff9bbaf5-b1da-47d4-89f3-158ed7aa5157.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpo4ssrtc6/files/f/6/0/dataset_f60dddd5-a2b5-48c9-b4bb-e571dae9bc45.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpo4ssrtc6/job_working_directory/000/27/outputs/dataset_01e72ad9-736a-4940-943b-939c373a071b.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpo4ssrtc6/files/6/c/8/dataset_6c872eba-4e48-468f-8d28-807445497d91.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmpo4ssrtc6/files/e/2/e/dataset_e2e8b076-3f79-4238-aefe-740ae1adf036.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/tmp/tmpo4ssrtc6/files/e/1/c/dataset_e1c788b0-e010-47a6-b862-c38019631342.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmpo4ssrtc6/files/c/5/f/dataset_c5fb1d48-4ee9-4cc9-a8d7-4e40d10f86f1.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_1/file_1' && ln -s '/tmp/tmpo4ssrtc6/files/0/5/2/dataset_0529d9da-e8a0-42fa-88ac-d7f2a5ae28f3.dat' 'multiqc_WDir/fastqc_0/data_1/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmpo4ssrtc6/files/3/b/a/dataset_3ba363a1-8131-4457-bdcb-0ee759f6579a.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_2/file_1' && ln -s '/tmp/tmpo4ssrtc6/files/c/1/9/dataset_c190bf74-f656-49c6-936f-7f404e3d7c32.dat' 'multiqc_WDir/fastqc_0/data_2/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmpo4ssrtc6/files/f/f/9/dataset_ff9bbaf5-b1da-47d4-89f3-158ed7aa5157.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_3/file_1' && ln -s '/tmp/tmpo4ssrtc6/files/0/1/e/dataset_01e72ad9-736a-4940-943b-939c373a071b.dat' 'multiqc_WDir/fastqc_0/data_3/file_1/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpo4ssrtc6/job_working_directory/000/28/working/multiqc_WDir
|            fastqc | Found 8 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 8/8

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled
Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpo4ssrtc6/job_working_directory/000/1/configs/tmpcoev3ma7' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-05T08:55:46 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-05T08:55:46 prefetch.3.0.8: 1) Downloading 'DRR011051'...
2024-03-05T08:55:46 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-05T08:55:46 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-05T08:55:46 prefetch.3.0.8:  HTTPS download succeed
2024-03-05T08:55:46 prefetch.3.0.8:  'DRR011051' is valid
2024-03-05T08:55:46 prefetch.3.0.8: 1) 'DRR011051' was downloaded successfully
2024-03-05T08:55:46 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-05T08:55:46 prefetch.3.0.8: 1) Downloading 'DRR010705'...
2024-03-05T08:55:46 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-05T08:55:46 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-05T08:55:46 prefetch.3.0.8:  HTTPS download succeed
2024-03-05T08:55:46 prefetch.3.0.8:  'DRR010705' is valid
2024-03-05T08:55:46 prefetch.3.0.8: 1) 'DRR010705' was downloaded successfully

Standard Output:

Downloading accession: DRR011051...

Rejected 270 READS because of filtering out non-biological READS
Read 90 spots for DRR011051
Written 90 spots for DRR011051
Downloading accession: DRR010705...

Rejected 588 READS because of filtering out non-biological READS
Read 196 spots for DRR010705
Written 196 spots for DRR010705
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"1cdd0794dace11eeaf8e0fb88749656a"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpo4ssrtc6/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- history_id
  - 4fcc97fa5f772a9d
- history_state
  - ok
- invocation_id
  - 4fcc97fa5f772a9d
- invocation_state
  - scheduled
- workflow_id
  - 4fcc97fa5f772a9d

github-actions · 2024-03-05T13:08:52Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	4
Passed	2
Error	1
Failure	1
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: clan info file:
- step_state: scheduled

Step 11: SSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 12: LSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 13: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "78158411daef11eebd289f556224bdc2"
      
      input {"values": [{"id": 12, "src": "hdca"}]}
Step 14: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "78158411daef11eebd289f556224bdc2"
      
      input {"values": [{"id": 13, "src": "hdca"}]}

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpcqjav5qq/job_working_directory/000/27/configs/tmp0a9dfp7o' '/tmp/tmpcqjav5qq/job_working_directory/000/27/outputs/dataset_2796b811-cc11-47fc-a68f-3b0cc6b33f32.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 15, "src": "hdca"}]}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpcqjav5qq/job_working_directory/000/28/configs/tmplksmizpy' '/tmp/tmpcqjav5qq/job_working_directory/000/28/outputs/dataset_e25d2b24-1ce8-4ab7-aafd-0dedab554606.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 16, "src": "hdca"}]}`

Step 18: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "78158411daef11eebd289f556224bdc2"
      
      input {"values": [{"id": 14, "src": "hdca"}]}

Step 19: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 31, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 20: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 32, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: covariance models:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpcqjav5qq/job_working_directory/000/30/configs/tmpfkyi7dfg' '/tmp/tmpcqjav5qq/job_working_directory/000/30/outputs/dataset_00a3eddf-719a-4196-8250-eb882c0a0a86.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: Unlabelled step:
- step_state: scheduled
Step 23: Unlabelled step:
- step_state: scheduled

Step 24: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 33, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 25: Unlabelled step:
- step_state: scheduled
Step 26: Unlabelled step:
- step_state: scheduled
Step 27: Unlabelled step:
- step_state: scheduled
Step 28: HDF5 SSU SILVA:
- step_state: scheduled
Step 29: JSON SSU SILVA:
- step_state: scheduled

Step 30: Krona SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709644054_2452135_77266.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709644054_2081466_43456.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 27, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpcqjav5qq/files/f/d/c/dataset_fdc5163e-3f64-43a3-a9bc-b626f547ae02.dat '/tmp/tmpcqjav5qq/files/e/8/0/dataset_e8038d42-cb42-44f2-85a7-deb68ee8081c.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpcqjav5qq/job_working_directory/000/5/outputs/dataset_aeeaba05-8c4f-4c55-8cf1-89485fcbd387.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpcqjav5qq/files/f/d/c/dataset_fdc5163e-3f64-43a3-a9bc-b626f547ae02.dat '/tmp/tmpcqjav5qq/files/f/e/6/dataset_fe690f20-8f19-439c-af23-16f14214bcf7.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpcqjav5qq/job_working_directory/000/6/outputs/dataset_c1a445dc-29e0-4bcc-8814-08ecea22cd99.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 31: HDF5 LSU SILVA:
- step_state: scheduled
Step 32: JSON LSU SILVA:
- step_state: scheduled

Step 33: Krona LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709644054_3233075_73368.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709644054_2081466_43456.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 31, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 34: Unlabelled step:
- step_state: scheduled
Step 35: Unlabelled step:
- step_state: scheduled
Step 36: HDF5 ITSonedb:
- step_state: scheduled
Step 37: JSON ITSonedb:
- step_state: scheduled

Step 38: Krona ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709644055_3624215_78780.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709644054_2081466_43456.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 39: HDF5 ITS UNITE:
- step_state: scheduled
Step 40: JSON ITS UNITE:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpcqjav5qq/files/c/5/c/dataset_c5c7e60c-651f-49e3-9e41-1098bef4fcc7.dat' clan_info && ln -s '/tmp/tmpcqjav5qq/files/a/e/e/dataset_aeeaba05-8c4f-4c55-8cf1-89485fcbd387.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpcqjav5qq/job_working_directory/000/7/outputs/dataset_886344ad-5ae1-454b-8687-6657dedc15e1.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpcqjav5qq/files/c/5/c/dataset_c5c7e60c-651f-49e3-9e41-1098bef4fcc7.dat' clan_info && ln -s '/tmp/tmpcqjav5qq/files/c/1/a/dataset_c1a445dc-29e0-4bcc-8814-08ecea22cd99.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpcqjav5qq/job_working_directory/000/8/outputs/dataset_edd7066e-0f24-4a7a-8422-7169457d48eb.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 41: Krona ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709644056_4201205_41567.py", line 92, in respond
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1259, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 585, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
           ^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/tools/evaluation.py", line 608, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 134, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpcqjav5qq/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/home/runner/.planemo/gx_venv_3.7_release_23.2/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1709644054_2081466_43456.py", line 89, in respond
IndexError: list index out of range

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 46, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmpcqjav5qq/job_working_directory/000/9/configs/tmpptonxoo0' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpcqjav5qq/job_working_directory/000/9/configs/tmpkide16z9' -Q '/tmp/tmpcqjav5qq/job_working_directory/000/9/configs/tmpptonxoo0'   --no_header   -o '/tmp/tmpcqjav5qq/job_working_directory/000/9/outputs/dataset_0186144f-42c0-42dd-8cab-d711eee1a6a3.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpcqjav5qq/files/8/8/6/dataset_886344ad-5ae1-454b-8687-6657dedc15e1.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is error

Command Line:

cat '/tmp/tmpcqjav5qq/job_working_directory/000/10/configs/tmpy20s9uxs' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmpcqjav5qq/job_working_directory/000/10/configs/tmpfsbuqjz0' -Q '/tmp/tmpcqjav5qq/job_working_directory/000/10/configs/tmpy20s9uxs'   --no_header   -o '/tmp/tmpcqjav5qq/job_working_directory/000/10/outputs/dataset_06ee1ade-07d5-44d8-9b04-f49a2ad99a7b.dat'

Exit Code:

```
1
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmpcqjav5qq/files/e/d/d/dataset_edd7066e-0f24-4a7a-8422-7169457d48eb.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}
Error: no such column: c9

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Step 7: SSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 8: SSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Step 9: LSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 10: LSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"78158411daef11eebd289f556224bdc2"`
chromInfo	`"/tmp/tmpcqjav5qq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - cdf9dae5ce091015
- history_state
  - error
- invocation_id
  - cdf9dae5ce091015
- invocation_state
  - scheduled
- workflow_id
  - cdf9dae5ce091015

Failed Tests

❌ testing_query_tabular.ga_0

Problems:

Output with path /tmp/tmpptcj7e6z/deoverlapped_matches__404c2c2d-9f2c-4f65-b967-a017eb45b589 different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/microbiome/testing-query-tabular/test-data/deoverlapped_matches.tabular v. /tmp/tmpesimy5ykdeoverlapped_matches.tabular )
--- local_file
+++ history_data
@@ -1,30 +1,30 @@
-DRR010481.1-HUMWT9A01C6SDL-4	-	LSU_rRNA_eukarya	RF02543	cm	1	180	236	414	+	3'	3	0.49	0.0	123.4	2e-31	!	-
-DRR010481.1-HUMWT9A01C6SDL-4	-	5_8S_rRNA	RF00002	cm	54	154	1	99	+	5'	2	0.51	0.0	76.5	1.2e-21	!	-
-DRR010481.10-HUMWT9A01CLKTT-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.11-HUMWT9A01A55N6-4	-	5_8S_rRNA	RF00002	cm	54	154	1	101	+	5'	2	0.46	0.0	86.6	1.5e-24	!	-
-DRR010481.12-HUMWT9A01DQZ35-4	-	5_8S_rRNA	RF00002	cm	53	154	1	100	+	5'	2	0.51	0.0	76.0	1.6e-21	!	-
-DRR010481.13-HUMWT9A01CWWE7-4	-	LSU_rRNA_eukarya	RF02543	cm	1	173	237	408	+	3'	3	0.48	0.0	122.4	3.6e-31	!	-
-DRR010481.13-HUMWT9A01CWWE7-4	-	5_8S_rRNA	RF00002	cm	53	154	1	100	+	5'	2	0.51	0.0	76.0	1.6e-21	!	-
-DRR010481.14-HUMWT9A01CWM7O-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.15-HUMWT9A01C6KQE-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.15-HUMWT9A01C6KQE-4	-	LSU_rRNA_eukarya	RF02543	cm	1	53	313	365	+	3'	3	0.45	0.0	49.2	2.8e-12	!	-
-DRR010481.16-HUMWT9A01BP5YQ-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.16-HUMWT9A01BP5YQ-4	-	LSU_rRNA_eukarya	RF02543	cm	1	54	313	366	+	3'	3	0.44	0.0	50.9	1e-12	!	-
-DRR010481.17-HUMWT9A01CLKK7-4	-	5_8S_rRNA	RF00002	cm	54	154	1	99	+	5'	2	0.51	0.0	76.5	1.2e-21	!	-
-DRR010481.17-HUMWT9A01CLKK7-4	-	LSU_rRNA_eukarya	RF02543	cm	1	56	236	291	+	3'	3	0.50	0.0	47.1	9.8e-12	!	-
-DRR010481.18-HUMWT9A01ATALC-4	-	5_8S_rRNA	RF00002	cm	54	154	1	101	+	5'	2	0.47	0.0	91.4	6.5e-26	!	-
-DRR010481.2-HUMWT9A01A6FHU-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.47	0.0	91.8	5.1e-26	!	-
-DRR010481.20-HUMWT9A01C8FXI-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.21-HUMWT9A01A9JR7-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.23-HUMWT9A01AM5Q3-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.24-HUMWT9A01CYLUO-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.25-HUMWT9A01A3MBZ-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.3-HUMWT9A01CEMJS-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
********
*SNIP *
********
+DRR010481.13-HUMWT9A01CWWE7-4 - LSU_rRNA_eukarya RF02543 cm 1 173 237 408 + 3' 3 0.48 0.0 122.4 3.6e-31 ! -
+DRR010481.13-HUMWT9A01CWWE7-4 - 5_8S_rRNA RF00002 cm 53 154 1 100 + 5' 2 0.51 0.0 76.0 1.6e-21 ! -
+DRR010481.14-HUMWT9A01CWM7O-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.15-HUMWT9A01C6KQE-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.15-HUMWT9A01C6KQE-4 - LSU_rRNA_eukarya RF02543 cm 1 53 313 365 + 3' 3 0.45 0.0 49.2 2.8e-12 ! -
+DRR010481.16-HUMWT9A01BP5YQ-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.16-HUMWT9A01BP5YQ-4 - LSU_rRNA_eukarya RF02543 cm 1 54 313 366 + 3' 3 0.44 0.0 50.9 1e-12 ! -
+DRR010481.17-HUMWT9A01CLKK7-4 - 5_8S_rRNA RF00002 cm 54 154 1 99 + 5' 2 0.51 0.0 76.5 1.2e-21 ! -
+DRR010481.17-HUMWT9A01CLKK7-4 - LSU_rRNA_eukarya RF02543 cm 1 56 236 291 + 3' 3 0.50 0.0 47.1 9.8e-12 ! -
+DRR010481.18-HUMWT9A01ATALC-4 - 5_8S_rRNA RF00002 cm 54 154 1 101 + 5' 2 0.47 0.0 91.4 6.5e-26 ! -
+DRR010481.2-HUMWT9A01A6FHU-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.47 0.0 91.8 5.1e-26 ! -
+DRR010481.20-HUMWT9A01C8FXI-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.21-HUMWT9A01A9JR7-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.23-HUMWT9A01AM5Q3-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.24-HUMWT9A01CYLUO-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.25-HUMWT9A01A3MBZ-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.3-HUMWT9A01CEMJS-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.31-HUMWT9A01CFUVG-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.32-HUMWT9A01BTRXI-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.33-HUMWT9A01BUFRP-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.4-HUMWT9A01BRR8F-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.5-HUMWT9A01A29S1-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.6-HUMWT9A01CMBDY-4 - 5_8S_rRNA RF00002 cm 54 154 1 101 + 5' 2 0.47 0.0 91.4 6.5e-26 ! -
+DRR010481.7-HUMWT9A01DMCR3-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.8-HUMWT9A01A36AF-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: covariance models:
- step_state: scheduled
Step 3: clan info file:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpb4hpffbo/files/2/8/8/dataset_288a0a0c-f3b2-4c1e-80b0-24fc1ba7f954.dat '/tmp/tmpb4hpffbo/files/7/9/f/dataset_79fcf714-10a8-42ba-816c-764f61795f02.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpb4hpffbo/job_working_directory/000/4/outputs/dataset_9e115fc6-a746-4831-a707-a05d6ad79873.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"611f2857daef11eeb87aab4c2e7068e8"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpb4hpffbo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 3, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpb4hpffbo/files/5/6/1/dataset_561b15e6-3ef7-4b98-9715-4613f441ae3a.dat' clan_info && ln -s '/tmp/tmpb4hpffbo/files/9/e/1/dataset_9e115fc6-a746-4831-a707-a05d6ad79873.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpb4hpffbo/job_working_directory/000/5/outputs/dataset_404c2c2d-9f2c-4f65-b967-a017eb45b589.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"611f2857daef11eeb87aab4c2e7068e8"`
chromInfo	`"/tmp/tmpb4hpffbo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Other invocation details
- history_id
  - c7c3c2c1f31c7dd1
- history_state
  - ok
- invocation_id
  - c7c3c2c1f31c7dd1
- invocation_state
  - scheduled
- workflow_id
  - c7c3c2c1f31c7dd1

Passed Tests

✅ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmps1m076h1/job_working_directory/000/1/configs/tmprxxy96i4' ~/.ncbi/user-settings.mkfg &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-05T12:53:43 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-05T12:53:43 prefetch.3.0.8: 1) Downloading 'DRR218540'...
2024-03-05T12:53:43 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-05T12:53:43 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-05T12:53:43 prefetch.3.0.8:  HTTPS download succeed
2024-03-05T12:53:43 prefetch.3.0.8:  'DRR218540' is valid
2024-03-05T12:53:43 prefetch.3.0.8: 1) 'DRR218540' was downloaded successfully
2024-03-05T12:53:43 prefetch.3.0.8: 'DRR218540' has 0 unresolved dependencies

Standard Output:

Downloading accession: DRR218540...

Read 67485 spots for DRR218540
Written 67485 spots for DRR218540
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "5a6cb854daef11eeb4c0051baf89ae85"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmps1m076h1/files/8/7/6/dataset_87642f9f-e4a5-4466-8348-bf7fb91ab1b6.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmps1m076h1/files/3/0/7/dataset_307d3b30-2f30-4e5d-81a4-13a86a58b65c.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmps1m076h1/job_working_directory/000/3/outputs/dataset_c596a84e-cec8-4229-ad6b-5ce7e45168a7.dat' && mv second.fastq.gz '/tmp/tmps1m076h1/job_working_directory/000/3/outputs/dataset_b7bf1c56-9f57-4342-b5c7-e6f299723baf.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 25 seconds

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmps1m076h1/files/c/5/9/dataset_c596a84e-cec8-4229-ad6b-5ce7e45168a7.dat' -r '/tmp/tmps1m076h1/files/b/7/b/dataset_b7bf1c56-9f57-4342-b5c7-e6f299723baf.dat' -1 '/tmp/tmps1m076h1/job_working_directory/000/6/outputs/dataset_113505f8-eb53-496f-99f8-8a728917d870.dat' -2 '/tmp/tmps1m076h1/job_working_directory/000/6/outputs/dataset_9c3a40e3-014d-4e48-a908-e36661222085.dat'  -s '/tmp/tmps1m076h1/job_working_directory/000/6/outputs/dataset_9090215e-a653-4df1-b80f-a8470ab50ec6.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020749

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmps1m076h1/files/9/0/9/dataset_9090215e-a653-4df1-b80f-a8470ab50ec6.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmps1m076h1/job_working_directory/000/7/outputs/dataset_4b99da80-ca05-44e6-934d-760740953cd1.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 6434 Surviving: 6432 (99.97%) Dropped: 2 (0.03%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmps1m076h1/files/9/0/9/dataset_9090215e-a653-4df1-b80f-a8470ab50ec6.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmps1m076h1/job_working_directory/000/8/outputs/dataset_74bcbc55-d2c6-4ca5-b603-937a1af79681_files' && fastqc --outdir '/tmp/tmps1m076h1/job_working_directory/000/8/outputs/dataset_74bcbc55-d2c6-4ca5-b603-937a1af79681_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmps1m076h1/job_working_directory/000/8/outputs/dataset_74bcbc55-d2c6-4ca5-b603-937a1af79681_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmps1m076h1/job_working_directory/000/8/outputs/dataset_74bcbc55-d2c6-4ca5-b603-937a1af79681_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
adapters	`None`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmps1m076h1/files/4/b/9/dataset_4b99da80-ca05-44e6-934d-760740953cd1.dat' '/tmp/tmps1m076h1/job_working_directory/000/9/configs/tmp109mtawj' '/tmp/tmps1m076h1/job_working_directory/000/9/outputs/dataset_2930e3e3-ddeb-42f9-862b-001e30af06db.dat' '/tmp/tmps1m076h1/job_working_directory/000/9/outputs/dataset_2930e3e3-ddeb-42f9-862b-001e30af06db_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 6432 of 6432 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmps1m076h1/files/4/b/9/dataset_4b99da80-ca05-44e6-934d-760740953cd1.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmps1m076h1/job_working_directory/000/10/outputs/dataset_ede761b4-2457-46c9-b377-78b5361f1771_files' && fastqc --outdir '/tmp/tmps1m076h1/job_working_directory/000/10/outputs/dataset_ede761b4-2457-46c9-b377-78b5361f1771_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmps1m076h1/job_working_directory/000/10/outputs/dataset_ede761b4-2457-46c9-b377-78b5361f1771_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmps1m076h1/job_working_directory/000/10/outputs/dataset_ede761b4-2457-46c9-b377-78b5361f1771_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
adapters	`None`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmps1m076h1/job_working_directory/000/11/outputs/dataset_f1e6f6c6-b525-4935-b55c-728b43a96521.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmps1m076h1/files/0/d/7/dataset_0d71b9a2-1400-435b-aea1-81bb49b2feda.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmps1m076h1/files/2/9/3/dataset_2930e3e3-ddeb-42f9-862b-001e30af06db.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmps1m076h1/job_working_directory/000/12/outputs/dataset_9b5a16b2-f0fc-495a-8725-b7237d89d495_files' && fastqc --outdir '/tmp/tmps1m076h1/job_working_directory/000/12/outputs/dataset_9b5a16b2-f0fc-495a-8725-b7237d89d495_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmps1m076h1/job_working_directory/000/12/outputs/dataset_9b5a16b2-f0fc-495a-8725-b7237d89d495_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmps1m076h1/job_working_directory/000/12/outputs/dataset_9b5a16b2-f0fc-495a-8725-b7237d89d495_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
adapters	`None`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmps1m076h1/files/2/9/3/dataset_2930e3e3-ddeb-42f9-862b-001e30af06db.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 6,432
	Input bases: 2,151,394
	Input mean length: 334.48
	Good sequences: 6,432 (100.00%)
	Good bases: 2,151,394
	Good mean length: 334.48
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmps1m076h1/job_working_directory/000/14/outputs/dataset_44e8e5d0-85a2-462a-8cc8-79ec8e5fcea0.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmps1m076h1/files/e/8/0/dataset_e80e4e9a-367f-4864-9669-75245b8eb388.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmps1m076h1/job_working_directory/000/15/outputs/dataset_9591e2df-943f-4f3b-ba07-c7bcf5bf9696.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmps1m076h1/files/e/8/1/dataset_e8101779-dc73-4d64-b085-81f7c76003d0.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmps1m076h1/files/7/b/d/dataset_7bd51a61-f141-4289-b916-f70d00cd05b1.dat' '/tmp/tmps1m076h1/job_working_directory/000/16/outputs/dataset_aa370c0d-79fd-4b7e-bdd6-2e6e3b609497.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

6432 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmps1m076h1/files/7/b/d/dataset_7bd51a61-f141-4289-b916-f70d00cd05b1.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmps1m076h1/job_working_directory/000/17/outputs/dataset_83d72010-c1df-46b1-a095-9dc5706f6591_files' && fastqc --outdir '/tmp/tmps1m076h1/job_working_directory/000/17/outputs/dataset_83d72010-c1df-46b1-a095-9dc5706f6591_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmps1m076h1/job_working_directory/000/17/outputs/dataset_83d72010-c1df-46b1-a095-9dc5706f6591_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmps1m076h1/job_working_directory/000/17/outputs/dataset_83d72010-c1df-46b1-a095-9dc5706f6591_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
adapters	`None`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmps1m076h1/files/a/a/3/dataset_aa370c0d-79fd-4b7e-bdd6-2e6e3b609497.dat' | fasta_formatter -w 0 -o '/tmp/tmps1m076h1/job_working_directory/000/18/outputs/dataset_b6809e50-6c5c-462f-8ea6-bafd096a4c97.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmps1m076h1/job_working_directory/000/19/outputs/dataset_3a6001dd-f6de-4992-ab43-4c356e043403.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmps1m076h1/files/e/6/5/dataset_e65ecb73-398a-4951-9ad2-178547abf0fe.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmps1m076h1/files/f/1/e/dataset_f1e6f6c6-b525-4935-b55c-728b43a96521.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmps1m076h1/files/4/4/e/dataset_44e8e5d0-85a2-462a-8cc8-79ec8e5fcea0.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmps1m076h1/files/9/5/9/dataset_9591e2df-943f-4f3b-ba07-c7bcf5bf9696.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmps1m076h1/files/3/a/6/dataset_3a6001dd-f6de-4992-ab43-4c356e043403.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmps1m076h1/job_working_directory/000/20/working/multiqc_WDir
|            fastqc | Found 4 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5a6cb854daef11eeb4c0051baf89ae85"`
chromInfo	`"/tmp/tmps1m076h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 23, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- history_id
  - adde89ce97f9f11b
- history_state
  - ok
- invocation_id
  - adde89ce97f9f11b
- invocation_state
  - scheduled
- workflow_id
  - adde89ce97f9f11b

✅ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled

Step 11: Trimming:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpeh37nsgc/files/f/b/6/dataset_fb6556fc-470a-40dd-a8dc-81469f3a8409.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpeh37nsgc/job_working_directory/000/2/outputs/dataset_3079268d-f7c0-4d89-8df5-1d5f1b6dbfb5.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 196 Surviving: 184 (93.88%) Dropped: 12 (6.12%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 1, "src": "dce"}]}, "single_or_paired": "se"}`

Job 2:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpeh37nsgc/files/b/0/1/dataset_b01382c8-2347-4860-a9c6-9e7bd705f00c.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpeh37nsgc/job_working_directory/000/3/outputs/dataset_99eb3909-2a4d-4553-bf0e-dba0f249e659.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 90 Surviving: 90 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 2, "src": "dce"}]}, "single_or_paired": "se"}`

Step 12: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpeh37nsgc/files/f/b/6/dataset_fb6556fc-470a-40dd-a8dc-81469f3a8409.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpeh37nsgc/job_working_directory/000/4/outputs/dataset_9b6af517-1d61-494f-b7e7-5c953c821a00_files' && fastqc --outdir '/tmp/tmpeh37nsgc/job_working_directory/000/4/outputs/dataset_9b6af517-1d61-494f-b7e7-5c953c821a00_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpeh37nsgc/job_working_directory/000/4/outputs/dataset_9b6af517-1d61-494f-b7e7-5c953c821a00_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpeh37nsgc/job_working_directory/000/4/outputs/dataset_9b6af517-1d61-494f-b7e7-5c953c821a00_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adapters	`None`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpeh37nsgc/files/b/0/1/dataset_b01382c8-2347-4860-a9c6-9e7bd705f00c.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpeh37nsgc/job_working_directory/000/5/outputs/dataset_e166cdb9-672a-45db-898c-e9029225c5c0_files' && fastqc --outdir '/tmp/tmpeh37nsgc/job_working_directory/000/5/outputs/dataset_e166cdb9-672a-45db-898c-e9029225c5c0_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpeh37nsgc/job_working_directory/000/5/outputs/dataset_e166cdb9-672a-45db-898c-e9029225c5c0_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpeh37nsgc/job_working_directory/000/5/outputs/dataset_e166cdb9-672a-45db-898c-e9029225c5c0_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adapters	`None`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 13: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpeh37nsgc/files/3/0/7/dataset_3079268d-f7c0-4d89-8df5-1d5f1b6dbfb5.dat' '/tmp/tmpeh37nsgc/job_working_directory/000/6/configs/tmpxq8goabl' '/tmp/tmpeh37nsgc/job_working_directory/000/6/outputs/dataset_be9a6c2e-a2fe-46c3-bad1-3b3a91f0c158.dat' '/tmp/tmpeh37nsgc/job_working_directory/000/6/outputs/dataset_be9a6c2e-a2fe-46c3-bad1-3b3a91f0c158_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 184 of 184 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Job 2:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpeh37nsgc/files/9/9/e/dataset_99eb3909-2a4d-4553-bf0e-dba0f249e659.dat' '/tmp/tmpeh37nsgc/job_working_directory/000/7/configs/tmpor6nw7f_' '/tmp/tmpeh37nsgc/job_working_directory/000/7/outputs/dataset_e815e4eb-f8c2-44eb-810f-6ac6166bdc66.dat' '/tmp/tmpeh37nsgc/job_working_directory/000/7/outputs/dataset_e815e4eb-f8c2-44eb-810f-6ac6166bdc66_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 90 of 90 reads (100.00%).
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpeh37nsgc/files/3/0/7/dataset_3079268d-f7c0-4d89-8df5-1d5f1b6dbfb5.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpeh37nsgc/job_working_directory/000/8/outputs/dataset_574ac69e-8b23-47ed-9586-96f38d4d50ac_files' && fastqc --outdir '/tmp/tmpeh37nsgc/job_working_directory/000/8/outputs/dataset_574ac69e-8b23-47ed-9586-96f38d4d50ac_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpeh37nsgc/job_working_directory/000/8/outputs/dataset_574ac69e-8b23-47ed-9586-96f38d4d50ac_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpeh37nsgc/job_working_directory/000/8/outputs/dataset_574ac69e-8b23-47ed-9586-96f38d4d50ac_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adapters	`None`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpeh37nsgc/files/9/9/e/dataset_99eb3909-2a4d-4553-bf0e-dba0f249e659.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpeh37nsgc/job_working_directory/000/9/outputs/dataset_2014852a-6098-49d4-8a0f-0272cb8f655f_files' && fastqc --outdir '/tmp/tmpeh37nsgc/job_working_directory/000/9/outputs/dataset_2014852a-6098-49d4-8a0f-0272cb8f655f_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpeh37nsgc/job_working_directory/000/9/outputs/dataset_2014852a-6098-49d4-8a0f-0272cb8f655f_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpeh37nsgc/job_working_directory/000/9/outputs/dataset_2014852a-6098-49d4-8a0f-0272cb8f655f_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adapters	`None`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpeh37nsgc/job_working_directory/000/10/outputs/dataset_76d82a78-df58-44db-aaf3-ff421b544c42.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpeh37nsgc/files/5/7/0/dataset_570802b4-1967-48aa-ab19-f6dc35d1c214.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpeh37nsgc/job_working_directory/000/11/outputs/dataset_f62744eb-a71b-4031-9bf6-f909c86485a8.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpeh37nsgc/files/2/9/b/dataset_29bbc3b5-a12d-4f17-b4cf-4711e0b2aa12.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 16: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpeh37nsgc/files/b/e/9/dataset_be9a6c2e-a2fe-46c3-bad1-3b3a91f0c158.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 184
	Input bases: 46,942
	Input mean length: 255.12
	Good sequences: 184 (100.00%)
	Good bases: 46,942
	Good mean length: 255.12
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 9, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Job 2:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpeh37nsgc/files/e/8/1/dataset_e815e4eb-f8c2-44eb-810f-6ac6166bdc66.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 90
	Input bases: 31,735
	Input mean length: 352.61
	Good sequences: 90 (100.00%)
	Good bases: 31,735
	Good mean length: 352.61
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 10, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpeh37nsgc/files/b/e/9/dataset_be9a6c2e-a2fe-46c3-bad1-3b3a91f0c158.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpeh37nsgc/job_working_directory/000/14/outputs/dataset_48810908-538a-4743-9a28-a0547154439e_files' && fastqc --outdir '/tmp/tmpeh37nsgc/job_working_directory/000/14/outputs/dataset_48810908-538a-4743-9a28-a0547154439e_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpeh37nsgc/job_working_directory/000/14/outputs/dataset_48810908-538a-4743-9a28-a0547154439e_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpeh37nsgc/job_working_directory/000/14/outputs/dataset_48810908-538a-4743-9a28-a0547154439e_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adapters	`None`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpeh37nsgc/files/e/8/1/dataset_e815e4eb-f8c2-44eb-810f-6ac6166bdc66.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpeh37nsgc/job_working_directory/000/15/outputs/dataset_4ef51644-6216-4d86-9b2a-bfddeee249d0_files' && fastqc --outdir '/tmp/tmpeh37nsgc/job_working_directory/000/15/outputs/dataset_4ef51644-6216-4d86-9b2a-bfddeee249d0_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpeh37nsgc/job_working_directory/000/15/outputs/dataset_4ef51644-6216-4d86-9b2a-bfddeee249d0_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpeh37nsgc/job_working_directory/000/15/outputs/dataset_4ef51644-6216-4d86-9b2a-bfddeee249d0_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adapters	`None`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpeh37nsgc/job_working_directory/000/16/outputs/dataset_da0889be-26ce-42e0-b281-e1ebfb19f646.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpeh37nsgc/files/5/f/8/dataset_5f89bc72-89f2-4122-a01d-7c192a44f83f.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpeh37nsgc/job_working_directory/000/17/outputs/dataset_8a66c81e-9e21-4371-9040-4f30009a5c55.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpeh37nsgc/files/b/2/0/dataset_b201fb8c-f14b-4859-8839-e06eca07904b.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpeh37nsgc/files/c/0/f/dataset_c0f7102f-f18e-4e58-bb2e-bc3b79a3b5a3.dat' '/tmp/tmpeh37nsgc/job_working_directory/000/18/outputs/dataset_5e18d8aa-0721-4cc2-b877-a635f486f4ee.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

184 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpeh37nsgc/files/2/0/6/dataset_206c1898-fa45-444b-ac96-6cd55b34d8e9.dat' '/tmp/tmpeh37nsgc/job_working_directory/000/19/outputs/dataset_a87bbf3c-0f1c-437b-88d2-95538289f3ce.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

90 FASTQ reads were converted to FASTA.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpeh37nsgc/files/c/0/f/dataset_c0f7102f-f18e-4e58-bb2e-bc3b79a3b5a3.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpeh37nsgc/job_working_directory/000/20/outputs/dataset_2d7cd142-c05f-4739-b95b-64609ad0ded4_files' && fastqc --outdir '/tmp/tmpeh37nsgc/job_working_directory/000/20/outputs/dataset_2d7cd142-c05f-4739-b95b-64609ad0ded4_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpeh37nsgc/job_working_directory/000/20/outputs/dataset_2d7cd142-c05f-4739-b95b-64609ad0ded4_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpeh37nsgc/job_working_directory/000/20/outputs/dataset_2d7cd142-c05f-4739-b95b-64609ad0ded4_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adapters	`None`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpeh37nsgc/files/2/0/6/dataset_206c1898-fa45-444b-ac96-6cd55b34d8e9.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpeh37nsgc/job_working_directory/000/21/outputs/dataset_d0c91cb8-2859-4fd7-9bf8-31da18dacca6_files' && fastqc --outdir '/tmp/tmpeh37nsgc/job_working_directory/000/21/outputs/dataset_d0c91cb8-2859-4fd7-9bf8-31da18dacca6_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpeh37nsgc/job_working_directory/000/21/outputs/dataset_d0c91cb8-2859-4fd7-9bf8-31da18dacca6_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpeh37nsgc/job_working_directory/000/21/outputs/dataset_d0c91cb8-2859-4fd7-9bf8-31da18dacca6_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adapters	`None`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 3: Trimmomatic - LEADING:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpeh37nsgc/job_working_directory/000/22/outputs/dataset_09033544-72fd-4adb-8b3b-a35ea154e832.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpeh37nsgc/files/9/c/2/dataset_9c2d80d7-8cb8-4efc-a3fe-5112493ab3e6.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpeh37nsgc/job_working_directory/000/23/outputs/dataset_c3e093d0-7794-4f24-917a-e002ad112924.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpeh37nsgc/files/c/6/0/dataset_c6001d83-7833-4c57-bdcb-ed90a722539d.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpeh37nsgc/files/5/e/1/dataset_5e18d8aa-0721-4cc2-b877-a635f486f4ee.dat' | fasta_formatter -w 60 -o '/tmp/tmpeh37nsgc/job_working_directory/000/24/outputs/dataset_0c48465a-d91a-423d-9e17-f7262e711cb0.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Job 2:

Job state is ok

Command Line:

cat '/tmp/tmpeh37nsgc/files/a/8/7/dataset_a87bbf3c-0f1c-437b-88d2-95538289f3ce.dat' | fasta_formatter -w 60 -o '/tmp/tmpeh37nsgc/job_working_directory/000/25/outputs/dataset_9f3da782-08bb-4d0c-9899-bf7ba19552f5.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpeh37nsgc/job_working_directory/000/26/outputs/dataset_a2848f94-822d-4f48-bf4d-79f6b70690cd.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpeh37nsgc/files/f/1/d/dataset_f1d10a47-95ac-481b-8c13-068a0fe52e3d.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpeh37nsgc/job_working_directory/000/27/outputs/dataset_0b071e38-92dc-49d5-92d4-89d1f2812c9e.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpeh37nsgc/files/e/5/3/dataset_e53b68c6-3faa-4492-9229-739a17ca9102.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmpeh37nsgc/files/7/6/d/dataset_76d82a78-df58-44db-aaf3-ff421b544c42.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/tmp/tmpeh37nsgc/files/f/6/2/dataset_f62744eb-a71b-4031-9bf6-f909c86485a8.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmpeh37nsgc/files/d/a/0/dataset_da0889be-26ce-42e0-b281-e1ebfb19f646.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_1/file_1' && ln -s '/tmp/tmpeh37nsgc/files/8/a/6/dataset_8a66c81e-9e21-4371-9040-4f30009a5c55.dat' 'multiqc_WDir/fastqc_0/data_1/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmpeh37nsgc/files/0/9/0/dataset_09033544-72fd-4adb-8b3b-a35ea154e832.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_2/file_1' && ln -s '/tmp/tmpeh37nsgc/files/c/3/e/dataset_c3e093d0-7794-4f24-917a-e002ad112924.dat' 'multiqc_WDir/fastqc_0/data_2/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmpeh37nsgc/files/a/2/8/dataset_a2848f94-822d-4f48-bf4d-79f6b70690cd.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_3/file_1' && ln -s '/tmp/tmpeh37nsgc/files/0/b/0/dataset_0b071e38-92dc-49d5-92d4-89d1f2812c9e.dat' 'multiqc_WDir/fastqc_0/data_3/file_1/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpeh37nsgc/job_working_directory/000/28/working/multiqc_WDir
|            fastqc | Found 8 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 8/8

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled
Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpeh37nsgc/job_working_directory/000/1/configs/tmp2g823h1b' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-05T12:56:37 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-05T12:56:37 prefetch.3.0.8: 1) Downloading 'DRR011051'...
2024-03-05T12:56:37 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-05T12:56:37 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-05T12:56:38 prefetch.3.0.8:  HTTPS download succeed
2024-03-05T12:56:38 prefetch.3.0.8:  'DRR011051' is valid
2024-03-05T12:56:38 prefetch.3.0.8: 1) 'DRR011051' was downloaded successfully
2024-03-05T12:56:39 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-05T12:56:39 prefetch.3.0.8: 1) Downloading 'DRR010705'...
2024-03-05T12:56:39 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-05T12:56:39 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-05T12:56:40 prefetch.3.0.8:  HTTPS download succeed
2024-03-05T12:56:40 prefetch.3.0.8:  'DRR010705' is valid
2024-03-05T12:56:40 prefetch.3.0.8: 1) 'DRR010705' was downloaded successfully

Standard Output:

Downloading accession: DRR011051...

Rejected 270 READS because of filtering out non-biological READS
Read 90 spots for DRR011051
Written 90 spots for DRR011051
Downloading accession: DRR010705...

Rejected 588 READS because of filtering out non-biological READS
Read 196 spots for DRR010705
Written 196 spots for DRR010705
Done with all accessions.

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9d1200ecdaef11eebc022f97b4af4286"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpeh37nsgc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- history_id
  - 1885725d2c2dfc2d
- history_state
  - ok
- invocation_id
  - 1885725d2c2dfc2d
- invocation_state
  - scheduled
- workflow_id
  - 1885725d2c2dfc2d

github-actions · 2024-03-18T12:56:14Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	4
Passed	2
Error	1
Failure	1
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy1 (version 0.08+galaxy1)","err_code":0}

Failed Tests

❌ testing_query_tabular.ga_0

Problems:

Output with path /tmp/tmpn6y54uq3/deoverlapped_matches__27112cfc-b246-4e06-bf37-2b9758c49a51 different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/microbiome/testing-query-tabular/test-data/deoverlapped_matches.tabular v. /tmp/tmpzz_819ncdeoverlapped_matches.tabular )
--- local_file
+++ history_data
@@ -1,30 +1,30 @@
-DRR010481.1-HUMWT9A01C6SDL-4	-	LSU_rRNA_eukarya	RF02543	cm	1	180	236	414	+	3'	3	0.49	0.0	123.4	2e-31	!	-
-DRR010481.1-HUMWT9A01C6SDL-4	-	5_8S_rRNA	RF00002	cm	54	154	1	99	+	5'	2	0.51	0.0	76.5	1.2e-21	!	-
-DRR010481.10-HUMWT9A01CLKTT-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.11-HUMWT9A01A55N6-4	-	5_8S_rRNA	RF00002	cm	54	154	1	101	+	5'	2	0.46	0.0	86.6	1.5e-24	!	-
-DRR010481.12-HUMWT9A01DQZ35-4	-	5_8S_rRNA	RF00002	cm	53	154	1	100	+	5'	2	0.51	0.0	76.0	1.6e-21	!	-
-DRR010481.13-HUMWT9A01CWWE7-4	-	LSU_rRNA_eukarya	RF02543	cm	1	173	237	408	+	3'	3	0.48	0.0	122.4	3.6e-31	!	-
-DRR010481.13-HUMWT9A01CWWE7-4	-	5_8S_rRNA	RF00002	cm	53	154	1	100	+	5'	2	0.51	0.0	76.0	1.6e-21	!	-
-DRR010481.14-HUMWT9A01CWM7O-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.15-HUMWT9A01C6KQE-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.15-HUMWT9A01C6KQE-4	-	LSU_rRNA_eukarya	RF02543	cm	1	53	313	365	+	3'	3	0.45	0.0	49.2	2.8e-12	!	-
-DRR010481.16-HUMWT9A01BP5YQ-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.16-HUMWT9A01BP5YQ-4	-	LSU_rRNA_eukarya	RF02543	cm	1	54	313	366	+	3'	3	0.44	0.0	50.9	1e-12	!	-
-DRR010481.17-HUMWT9A01CLKK7-4	-	5_8S_rRNA	RF00002	cm	54	154	1	99	+	5'	2	0.51	0.0	76.5	1.2e-21	!	-
-DRR010481.17-HUMWT9A01CLKK7-4	-	LSU_rRNA_eukarya	RF02543	cm	1	56	236	291	+	3'	3	0.50	0.0	47.1	9.8e-12	!	-
-DRR010481.18-HUMWT9A01ATALC-4	-	5_8S_rRNA	RF00002	cm	54	154	1	101	+	5'	2	0.47	0.0	91.4	6.5e-26	!	-
-DRR010481.2-HUMWT9A01A6FHU-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.47	0.0	91.8	5.1e-26	!	-
-DRR010481.20-HUMWT9A01C8FXI-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.21-HUMWT9A01A9JR7-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.23-HUMWT9A01AM5Q3-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.24-HUMWT9A01CYLUO-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.25-HUMWT9A01A3MBZ-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.3-HUMWT9A01CEMJS-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
********
*SNIP *
********
+DRR010481.13-HUMWT9A01CWWE7-4 - LSU_rRNA_eukarya RF02543 cm 1 173 237 408 + 3' 3 0.48 0.0 122.4 3.6e-31 ! -
+DRR010481.13-HUMWT9A01CWWE7-4 - 5_8S_rRNA RF00002 cm 53 154 1 100 + 5' 2 0.51 0.0 76.0 1.6e-21 ! -
+DRR010481.14-HUMWT9A01CWM7O-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.15-HUMWT9A01C6KQE-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.15-HUMWT9A01C6KQE-4 - LSU_rRNA_eukarya RF02543 cm 1 53 313 365 + 3' 3 0.45 0.0 49.2 2.8e-12 ! -
+DRR010481.16-HUMWT9A01BP5YQ-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.16-HUMWT9A01BP5YQ-4 - LSU_rRNA_eukarya RF02543 cm 1 54 313 366 + 3' 3 0.44 0.0 50.9 1e-12 ! -
+DRR010481.17-HUMWT9A01CLKK7-4 - 5_8S_rRNA RF00002 cm 54 154 1 99 + 5' 2 0.51 0.0 76.5 1.2e-21 ! -
+DRR010481.17-HUMWT9A01CLKK7-4 - LSU_rRNA_eukarya RF02543 cm 1 56 236 291 + 3' 3 0.50 0.0 47.1 9.8e-12 ! -
+DRR010481.18-HUMWT9A01ATALC-4 - 5_8S_rRNA RF00002 cm 54 154 1 101 + 5' 2 0.47 0.0 91.4 6.5e-26 ! -
+DRR010481.2-HUMWT9A01A6FHU-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.47 0.0 91.8 5.1e-26 ! -
+DRR010481.20-HUMWT9A01C8FXI-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.21-HUMWT9A01A9JR7-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.23-HUMWT9A01AM5Q3-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.24-HUMWT9A01CYLUO-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.25-HUMWT9A01A3MBZ-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.3-HUMWT9A01CEMJS-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.31-HUMWT9A01CFUVG-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.32-HUMWT9A01BTRXI-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.33-HUMWT9A01BUFRP-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.4-HUMWT9A01BRR8F-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.5-HUMWT9A01A29S1-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.6-HUMWT9A01CMBDY-4 - 5_8S_rRNA RF00002 cm 54 154 1 101 + 5' 2 0.47 0.0 91.4 6.5e-26 ! -
+DRR010481.7-HUMWT9A01DMCR3-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.8-HUMWT9A01A36AF-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: covariance models:
- step_state: scheduled
Step 3: clan info file:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmp56jhrx15/files/e/6/2/dataset_e62a9f9d-459c-4cf7-ba78-74b38b26c881.dat '/tmp/tmp56jhrx15/files/c/b/0/dataset_cb047a9e-e91e-4a9c-a125-ed486ad032ff.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmp56jhrx15/job_working_directory/000/4/outputs/dataset_9fc5ab97-f856-41c7-a145-2732675fe61b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"d366b1bee52511eeb2fc6bf3232c0333"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmp56jhrx15/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 3, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp56jhrx15/files/c/7/7/dataset_c773ee59-2039-4803-a9ff-35865517cc4e.dat' clan_info && ln -s '/tmp/tmp56jhrx15/files/9/f/c/dataset_9fc5ab97-f856-41c7-a145-2732675fe61b.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmp56jhrx15/job_working_directory/000/5/outputs/dataset_27112cfc-b246-4e06-bf37-2b9758c49a51.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d366b1bee52511eeb2fc6bf3232c0333"`
chromInfo	`"/tmp/tmp56jhrx15/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Other invocation details
- history_id
  - 9a6fbca68edb0158
- history_state
  - ok
- invocation_id
  - 9a6fbca68edb0158
- invocation_state
  - scheduled
- workflow_id
  - 9a6fbca68edb0158

Passed Tests

✅ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmp4jr2tggt/job_working_directory/000/1/configs/tmpfqqcf971' ~/.ncbi/user-settings.mkfg &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-18T12:51:53 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-18T12:51:53 prefetch.3.0.8: 1) Downloading 'DRR218540'...
2024-03-18T12:51:53 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-18T12:51:53 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-18T12:51:55 prefetch.3.0.8:  HTTPS download succeed
2024-03-18T12:51:55 prefetch.3.0.8:  'DRR218540' is valid
2024-03-18T12:51:55 prefetch.3.0.8: 1) 'DRR218540' was downloaded successfully
2024-03-18T12:51:55 prefetch.3.0.8: 'DRR218540' has 0 unresolved dependencies

Standard Output:

Downloading accession: DRR218540...

Read 67485 spots for DRR218540
Written 67485 spots for DRR218540
Done with all accessions.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "2721679ae52611ee89fd8d825e54c327"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4jr2tggt/files/9/b/0/dataset_9b08ab87-dfcf-4ef4-a8fa-7f815956133a.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmp4jr2tggt/files/f/5/1/dataset_f5197c41-608b-4bda-ace7-528bd3471a6f.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmp4jr2tggt/job_working_directory/000/3/outputs/dataset_ba7d02d8-2376-407d-8386-ff4b089fdcc9.dat' && mv second.fastq.gz '/tmp/tmp4jr2tggt/job_working_directory/000/3/outputs/dataset_a1c99f6b-dcbe-424d-9e96-44a653d5ff68.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 26 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmp4jr2tggt/files/b/a/7/dataset_ba7d02d8-2376-407d-8386-ff4b089fdcc9.dat' -r '/tmp/tmp4jr2tggt/files/a/1/c/dataset_a1c99f6b-dcbe-424d-9e96-44a653d5ff68.dat' -1 '/tmp/tmp4jr2tggt/job_working_directory/000/6/outputs/dataset_dfacbb7c-df8e-414d-955b-a7e325e7c855.dat' -2 '/tmp/tmp4jr2tggt/job_working_directory/000/6/outputs/dataset_d9baa55d-cbba-4041-9336-9045254d7c62.dat'  -s '/tmp/tmp4jr2tggt/job_working_directory/000/6/outputs/dataset_b1f01cf0-1d34-4573-a84f-cec601e8d7a5.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020721

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmp4jr2tggt/files/b/1/f/dataset_b1f01cf0-1d34-4573-a84f-cec601e8d7a5.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmp4jr2tggt/job_working_directory/000/7/outputs/dataset_ca138d12-83fe-492f-98d5-cc0d79d0b98d.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 6434 Surviving: 6432 (99.97%) Dropped: 2 (0.03%)
TrimmomaticSE: Completed successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4jr2tggt/files/b/1/f/dataset_b1f01cf0-1d34-4573-a84f-cec601e8d7a5.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmp4jr2tggt/job_working_directory/000/8/outputs/dataset_84785904-0672-4cb9-829f-908e58821190_files' && fastqc --outdir '/tmp/tmp4jr2tggt/job_working_directory/000/8/outputs/dataset_84785904-0672-4cb9-829f-908e58821190_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmp4jr2tggt/job_working_directory/000/8/outputs/dataset_84785904-0672-4cb9-829f-908e58821190_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp4jr2tggt/job_working_directory/000/8/outputs/dataset_84785904-0672-4cb9-829f-908e58821190_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
adapters	`None`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmp4jr2tggt/files/c/a/1/dataset_ca138d12-83fe-492f-98d5-cc0d79d0b98d.dat' '/tmp/tmp4jr2tggt/job_working_directory/000/9/configs/tmp_2v1jh31' '/tmp/tmp4jr2tggt/job_working_directory/000/9/outputs/dataset_d0a26ad4-1b9e-4075-b62b-6da6f85354df.dat' '/tmp/tmp4jr2tggt/job_working_directory/000/9/outputs/dataset_d0a26ad4-1b9e-4075-b62b-6da6f85354df_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 6432 of 6432 reads (100.00%).
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4jr2tggt/files/c/a/1/dataset_ca138d12-83fe-492f-98d5-cc0d79d0b98d.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmp4jr2tggt/job_working_directory/000/10/outputs/dataset_cbeac128-926b-4b2c-b0bb-26b7e83a5104_files' && fastqc --outdir '/tmp/tmp4jr2tggt/job_working_directory/000/10/outputs/dataset_cbeac128-926b-4b2c-b0bb-26b7e83a5104_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmp4jr2tggt/job_working_directory/000/10/outputs/dataset_cbeac128-926b-4b2c-b0bb-26b7e83a5104_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp4jr2tggt/job_working_directory/000/10/outputs/dataset_cbeac128-926b-4b2c-b0bb-26b7e83a5104_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
adapters	`None`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp4jr2tggt/job_working_directory/000/11/outputs/dataset_b86c6b25-7cf5-462e-93bd-8e7521349ca4.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmp4jr2tggt/files/b/f/b/dataset_bfb344ef-d673-49f6-9e8a-935c1fe3fb91.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4jr2tggt/files/d/0/a/dataset_d0a26ad4-1b9e-4075-b62b-6da6f85354df.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmp4jr2tggt/job_working_directory/000/12/outputs/dataset_eb9ce73e-30ef-4887-95ad-db4403376c1e_files' && fastqc --outdir '/tmp/tmp4jr2tggt/job_working_directory/000/12/outputs/dataset_eb9ce73e-30ef-4887-95ad-db4403376c1e_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmp4jr2tggt/job_working_directory/000/12/outputs/dataset_eb9ce73e-30ef-4887-95ad-db4403376c1e_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp4jr2tggt/job_working_directory/000/12/outputs/dataset_eb9ce73e-30ef-4887-95ad-db4403376c1e_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
adapters	`None`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmp4jr2tggt/files/d/0/a/dataset_d0a26ad4-1b9e-4075-b62b-6da6f85354df.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 6,432
	Input bases: 2,151,394
	Input mean length: 334.48
	Good sequences: 6,432 (100.00%)
	Good bases: 2,151,394
	Good mean length: 334.48
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp4jr2tggt/job_working_directory/000/14/outputs/dataset_2d8e3498-0704-4c7c-840d-11c9ca704bff.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmp4jr2tggt/files/1/2/c/dataset_12c4426b-bd6f-4a42-b62e-ad753b381755.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp4jr2tggt/job_working_directory/000/15/outputs/dataset_c7c3a642-4e55-45e9-a8c2-115d28fd8d5a.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmp4jr2tggt/files/a/1/8/dataset_a182e036-9df4-4ee9-800c-a87f7260c04a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmp4jr2tggt/files/a/1/6/dataset_a163816b-b731-411b-a8ba-f18cbf7fd466.dat' '/tmp/tmp4jr2tggt/job_working_directory/000/16/outputs/dataset_a30e3b97-67ec-4fb5-8e20-3edc49a01c53.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

6432 FASTQ reads were converted to FASTA.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4jr2tggt/files/a/1/6/dataset_a163816b-b731-411b-a8ba-f18cbf7fd466.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmp4jr2tggt/job_working_directory/000/17/outputs/dataset_ece58b5d-657a-4186-8119-a0b9125cb920_files' && fastqc --outdir '/tmp/tmp4jr2tggt/job_working_directory/000/17/outputs/dataset_ece58b5d-657a-4186-8119-a0b9125cb920_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmp4jr2tggt/job_working_directory/000/17/outputs/dataset_ece58b5d-657a-4186-8119-a0b9125cb920_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp4jr2tggt/job_working_directory/000/17/outputs/dataset_ece58b5d-657a-4186-8119-a0b9125cb920_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
adapters	`None`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp4jr2tggt/files/a/3/0/dataset_a30e3b97-67ec-4fb5-8e20-3edc49a01c53.dat' | fasta_formatter -w 0 -o '/tmp/tmp4jr2tggt/job_working_directory/000/18/outputs/dataset_e4bf32ad-ca5f-4253-9532-8d6f5cb3c7e6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp4jr2tggt/job_working_directory/000/19/outputs/dataset_37dd3ee1-d7b8-4368-8e06-3e22582f491e.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmp4jr2tggt/files/8/7/3/dataset_87345e06-2c84-441e-aed9-5c8abc513a4b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmp4jr2tggt/files/b/8/6/dataset_b86c6b25-7cf5-462e-93bd-8e7521349ca4.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmp4jr2tggt/files/2/d/8/dataset_2d8e3498-0704-4c7c-840d-11c9ca704bff.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmp4jr2tggt/files/c/7/c/dataset_c7c3a642-4e55-45e9-a8c2-115d28fd8d5a.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmp4jr2tggt/files/3/7/d/dataset_37dd3ee1-d7b8-4368-8e06-3e22582f491e.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmp4jr2tggt/job_working_directory/000/20/working/multiqc_WDir
|            fastqc | Found 4 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2721679ae52611ee89fd8d825e54c327"`
chromInfo	`"/tmp/tmp4jr2tggt/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 23, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- history_id
  - f1c3eb7fc42c2f6c
- history_state
  - ok
- invocation_id
  - f1c3eb7fc42c2f6c
- invocation_state
  - scheduled
- workflow_id
  - f1c3eb7fc42c2f6c

✅ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled

Step 11: Trimming:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmprnm73jov/files/1/4/6/dataset_14620d1a-978c-4543-b657-9b3106381e5c.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmprnm73jov/job_working_directory/000/2/outputs/dataset_cea32407-0219-44fb-aa00-f4e1cd298212.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 196 Surviving: 184 (93.88%) Dropped: 12 (6.12%)
TrimmomaticSE: Completed successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 1, "src": "dce"}]}, "single_or_paired": "se"}`

Job 2:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmprnm73jov/files/2/7/8/dataset_278a1603-e5d7-4dae-89b1-47747c69fa90.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmprnm73jov/job_working_directory/000/3/outputs/dataset_7f137ee4-0423-4e5a-90b4-abc97acdc768.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 90 Surviving: 90 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 2, "src": "dce"}]}, "single_or_paired": "se"}`

Step 12: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprnm73jov/files/1/4/6/dataset_14620d1a-978c-4543-b657-9b3106381e5c.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmprnm73jov/job_working_directory/000/4/outputs/dataset_2de915ed-a513-49db-b537-c55b885fac06_files' && fastqc --outdir '/tmp/tmprnm73jov/job_working_directory/000/4/outputs/dataset_2de915ed-a513-49db-b537-c55b885fac06_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmprnm73jov/job_working_directory/000/4/outputs/dataset_2de915ed-a513-49db-b537-c55b885fac06_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprnm73jov/job_working_directory/000/4/outputs/dataset_2de915ed-a513-49db-b537-c55b885fac06_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adapters	`None`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmprnm73jov/files/2/7/8/dataset_278a1603-e5d7-4dae-89b1-47747c69fa90.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmprnm73jov/job_working_directory/000/5/outputs/dataset_6832ac5a-9657-447a-8395-1ec1e5430caa_files' && fastqc --outdir '/tmp/tmprnm73jov/job_working_directory/000/5/outputs/dataset_6832ac5a-9657-447a-8395-1ec1e5430caa_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmprnm73jov/job_working_directory/000/5/outputs/dataset_6832ac5a-9657-447a-8395-1ec1e5430caa_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprnm73jov/job_working_directory/000/5/outputs/dataset_6832ac5a-9657-447a-8395-1ec1e5430caa_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adapters	`None`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 13: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmprnm73jov/files/c/e/a/dataset_cea32407-0219-44fb-aa00-f4e1cd298212.dat' '/tmp/tmprnm73jov/job_working_directory/000/6/configs/tmp724uugzv' '/tmp/tmprnm73jov/job_working_directory/000/6/outputs/dataset_6774fd40-3667-477c-a3c3-b31b1fcf6bf0.dat' '/tmp/tmprnm73jov/job_working_directory/000/6/outputs/dataset_6774fd40-3667-477c-a3c3-b31b1fcf6bf0_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 184 of 184 reads (100.00%).
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Job 2:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmprnm73jov/files/7/f/1/dataset_7f137ee4-0423-4e5a-90b4-abc97acdc768.dat' '/tmp/tmprnm73jov/job_working_directory/000/7/configs/tmpwjlrxf4r' '/tmp/tmprnm73jov/job_working_directory/000/7/outputs/dataset_b48140d9-e530-47ba-a85a-a388fd6e1b69.dat' '/tmp/tmprnm73jov/job_working_directory/000/7/outputs/dataset_b48140d9-e530-47ba-a85a-a388fd6e1b69_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 90 of 90 reads (100.00%).
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprnm73jov/files/c/e/a/dataset_cea32407-0219-44fb-aa00-f4e1cd298212.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmprnm73jov/job_working_directory/000/8/outputs/dataset_b01240b4-04cc-4950-9cad-12c506ebee18_files' && fastqc --outdir '/tmp/tmprnm73jov/job_working_directory/000/8/outputs/dataset_b01240b4-04cc-4950-9cad-12c506ebee18_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmprnm73jov/job_working_directory/000/8/outputs/dataset_b01240b4-04cc-4950-9cad-12c506ebee18_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprnm73jov/job_working_directory/000/8/outputs/dataset_b01240b4-04cc-4950-9cad-12c506ebee18_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adapters	`None`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmprnm73jov/files/7/f/1/dataset_7f137ee4-0423-4e5a-90b4-abc97acdc768.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmprnm73jov/job_working_directory/000/9/outputs/dataset_d3a7e31a-d70d-4839-b2f2-e81d75edb523_files' && fastqc --outdir '/tmp/tmprnm73jov/job_working_directory/000/9/outputs/dataset_d3a7e31a-d70d-4839-b2f2-e81d75edb523_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmprnm73jov/job_working_directory/000/9/outputs/dataset_d3a7e31a-d70d-4839-b2f2-e81d75edb523_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprnm73jov/job_working_directory/000/9/outputs/dataset_d3a7e31a-d70d-4839-b2f2-e81d75edb523_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adapters	`None`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprnm73jov/job_working_directory/000/10/outputs/dataset_13073768-3719-4b0a-bc72-7752d1d61427.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmprnm73jov/files/4/c/c/dataset_4cc98726-850e-46e1-b5b3-f11ef29107f9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprnm73jov/job_working_directory/000/11/outputs/dataset_1d22c2da-9655-4a8c-ab51-b3fc10a41adc.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmprnm73jov/files/4/b/e/dataset_4be4729e-d7aa-4745-9054-d8e9336f9b03.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 16: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmprnm73jov/files/6/7/7/dataset_6774fd40-3667-477c-a3c3-b31b1fcf6bf0.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 184
	Input bases: 46,942
	Input mean length: 255.12
	Good sequences: 184 (100.00%)
	Good bases: 46,942
	Good mean length: 255.12
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 9, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Job 2:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmprnm73jov/files/b/4/8/dataset_b48140d9-e530-47ba-a85a-a388fd6e1b69.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 90
	Input bases: 31,735
	Input mean length: 352.61
	Good sequences: 90 (100.00%)
	Good bases: 31,735
	Good mean length: 352.61
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 10, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprnm73jov/files/6/7/7/dataset_6774fd40-3667-477c-a3c3-b31b1fcf6bf0.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmprnm73jov/job_working_directory/000/14/outputs/dataset_87016498-370c-4076-976d-c05ff40bc911_files' && fastqc --outdir '/tmp/tmprnm73jov/job_working_directory/000/14/outputs/dataset_87016498-370c-4076-976d-c05ff40bc911_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmprnm73jov/job_working_directory/000/14/outputs/dataset_87016498-370c-4076-976d-c05ff40bc911_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprnm73jov/job_working_directory/000/14/outputs/dataset_87016498-370c-4076-976d-c05ff40bc911_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adapters	`None`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmprnm73jov/files/b/4/8/dataset_b48140d9-e530-47ba-a85a-a388fd6e1b69.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmprnm73jov/job_working_directory/000/15/outputs/dataset_75bf4bbe-4723-43ab-87bb-dd05a81becab_files' && fastqc --outdir '/tmp/tmprnm73jov/job_working_directory/000/15/outputs/dataset_75bf4bbe-4723-43ab-87bb-dd05a81becab_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmprnm73jov/job_working_directory/000/15/outputs/dataset_75bf4bbe-4723-43ab-87bb-dd05a81becab_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprnm73jov/job_working_directory/000/15/outputs/dataset_75bf4bbe-4723-43ab-87bb-dd05a81becab_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adapters	`None`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprnm73jov/job_working_directory/000/16/outputs/dataset_e12858e5-b5cb-4c7a-ba31-a7eb7eb1532c.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmprnm73jov/files/4/8/d/dataset_48d265cc-ca8e-41ff-b267-c4ec4173e89d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprnm73jov/job_working_directory/000/17/outputs/dataset_3e14f96c-b923-4fa9-98e1-5f517b080654.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmprnm73jov/files/b/c/c/dataset_bccae83d-b497-4294-b157-f9e74e09eab1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmprnm73jov/files/f/2/6/dataset_f26647b9-17b2-48c9-9fa1-c7567af1552a.dat' '/tmp/tmprnm73jov/job_working_directory/000/18/outputs/dataset_b2759a30-8542-4116-a2b8-ffdca4ca7f95.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

184 FASTQ reads were converted to FASTA.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmprnm73jov/files/7/b/a/dataset_7baedf0d-ef30-4e9e-a997-8ee4511260dc.dat' '/tmp/tmprnm73jov/job_working_directory/000/19/outputs/dataset_fd1af47e-a4e5-4aa8-97f0-f934eec74a05.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

90 FASTQ reads were converted to FASTA.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprnm73jov/files/f/2/6/dataset_f26647b9-17b2-48c9-9fa1-c7567af1552a.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmprnm73jov/job_working_directory/000/20/outputs/dataset_02f63552-5d20-4a37-94db-d95f82953606_files' && fastqc --outdir '/tmp/tmprnm73jov/job_working_directory/000/20/outputs/dataset_02f63552-5d20-4a37-94db-d95f82953606_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmprnm73jov/job_working_directory/000/20/outputs/dataset_02f63552-5d20-4a37-94db-d95f82953606_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprnm73jov/job_working_directory/000/20/outputs/dataset_02f63552-5d20-4a37-94db-d95f82953606_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adapters	`None`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmprnm73jov/files/7/b/a/dataset_7baedf0d-ef30-4e9e-a997-8ee4511260dc.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmprnm73jov/job_working_directory/000/21/outputs/dataset_1da5cb02-3ae6-427d-b7d9-48be60c2a51c_files' && fastqc --outdir '/tmp/tmprnm73jov/job_working_directory/000/21/outputs/dataset_1da5cb02-3ae6-427d-b7d9-48be60c2a51c_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmprnm73jov/job_working_directory/000/21/outputs/dataset_1da5cb02-3ae6-427d-b7d9-48be60c2a51c_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmprnm73jov/job_working_directory/000/21/outputs/dataset_1da5cb02-3ae6-427d-b7d9-48be60c2a51c_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adapters	`None`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 3: Trimmomatic - LEADING:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprnm73jov/job_working_directory/000/22/outputs/dataset_231e112a-5b7c-4031-a619-7ffedbb53c21.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmprnm73jov/files/d/9/4/dataset_d948395c-4769-4aaa-b49d-cb83243352c8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprnm73jov/job_working_directory/000/23/outputs/dataset_68946b3e-d010-4204-a376-17b0d2fd8bb2.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmprnm73jov/files/c/a/d/dataset_cad5dbf4-3fc9-4786-b854-684893f4d382.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmprnm73jov/files/b/2/7/dataset_b2759a30-8542-4116-a2b8-ffdca4ca7f95.dat' | fasta_formatter -w 60 -o '/tmp/tmprnm73jov/job_working_directory/000/24/outputs/dataset_f46048cf-954c-4f35-8281-45aa15e75ac2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Job 2:

Job state is ok

Command Line:

cat '/tmp/tmprnm73jov/files/f/d/1/dataset_fd1af47e-a4e5-4aa8-97f0-f934eec74a05.dat' | fasta_formatter -w 60 -o '/tmp/tmprnm73jov/job_working_directory/000/25/outputs/dataset_b57fff43-d182-4064-8527-1479ce3dabac.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprnm73jov/job_working_directory/000/26/outputs/dataset_0b711e62-7765-4704-b911-4e91cd6a24a6.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmprnm73jov/files/c/0/2/dataset_c02fa298-81b9-42b6-8c9a-034ff4063224.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmprnm73jov/job_working_directory/000/27/outputs/dataset_9cc612b3-24e0-45f6-9917-2ccf2d721e4d.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmprnm73jov/files/8/d/4/dataset_8d460a42-1119-469a-bbf5-46e944296a52.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmprnm73jov/files/1/3/0/dataset_13073768-3719-4b0a-bc72-7752d1d61427.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/tmp/tmprnm73jov/files/1/d/2/dataset_1d22c2da-9655-4a8c-ab51-b3fc10a41adc.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmprnm73jov/files/e/1/2/dataset_e12858e5-b5cb-4c7a-ba31-a7eb7eb1532c.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_1/file_1' && ln -s '/tmp/tmprnm73jov/files/3/e/1/dataset_3e14f96c-b923-4fa9-98e1-5f517b080654.dat' 'multiqc_WDir/fastqc_0/data_1/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmprnm73jov/files/2/3/1/dataset_231e112a-5b7c-4031-a619-7ffedbb53c21.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_2/file_1' && ln -s '/tmp/tmprnm73jov/files/6/8/9/dataset_68946b3e-d010-4204-a376-17b0d2fd8bb2.dat' 'multiqc_WDir/fastqc_0/data_2/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmprnm73jov/files/0/b/7/dataset_0b711e62-7765-4704-b911-4e91cd6a24a6.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_3/file_1' && ln -s '/tmp/tmprnm73jov/files/9/c/c/dataset_9cc612b3-24e0-45f6-9917-2ccf2d721e4d.dat' 'multiqc_WDir/fastqc_0/data_3/file_1/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmprnm73jov/job_working_directory/000/28/working/multiqc_WDir
|            fastqc | Found 8 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 8/8

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled
Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmprnm73jov/job_working_directory/000/1/configs/tmpe3edgzpt' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-18T12:52:57 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-18T12:52:57 prefetch.3.0.8: 1) Downloading 'DRR011051'...
2024-03-18T12:52:57 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-18T12:52:57 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-18T12:52:58 prefetch.3.0.8:  HTTPS download succeed
2024-03-18T12:52:58 prefetch.3.0.8:  'DRR011051' is valid
2024-03-18T12:52:58 prefetch.3.0.8: 1) 'DRR011051' was downloaded successfully
2024-03-18T12:52:58 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-18T12:52:59 prefetch.3.0.8: 1) Downloading 'DRR010705'...
2024-03-18T12:52:59 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-18T12:52:59 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-18T12:52:59 prefetch.3.0.8:  HTTPS download succeed
2024-03-18T12:52:59 prefetch.3.0.8:  'DRR010705' is valid
2024-03-18T12:52:59 prefetch.3.0.8: 1) 'DRR010705' was downloaded successfully

Standard Output:

Downloading accession: DRR011051...

Rejected 270 READS because of filtering out non-biological READS
Read 90 spots for DRR011051
Written 90 spots for DRR011051
Downloading accession: DRR010705...

Rejected 588 READS because of filtering out non-biological READS
Read 196 spots for DRR010705
Written 196 spots for DRR010705
Done with all accessions.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e36d7b6e52611eeaa0a252bf652e966"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmprnm73jov/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- history_id
  - 687589b6bb00f245
- history_state
  - ok
- invocation_id
  - 687589b6bb00f245
- invocation_state
  - scheduled
- workflow_id
  - 687589b6bb00f245

github-actions · 2024-03-20T11:46:38Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	4
Passed	1
Error	1
Failure	2
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled
Step 11: Trimming:
- step_state: scheduled
Step 12: Unlabelled step:
- step_state: scheduled
Step 13: Length filtering:
- step_state: scheduled
Step 14: Unlabelled step:
- step_state: scheduled
Step 15: Unlabelled step:
- step_state: scheduled
Step 16: Ambiguity filtering:
- step_state: scheduled
Step 17: Unlabelled step:
- step_state: scheduled
Step 18: Unlabelled step:
- step_state: scheduled
Step 19: Unlabelled step:
- step_state: scheduled
Step 20: Unlabelled step:
- step_state: scheduled
Step 3: Trimmomatic - LEADING:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: scheduled
Step 22: Unlabelled step:
- step_state: scheduled
Step 23: Unlabelled step:
- step_state: scheduled

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9002b48ae6ac11ee8f1375f1524273ef"`
chromInfo	`"/tmp/tmpyx6eldw7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled
Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpyx6eldw7/job_working_directory/000/1/configs/tmpuczq_6a8' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
2
```

Standard Error:

/tmp/tmpyx6eldw7/job_working_directory/000/1/tool_script.sh: line 10: fastq-dump: command not found
/tmp/tmpyx6eldw7/job_working_directory/000/1/tool_script.sh: line 11: prefetch: command not found
ls: cannot access './*.fast*': No such file or directory

Standard Output:

```
Downloading accession: DRR011051...
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9002b48ae6ac11ee8f1375f1524273ef"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpyx6eldw7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 2525cdfda08a9945
- history_state
  - error
- invocation_id
  - 2525cdfda08a9945
- invocation_state
  - scheduled
- workflow_id
  - 2525cdfda08a9945

Failed Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Problems:

Output with path /tmp/tmpl8mqsjln/Classifications_SSU_SILVA__dc4c4fd6-ab07-491b-9641-012b3a568db1 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/Classifications_SSU_SILVA/ERR2715528_MERGED_FASTQ.fasta.tabular v. /tmp/tmp4t17__5pERR2715528_MERGED_FASTQ.fasta.tabular )
Failed to find 'ERR2715528.10-M00969:265:000000000-ANYDA:1:1101:24166:4465-1:0-46	CVKT01004482.883.2203	46	1	46	0	0	0	46	1275	1321	+		sk__Eukaryota	' in history data. (lines_diff=0).

Output with path /tmp/tmpjfp05ise/OTU_SSU_SILVA__7aeeb4c7-2bca-4622-b06a-8a97f03c4a3b different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/OTU_SSU_SILVA/ERR2715528_MERGED_FASTQ.fasta.tabular v. /tmp/tmpf6r4a7dsERR2715528_MERGED_FASTQ.fasta.tabular )
Failed to find '100053	471.0	sk__Eukaryota	2759' in history data. (lines_diff=0).

Output with path /tmp/tmp66pa8157/Classifications_LSU_SILVA__1d202f02-7de3-442b-aa5d-6cc7382324aa different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/Classifications_LSU_SILVA/DRR010481_FASTQ.fasta.tabular v. /tmp/tmp9myig3pqDRR010481_FASTQ.fasta.tabular )
Failed to find 'DRR010481.15-HUMWT9A01C6KQE-4:312-365	AYUK01000002.1610616.1614250	53	1	53	0	0	0	53	361	414	+		sk__Eukaryota;k__Fungi	' in history data. (lines_diff=0).

Output with path /tmp/tmpxakmi1vo/HDF5_SSU_SILVA__16b5bf9e-e17f-44eb-b470-ca8b60d9c1ad different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/HDF5_SSU_SILVA/ERR2715528_MERGED_FASTQ.fasta.biom1 v. /tmp/tmp4j1hi4jpERR2715528_MERGED_FASTQ.fasta.biom1 )
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Table ID\x00\x00\x00\x00\x00\x02\x00\x00\x00\x00\x00\x00\x00\t\x00\x00\x00\x00\x00\x00\x00OTU table\x00\x00\x00\x00\x00\x00\x00\x03\x00\x00\x00\x00\x00\x00\x00\x16\x00\x00\x00\x00\x00\x00\x00http://biom-format.org\x00\x00\x04\x00\x00\x00\x00\x00\x00\x00\x12\x00\x00\x00\x00\x00\x00\x00BIOM-Format 2.1.15\x00\x00\x00\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x1a\x00\x00\x00\x00\x00\x00\x002024-02-16T12:41:51.708336\x00\x00\x00\x00\x00\x00\x06\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x07\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x08\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\t\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'' in history data. (lines_diff=0).

Output with path /tmp/tmpgcsg47dw/JSON_SSU_SILVA__954c1b01-b0bc-4a83-b5f0-a59b2f550488 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/JSON_SSU_SILVA/ERR2715528_MERGED_FASTQ.fasta.biom1 v. /tmp/tmpydqh364vERR2715528_MERGED_FASTQ.fasta.biom1 )
Failed to find '{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.15","date": "2024-02-16T12:42:00.233757","type": "OTU table","matrix_element_type": "float","shape": [9, 1],"data": [[0,0,471.0],[1,0,3.0],[2,0,46.0],[3,0,1616.0],[4,0,54.0],[5,0,1.0],[6,0,1.0],[7,0,1.0],[8,0,14.0]],"rows": [{"id": "100053", "metadata": {"taxonomy": ["sk__Eukaryota"]}},{"id": "25778", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi"]}},{"id": "229700", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota"]}},{"id": "121326", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota", "c__Sordariomycetes"]}},{"id": "46745", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Chytridiomycota", "c__Chytridiomycetes"]}},{"id": "167911", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Metazoa", "p__Annelida", "c__Polychaeta", "o__Phyllodocida", "f__Glyceridae", "g__Glycera", "s__Glycera_nicobarica"]}},{"id": "234433", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Metazoa", "p__Arthropoda", "c__Insecta"]}},{"id": "51027", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Viridiplantae"]}},{"id": "237552", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Viridiplantae", "p__Streptophyta", "c__Magnoliopsida", "o__Solanales", "f__Convolvulaceae", "g__Ipomoea"]}}],"columns": [{"id": "Unspecified", "metadata": null}]}' in history data. (lines_diff=0).

Output with path /tmp/tmpdgud2jgq/Krona_SSU_SILVA__45391aee-0053-4e90-b6b1-133a128ff025 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/Krona_SSU_SILVA.html v. /tmp/tmpr3dn2i1oKrona_SSU_SILVA.html )
Failed to find '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">' in history data. (lines_diff=0).

Output with path /tmp/tmpgn3mhfxm/HDF5 _LSU_SILVA__3da9b32c-41af-4340-9d8d-fcadc243f125 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/HDF5_LSU_SILVA/DRR010481_FASTQ.fasta.biom1 v. /tmp/tmphrkyq_23DRR010481_FASTQ.fasta.biom1 )
Failed to find 'b'\x00\x01\x00\x00\x00\x18\x00\x00\x00\x00\x00\x00\x00\x10\x00\x10\x00\x00\x00\x00\x00 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\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00GCOL\x01\x00\x00\x00\x00\x10\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x0b\x00\x00\x00\x00\x00\x00\x00No Table ID\x00\x00\x00\x00\x00\x02\x00\x00\x00\x00\x00\x00\x00\t\x00\x00\x00\x00\x00\x00\x00OTU table\x00\x00\x00\x00\x00\x00\x00\x03\x00\x00\x00\x00\x00\x00\x00\x16\x00\x00\x00\x00\x00\x00\x00http://biom-format.org\x00\x00\x04\x00\x00\x00\x00\x00\x00\x00\x12\x00\x00\x00\x00\x00\x00\x00BIOM-Format 2.1.15\x00\x00\x00\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x1a\x00\x00\x00\x00\x00\x00\x002024-02-16T12:40:56.683053\x00\x00\x00\x00\x00\x00\x06\x00\x00\x00\x00\x00\x00\x00\r\x00\x00\x00\x00\x00\x00\x00sk__Eukaryota\x00\x00\x00\x07\x00\x00\x00\x00\x00\x00\x00\x08\x00\x00\x00\x00\x00\x00\x00k__Fungi\x08\x00\x00\x00\x00\x00\x00\x00\r\x00\x00\x00\x00\x00\x00\x00p__Ascomycota\x00\x00\x00\t\x00\x00\x00\x00\x00\x00\x00\x11\x00\x00\x00\x00\x00\x00\x00c__Eurotiomycetes\x00\x00\x00\x00\x00\x00\x00'' in history data. (lines_diff=0).

Output with path /tmp/tmpxcn6isvd/JSON_LSU_SILVA__b61f3fbc-32a8-4edc-80cc-e5897de41ab1 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/JSON_LSU_SILVA/DRR010481_FASTQ.fasta.biom1 v. /tmp/tmphb0d1hu3DRR010481_FASTQ.fasta.biom1 )
Failed to find '{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.15","date": "2024-02-16T12:41:05.832816","type": "OTU table","matrix_element_type": "float","shape": [4, 1],"data": [[0,0,2.0],[1,0,1.0],[2,0,1.0],[3,0,1.0]],"rows": [{"id": "16424", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi"]}},{"id": "32279", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota"]}},{"id": "28998", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota", "c__Eurotiomycetes"]}},{"id": "30170", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Verrucariales", "f__Verrucariaceae"]}}],"columns": [{"id": "Unspecified", "metadata": null}]}' in history data. (lines_diff=0).

Output with path /tmp/tmpt19fqaez/Krona_LSU_SILVA__325c938e-92d4-406d-858b-7919205becbf different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/Krona_LSU_SILVA.html v. /tmp/tmplory2pvaKrona_LSU_SILVA.html )
Failed to find '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">' in history data. (lines_diff=0).

Output with path /tmp/tmprr19x2_s/Classifications_ITSonedb__1978fdc2-267c-4dad-b3db-cf76891f9643 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/Classifications_ITSonedb/DRR010481_FASTQ.fasta.tabular v. /tmp/tmpgkfnqp66DRR010481_FASTQ.fasta.tabular )
Failed to find 'DRR010481.13-HUMWT9A01CWWE7-4	EF434064	111	0.8452380895614624	142	23	3	0	165	217	385	+		sk__Eukaryota;k__Fungi	' in history data. (lines_diff=0).

Output with path /tmp/tmpawp3zila/OTU_ITSonedb__7dce3aa3-98b7-4a3e-a571-18dfcd1a3294 different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/OTU_ITSonedb/ERR2715528_MERGED_FASTQ.fasta.tabular v. /tmp/tmp4ptkc128ERR2715528_MERGED_FASTQ.fasta.tabular )
--- local_file
+++ history_data
@@ -1,16 +1,15 @@
 # Constructed from biom file
 # OTU ID	Unspecified	taxonomy	taxid
 1470	32.0	sk__Eukaryota;k__Fungi	
-1486	55.0	sk__Eukaryota;k__Fungi;p__Ascomycota	
+1486	57.0	sk__Eukaryota;k__Fungi;p__Ascomycota	
 1491	5.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__;o__;f__;g__;s__Ascomycota_sp	
-1726	4.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes	
+1726	3.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes	
 1730	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__;f__;g__;s__Dothideomycetes_sp	
 2230	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Capnodiales	
 2521	3.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Capnodiales;f__Mycosphaerellaceae;g__;s__Mycosphaerellaceae_sp	
 3630	3.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Capnodiales;f__Teratosphaeriaceae;g__;s__Teratosphaeriaceae_sp	
-4242	3.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales	
+4242	6.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales	
 4245	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__;g__;s__Pleosporales_sp	
-5692	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Pleosporaceae;g__Alternaria	
 5925	2.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Pleosporaceae;g__Alternaria;s__Alternaria_sp	
 6899	5.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Venturiales;f__Sympoventuriaceae;g__Fusicladium;s__Fusicladium_cordae	
 6972	3.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Venturiales;f__Venturiaceae	
@@ -34,7 +33,7 @@
 15578	20.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Leotiomycetes;o__Phacidiales;f__Phacidiaceae	
 15779	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Leotiomycetes;o__Thelebolales;f__Pseudeurotiaceae	
 15971	2.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Orbiliomycetes;o__Orbiliales;f__Orbiliaceae;g__Dactylella;s__Dactylella_candida	
-17177	17.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales	
+17177	15.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales	
 17371	2.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Lipomycetaceae;g__Lipomyces	
 17382	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Lipomycetaceae;g__Lipomyces;s__Lipomyces_sp	
 17395	3.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Metschnikowiaceae;g__Clavispora;s__Clavispora_lusitaniae	
@@ -51,8 +50,9 @@
 18623	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Coniochaetales;f__Coniochaetaceae;g__Coniochaeta;s__Coniochaeta_luteoviridis	
 18631	8.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Coniochaetales;f__Coniochaetaceae;g__Coniochaeta;s__Coniochaeta_sp	
 19961	3.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales	
-20431	6.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae	
-20542	1597.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma	
+20431	5.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae	
+20542	1596.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma	
+20590	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_citrinoviride

Output with path /tmp/tmp2y2uwep8/OTU_ITS_UNITE__dd4ac833-6491-4280-94aa-edb2f8420009 different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/OTU_ITS_UNITE/ERR2715528_MERGED_FASTQ.fasta.tabular v. /tmp/tmpc78uhosfERR2715528_MERGED_FASTQ.fasta.tabular )
--- local_file
+++ history_data
@@ -2,7 +2,7 @@
 # OTU ID	Unspecified	taxonomy	taxid
 32396	2.0	sk__Eukaryota;k__;p__Apicomplexa;c__Conoidasida;o__Eucoccidiorida;f__Cryptosporidiidae	35082
 18861	46.0	sk__Eukaryota;k__Fungi	4751
-169982	55.0	sk__Eukaryota;k__Fungi;p__Ascomycota	4890
+169982	56.0	sk__Eukaryota;k__Fungi;p__Ascomycota	4890
 83634	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__;o__;f__;g__;s__leaf_litter_ascomycete_strain_its286	194073
 73457	8.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__;o__;f__;g__;s__uncultured_Ascomycota	175243
 121688	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__;o__;f__;g__Xenochalara;s__Xenochalara_juniperi	104697
@@ -25,7 +25,8 @@
 148841	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae;g__Emericella	5071
 33260	121.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae;g__Penicillium	5073
 173381	2.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae;g__Penicillium;s__Penicillium_chrysogenum	5076
-46101	62.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Talaromyces	5094
+54890	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Thermoascaceae;g__Paecilomyces	33202
+46101	61.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Talaromyces	5094
 27453	3.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Leotiomycetes;o__;f__;g__Scytalidium;s__Scytalidium_sp._TMS-2011	942822
 93403	2.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Leotiomycetes;o__Helotiales	5178
 116081	1.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Leotiomycetes;o__Helotiales;f__;g__;s__Helotiales_sp.	1755440
@@ -33,7 +34,7 @@
 82236	2.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Orbiliomycetes;o__Orbiliales;f__Orbiliaceae	47021
 93700	2.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Debaryomycetaceae;g__Candida;s__Candida_albicans	5476
 5901	46.0	sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Debaryomycetaceae;g__Meyerozyma;s__Meyerozyma_guilliermondii	4929
********
*SNIP *
********
 9326	3.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius	34451
 127530	2.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Atheliales;f__Atheliaceae	80628
 91803	2.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Cantharellales;f__Ceratobasidiaceae	5250
@@ -69,18 +69,18 @@
 141989	3.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Polyporales;f__Phanerochaetaceae;g__Phanerochaete;s__Phanerochaete_chrysosporium	5306
 85484	1.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Peniophoraceae;g__Peniophora	40463
 146505	2.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Tomentella	56494
-100538	4.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Trechisporales;f__Hydnodontaceae;g__Trechispora	156596
+100538	5.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Trechisporales;f__Hydnodontaceae;g__Trechispora	156596
 172165	7.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Trechisporales;f__Hydnodontaceae;g__Trechispora;s__Trechispora_farinacea	156599
 447	2.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Agaricostilbomycetes;o__Agaricostilbales;f__Chionosphaeraceae	54740
 1470	7.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Microbotryomycetes;o__;f__;g__Curvibasidium	256806
 125725	6.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Microbotryomycetes;o__Sporidiobolales;f__Sporidiobolaceae;g__Rhodotorula;s__Rhodotorula_dairenensis	86832
-167681	6.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes	155616
+167681	7.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes	155616
+4827	1.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__;f__;g__;s__uncultured_Cryptococcus	526442
 112378	9.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Filobasidiales;f__Filobasidiaceae;g__Naganishia;s__Naganishia_adeliensis	92952
 55319	1.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Filobasidiales;f__Piskurozymaceae;g__Piskurozyma;s__Piskurozyma_cylindrica	104406
 39274	1.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Tremellales;f__Cryptococcaceae	1884633
 162156	2.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Tremellales;f__Cryptococcaceae;g__Kwoniella	490731
 165507	1.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Tremellales;f__Cryptococcaceae;g__Kwoniella;s__Kwoniella_europaea	1247712
-97980	1.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Tremellales;f__Rhynchogastremataceae;g__Papiliotrema;s__Papiliotrema_laurentii	5418
 110271	1.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Tremellales;f__Syzygosporaceae	509125
 110689	1.0	sk__Eukaryota;k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Trichosporonales	1851469
 64699	13.0	sk__Eukaryota;k__Fungi;p__Chytridiomycota;c__Neocallimastigomycetes;o__Neocallimastigales	29006

Output with path /tmp/tmp3bt0jm6c/Classifications_ITS_UNITE__65957033-e86d-4492-bb93-f6c0101492fb different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/Classifications_ITS_UNITE/DRR010481_FASTQ.fasta.tabular v. /tmp/tmpfxl8cu4oDRR010481_FASTQ.fasta.tabular )
Failed to find 'DRR010481.7-HUMWT9A01DMCR3-4	ITS1DB00487337|1810549|Diaporthe	107	0.902255654335022	120	13	0	0	133	238	371	+		sk__Eukaryota;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Diaporthales	' in history data. (lines_diff=0).

Output with path /tmp/tmpc0tfj2dl/HDF5_ITSonedb__35e5458f-96c3-44df-97ba-1d06171fa761 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/HDF5_ITSonedb/DRR010481_FASTQ.fasta.biom1 v. /tmp/tmpr_5g2g_7DRR010481_FASTQ.fasta.biom1 )
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Table ID\x00\x00\x00\x00\x00\x02\x00\x00\x00\x00\x00\x00\x00\t\x00\x00\x00\x00\x00\x00\x00OTU table\x00\x00\x00\x00\x00\x00\x00\x03\x00\x00\x00\x00\x00\x00\x00\x16\x00\x00\x00\x00\x00\x00\x00http://biom-format.org\x00\x00\x04\x00\x00\x00\x00\x00\x00\x00\x12\x00\x00\x00\x00\x00\x00\x00BIOM-Format 2.1.15\x00\x00\x00\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x1a\x00\x00\x00\x00\x00\x00\x002024-02-16T12:41:47.230605\x00\x00\x00\x00\x00\x00\x06\x00\x00\x00\x00\x00\x00\x00\r\x00\x00\x00\x00\x00\x00\x00sk__Eukaryota\x00\x00\x00\x07\x00\x00\x00\x00\x00\x00\x00\x08\x00\x00\x00\x00\x00\x00\x00k__Fungi\x08\x00\x00\x00\x00\x00\x00\x00\r\x00\x00\x00\x00\x00\x00\x00p__Ascomycota\x00\x00\x00\t\x00\x00\x00\x00\x00\x00\x00\x12\x00\x00\x00\x00\x00\x00\x00c__Dothideomycetes\x00\x00\x00\x00\x00\x00'' in history data. (lines_diff=0).

Output with path /tmp/tmpuvfp3u3d/JSON_ITSonedb__99ef8dff-038c-44ae-b674-1dc929284146 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/JSON_ITSonedb/DRR010481_FASTQ.fasta.biom1 v. /tmp/tmpai8jdva9DRR010481_FASTQ.fasta.biom1 )
Failed to find '{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.15","date": "2024-02-16T12:41:42.351328","type": "OTU table","matrix_element_type": "float","shape": [6, 1],"data": [[0,0,4.0],[1,0,1.0],[2,0,8.0],[3,0,9.0],[4,0,1.0],[5,0,2.0]],"rows": [{"id": "1470", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi"]}},{"id": "1486", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota"]}},{"id": "1491", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota", "c__", "o__", "f__", "g__", "s__Ascomycota_sp"]}},{"id": "6882", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Venturiales"]}},{"id": "25133", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales"]}},{"id": "29420", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Mycenaceae"]}}],"columns": [{"id": "Unspecified", "metadata": null}]}' in history data. (lines_diff=0).

Output with path /tmp/tmpiwns5xgz/Krona_ITSonedb__550b4fd2-2d2a-446b-ad8b-09d332ec44aa different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/Krona_ITSonedb.html v. /tmp/tmpl4_johy5Krona_ITSonedb.html )
Failed to find '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">' in history data. (lines_diff=0).

Output with path /tmp/tmpebwv0zhq/HDF5_ITS_UNITE__14aba8c6-09c9-409a-b99c-41c87bb22be6 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/HDF5_ITS_UNITE/DRR010481_FASTQ.fasta.biom1 v. /tmp/tmpzbadjfktDRR010481_FASTQ.fasta.biom1 )
Failed to find 'b'\x00\x01\x00\x00\x00\x18\x00\x00\x00\x00\x00\x00\x00\x10\x00\x10\x00\x00\x00\x00\x00 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\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00GCOL\x01\x00\x00\x00\x00\x10\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x0b\x00\x00\x00\x00\x00\x00\x00No Table ID\x00\x00\x00\x00\x00\x02\x00\x00\x00\x00\x00\x00\x00\t\x00\x00\x00\x00\x00\x00\x00OTU table\x00\x00\x00\x00\x00\x00\x00\x03\x00\x00\x00\x00\x00\x00\x00\x16\x00\x00\x00\x00\x00\x00\x00http://biom-format.org\x00\x00\x04\x00\x00\x00\x00\x00\x00\x00\x12\x00\x00\x00\x00\x00\x00\x00BIOM-Format 2.1.15\x00\x00\x00\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x1a\x00\x00\x00\x00\x00\x00\x002024-02-16T12:41:01.396413\x00\x00\x00\x00\x00\x00\x06\x00\x00\x00\x00\x00\x00\x00\x12\x00\x00\x00\x00\x00\x00\x00c__Sordariomycetes\x00\x00\x00\x00\x00\x00\x07\x00\x00\x00\x00\x00\x00\x00\x0f\x00\x00\x00\x00\x00\x00\x00o__Diaporthales\x00\x08\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\t\x00\x00\x00\x00\x00\x00\x00\r\x00\x00\x00\x00\x00\x00\x00sk__Eukaryota\x00\x00\x00'' in history data. (lines_diff=0).

Output with path /tmp/tmp77pudajf/JSON_ITS_UNITE__f5f797a7-2a24-4c13-bcb4-c3cc90bf288c different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/JSON_ITS_UNITE/DRR010481_FASTQ.fasta.biom1 v. /tmp/tmpjli9e9yxDRR010481_FASTQ.fasta.biom1 )
Failed to find '{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.15","date": "2024-02-16T12:40:11.842285","type": "OTU table","matrix_element_type": "float","shape": [5, 1],"data": [[0,0,6.0],[1,0,1.0],[2,0,16.0],[3,0,1.0],[4,0,1.0]],"rows": [{"id": "18861", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi"]}},{"id": "93403", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota", "c__Leotiomycetes", "o__Helotiales"]}},{"id": "141869", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Diaporthales"]}},{"id": "132284", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Diaporthales", "f__Diaporthaceae"]}},{"id": "84360", "metadata": {"taxonomy": ["sk__Eukaryota", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales"]}}],"columns": [{"id": "Unspecified", "metadata": null}]}' in history data. (lines_diff=0).

Output with path /tmp/tmpta2d1cdb/Krona_ITS_UNITE__83a95cd1-7333-465e-9544-548398a21bb0 different than expected, difference (using contains):
( /home/runner/work/iwc/iwc/workflows/microbiome/mgnify-amplicon-after-quality-control/test-data/Krona_ITS_UNITE.html v. /tmp/tmpeiqp0jneKrona_ITS_UNITE.html )
Failed to find '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">' in history data. (lines_diff=0).

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: clan info file:
- step_state: scheduled

Step 11: SSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/concat/73ca13a7ec5f/concat/gops_concat.py' '/tmp/tmps8cm08gj/files/d/7/1/dataset_d71e8fa1-70bb-4fd4-9f1a-54574a6b4b2d.dat' '/tmp/tmps8cm08gj/files/1/c/f/dataset_1cf58a2a-6155-421b-8b5e-1bd831084857.dat' '/tmp/tmps8cm08gj/job_working_directory/000/19/outputs/dataset_40a91a95-cabf-4e76-9580-adffff771129.dat' -1 1,2,3,0 -2 1,2,3,0 --sameformat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/concat/73ca13a7ec5f/concat/gops_concat.py' '/tmp/tmps8cm08gj/files/c/3/9/dataset_c392be44-018f-4f30-bbb1-b0216d6cf5bc.dat' '/tmp/tmps8cm08gj/files/2/a/f/dataset_2af4c4c9-3f02-4677-8629-6ff870dcb178.dat' '/tmp/tmps8cm08gj/job_working_directory/000/20/outputs/dataset_3d2a5bf4-ff67-4b81-93cc-51884eb5e04f.dat' -1 1,2,3,6 -2 1,2,3,0 --sameformat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 12: LSU BED:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/concat/73ca13a7ec5f/concat/gops_concat.py' '/tmp/tmps8cm08gj/files/6/e/3/dataset_6e34ae9a-8da1-411b-a67f-257935fce82f.dat' '/tmp/tmps8cm08gj/files/4/f/5/dataset_4f553136-5bb1-4e1f-8252-9c1613018237.dat' '/tmp/tmps8cm08gj/job_working_directory/000/21/outputs/dataset_2dc7e817-5a79-4087-9de8-46e3a821e188.dat' -1 1,2,3,6 -2 1,2,3,0 --sameformat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/concat/73ca13a7ec5f/concat/gops_concat.py' '/tmp/tmps8cm08gj/files/3/f/9/dataset_3f97edf7-2298-4b48-a07e-e617895b9d77.dat' '/tmp/tmps8cm08gj/files/0/5/1/dataset_051b2f73-d3b8-4f84-83b0-3c93ff0ba3f6.dat' '/tmp/tmps8cm08gj/job_working_directory/000/22/outputs/dataset_f8aecd95-6bce-4aa3-838d-509a2d2021ce.dat' -1 1,2,3,0 -2 1,2,3,0 --sameformat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 13: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "f5aba53ae6ac11ee8bf6f341fccaebc9"
      
      input {"values": [{"id": 12, "src": "hdca"}]}
Step 14: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "f5aba53ae6ac11ee8bf6f341fccaebc9"
      
      input {"values": [{"id": 13, "src": "hdca"}]}

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/concat/73ca13a7ec5f/concat/gops_concat.py' '/tmp/tmps8cm08gj/files/4/0/a/dataset_40a91a95-cabf-4e76-9580-adffff771129.dat' '/tmp/tmps8cm08gj/files/2/d/c/dataset_2dc7e817-5a79-4087-9de8-46e3a821e188.dat' '/tmp/tmps8cm08gj/job_working_directory/000/23/outputs/dataset_ff1df6ff-6a78-47d3-a8e4-8b70b57ae9f4.dat' -1 1,2,3,0 -2 1,2,3,6 --sameformat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Job 2:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/concat/73ca13a7ec5f/concat/gops_concat.py' '/tmp/tmps8cm08gj/files/3/d/2/dataset_3d2a5bf4-ff67-4b81-93cc-51884eb5e04f.dat' '/tmp/tmps8cm08gj/files/f/8/a/dataset_f8aecd95-6bce-4aa3-838d-509a2d2021ce.dat' '/tmp/tmps8cm08gj/job_working_directory/000/24/outputs/dataset_66cad80b-261d-4c9a-b0e6-b2d772229416.dat' -1 1,2,3,6 -2 1,2,3,0 --sameformat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
sameformat	`true`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmps8cm08gj/job_working_directory/000/27/configs/tmpie7rtul_' '/tmp/tmps8cm08gj/job_working_directory/000/27/outputs/dataset_b920866f-65d1-4c89-b050-6e8d9ab3141a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 15, "src": "hdca"}]}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmps8cm08gj/job_working_directory/000/28/configs/tmpn12ly5z1' '/tmp/tmps8cm08gj/job_working_directory/000/28/outputs/dataset_b2a7d1ca-d83f-41ea-9036-efe678d314c3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 16, "src": "hdca"}]}`

Step 18: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "f5aba53ae6ac11ee8bf6f341fccaebc9"
      
      input {"values": [{"id": 14, "src": "hdca"}]}

Step 19: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 33, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 20: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 34, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: covariance models:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmps8cm08gj/job_working_directory/000/32/configs/tmpidyc3tyy' '/tmp/tmps8cm08gj/job_working_directory/000/32/outputs/dataset_293f5387-714d-4779-b7d1-d7e05b30669b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 17, "src": "hdca"}]}`

Step 22: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmps8cm08gj/files/5/c/0/dataset_5c066c01-8905-428d-a2a6-22f4332050a9.dat' 'input.fasta' && bedtools getfasta      -fi 'input.fasta' -bed '/tmp/tmps8cm08gj/files/3/d/2/dataset_3d2a5bf4-ff67-4b81-93cc-51884eb5e04f.dat' -fo '/tmp/tmps8cm08gj/job_working_directory/000/33/outputs/dataset_01a031b8-dc23-4027-9bf8-a7d8be6faeb4.dat'

Exit Code:

```
0
```

Standard Error:

index file input.fasta.fai not found, generating...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fasta_source	`{"__current_case__": 0, "fasta": {"values": [{"id": 33, "src": "dce"}]}, "fasta_source_selector": "history"}`
name	`false`
nameOnly	`false`
split	`false`
strand	`false`
tab	`false`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmps8cm08gj/files/f/e/7/dataset_fe710ee9-ecf7-4550-bb18-7353d0ef7ce0.dat' 'input.fasta' && bedtools getfasta      -fi 'input.fasta' -bed '/tmp/tmps8cm08gj/files/2/d/c/dataset_2dc7e817-5a79-4087-9de8-46e3a821e188.dat' -fo '/tmp/tmps8cm08gj/job_working_directory/000/34/outputs/dataset_14b1ae48-fffa-4feb-af1a-edc7c3ed76da.dat'

Exit Code:

```
0
```

Standard Error:

index file input.fasta.fai not found, generating...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fasta_source	`{"__current_case__": 0, "fasta": {"values": [{"id": 35, "src": "dce"}]}, "fasta_source_selector": "history"}`
name	`false`
nameOnly	`false`
split	`false`
strand	`false`
tab	`false`

Step 24: __FILTER_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
how	`{"__current_case__": 0, "filter_source": {"values": [{"id": 41, "src": "hda"}]}, "how_filter": "remove_if_absent"}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_ssu_from_2023-09-26'/*.fasta db.fasta && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_ssu_from_2023-09-26'/*.txt taxonomy.txt && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_ssu_from_2023-09-26'/*.mscluster db.fasta.mscluster && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_ssu_from_2023-09-26'/*.otu db.otu &&    mapseq -nthreads ${GALAXY_SLOTS:-8} -tophits '80' -topotus '40' -minscore '30' -minid1 '1' -minid2 '1' -otulim '50' -outfmt 'simple' '/tmp/tmps8cm08gj/files/0/1/a/dataset_01a031b8-dc23-4027-9bf8-a7d8be6faeb4.dat' db.fasta taxonomy.txt > '/tmp/tmps8cm08gj/job_working_directory/000/35/outputs/dataset_dc4c4fd6-ab07-491b-9641-012b3a568db1.dat'  && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl' --otuTable db.otu --query '/tmp/tmps8cm08gj/job_working_directory/000/35/outputs/dataset_dc4c4fd6-ab07-491b-9641-012b3a568db1.dat' --outfile '/tmp/tmps8cm08gj/job_working_directory/000/35/outputs/dataset_7aeeb4c7-2bca-4622-b06a-8a97f03c4a3b.dat' --taxid --notaxidfile '/tmp/tmps8cm08gj/job_working_directory/000/35/outputs/dataset_9d90844f-82c4-4c77-804c-dd0022f36afd.dat' --krona '/tmp/tmps8cm08gj/job_working_directory/000/35/outputs/dataset_1422686e-3c99-489d-bd5b-cc735c28b7d3.dat'

Exit Code:

```
0
```

Standard Error:

# loaded 2019789 sequences
# loading taxonomy file: taxonomy.txt
# taxonomies: 1
# tax levels: 8
# tax: 0 level: 0 (3)
# tax: 0 level: 1 (4)
# tax: 0 level: 2 (205)
# tax: 0 level: 3 (347)
# tax: 0 level: 4 (1318)
# tax: 0 level: 5 (5905)
# tax: 0 level: 6 (24251)
# tax: 0 level: 7 (205715)
# fcount: 50 otukmercount: 261872
# processing input... 
# processing input... 2208
# done processing 2208 seqs (4.84108s)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
minid1	`"1"`
minid2	`"1"`
minscore	`"30"`
otulim	`"50"`
outfmt	`"simple"`
ref_db	`{"__current_case__": 0, "db_cached": "mgnify_ssu_from_2023-09-26", "db_source": "cached", "mapseq2biom": {"__current_case__": 0, "krona_input": true, "mapseq2biom": "yes"}}`
tophits	`"80"`
topotus	`"40"`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_lsu_from_2023-09-26'/*.fasta db.fasta && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_lsu_from_2023-09-26'/*.txt taxonomy.txt && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_lsu_from_2023-09-26'/*.mscluster db.fasta.mscluster && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_lsu_from_2023-09-26'/*.otu db.otu &&    mapseq -nthreads ${GALAXY_SLOTS:-8} -tophits '80' -topotus '40' -minscore '30' -minid1 '1' -minid2 '1' -otulim '50' -outfmt 'simple' '/tmp/tmps8cm08gj/files/1/4/b/dataset_14b1ae48-fffa-4feb-af1a-edc7c3ed76da.dat' db.fasta taxonomy.txt > '/tmp/tmps8cm08gj/job_working_directory/000/36/outputs/dataset_1d202f02-7de3-442b-aa5d-6cc7382324aa.dat'  && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl' --otuTable db.otu --query '/tmp/tmps8cm08gj/job_working_directory/000/36/outputs/dataset_1d202f02-7de3-442b-aa5d-6cc7382324aa.dat' --outfile '/tmp/tmps8cm08gj/job_working_directory/000/36/outputs/dataset_758edbc3-0c61-4e08-86b0-046eef1e8a77.dat' --taxid --notaxidfile '/tmp/tmps8cm08gj/job_working_directory/000/36/outputs/dataset_76ee0daa-398f-424a-b8d5-47b67c13764a.dat' --krona '/tmp/tmps8cm08gj/job_working_directory/000/36/outputs/dataset_afd208bd-5aa1-442c-b640-815e18132983.dat'

Exit Code:

```
0
```

Standard Error:

# loaded 183364 sequences
# loading taxonomy file: taxonomy.txt
# taxonomies: 1
# tax levels: 8
# tax: 0 level: 0 (3)
# tax: 0 level: 1 (4)
# tax: 0 level: 2 (203)
# tax: 0 level: 3 (294)
# tax: 0 level: 4 (867)
# tax: 0 level: 5 (2985)
# tax: 0 level: 6 (8373)
# tax: 0 level: 7 (24642)
# fcount: 9 otukmercount: 259379
# processing input... 
# processing input... 5
# done processing 5 seqs (0.046292s)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
minid1	`"1"`
minid2	`"1"`
minscore	`"30"`
otulim	`"50"`
outfmt	`"simple"`
ref_db	`{"__current_case__": 0, "db_cached": "mgnify_lsu_from_2023-09-26", "db_source": "cached", "mapseq2biom": {"__current_case__": 0, "krona_input": true, "mapseq2biom": "yes"}}`
tophits	`"80"`
topotus	`"40"`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

bedtools maskfasta  -mc 'N' -fi '/tmp/tmps8cm08gj/files/f/e/7/dataset_fe710ee9-ecf7-4550-bb18-7353d0ef7ce0.dat' -bed '/tmp/tmps8cm08gj/files/f/f/1/dataset_ff1df6ff-6a78-47d3-a8e4-8b70b57ae9f4.dat' -fo '/tmp/tmps8cm08gj/job_working_directory/000/44/outputs/dataset_1576ad91-714e-4785-a274-6cff4525c63e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fullheader	`false`
mc	`"N"`
soft	`false`

Job 2:

Job state is ok

Command Line:

bedtools maskfasta  -mc 'N' -fi '/tmp/tmps8cm08gj/files/5/c/0/dataset_5c066c01-8905-428d-a2a6-22f4332050a9.dat' -bed '/tmp/tmps8cm08gj/files/6/6/c/dataset_66cad80b-261d-4c9a-b0e6-b2d772229416.dat' -fo '/tmp/tmps8cm08gj/job_working_directory/000/45/outputs/dataset_af0f2608-e90a-421a-8212-77ec2ad2f432.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fullheader	`false`
mc	`"N"`
soft	`false`

Step 28: HDF5 SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/9/d/9/dataset_9d90844f-82c4-4c77-804c-dd0022f36afd.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/37/outputs/dataset_16b5bf9e-e17f-44eb-b470-ca8b60d9c1ad.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-hdf5

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 41, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 1, "collapsed_observations": false, "collapsed_samples": false, "selector": "hdf5"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Step 29: JSON SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/9/d/9/dataset_9d90844f-82c4-4c77-804c-dd0022f36afd.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/38/outputs/dataset_954c1b01-b0bc-4a83-b5f0-a59b2f550488.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-json

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 41, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 0, "selector": "json"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Step 30: Krona SSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ktImportText  -n 'Root' -o '/tmp/tmps8cm08gj/job_working_directory/000/39/outputs/dataset_45391aee-0053-4e90-b6b1-133a128ff025.dat'  '/tmp/tmps8cm08gj/files/1/4/2/dataset_1422686e-3c99-489d-bd5b-cc735c28b7d3.dat,ERR2715528_MERGED_FASTQ_fasta' && if [ -d '/tmp/tmps8cm08gj/job_working_directory/000/39/outputs/dataset_45391aee-0053-4e90-b6b1-133a128ff025.dat.files' ] ; then mkdir '/tmp/tmps8cm08gj/job_working_directory/000/39/outputs/dataset_45391aee-0053-4e90-b6b1-133a128ff025_files' && mv '/tmp/tmps8cm08gj/job_working_directory/000/39/outputs/dataset_45391aee-0053-4e90-b6b1-133a128ff025.dat.files' '/tmp/tmps8cm08gj/job_working_directory/000/39/outputs/dataset_45391aee-0053-4e90-b6b1-133a128ff025_files' ; fi

Exit Code:

```
0
```

Standard Output:

Writing /tmp/tmps8cm08gj/job_working_directory/000/39/outputs/dataset_45391aee-0053-4e90-b6b1-133a128ff025.dat...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 27, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmps8cm08gj/files/b/9/e/dataset_b9e98280-f767-49c3-9a54-3bfd430fa9b8.dat '/tmp/tmps8cm08gj/files/f/e/7/dataset_fe710ee9-ecf7-4550-bb18-7353d0ef7ce0.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmps8cm08gj/job_working_directory/000/5/outputs/dataset_4c015fb4-bf94-435d-b20e-9cbc636fe271.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Job 2:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmps8cm08gj/files/b/9/e/dataset_b9e98280-f767-49c3-9a54-3bfd430fa9b8.dat '/tmp/tmps8cm08gj/files/5/c/0/dataset_5c066c01-8905-428d-a2a6-22f4332050a9.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmps8cm08gj/job_working_directory/000/6/outputs/dataset_fba04728-a570-4c03-808a-55ff9b0094be.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 4, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 31: HDF5 LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/7/6/e/dataset_76ee0daa-398f-424a-b8d5-47b67c13764a.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/40/outputs/dataset_3da9b32c-41af-4340-9d8d-fcadc243f125.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-hdf5

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 45, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 1, "collapsed_observations": false, "collapsed_samples": false, "selector": "hdf5"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Step 32: JSON LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/7/6/e/dataset_76ee0daa-398f-424a-b8d5-47b67c13764a.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/41/outputs/dataset_b61f3fbc-32a8-4edc-80cc-e5897de41ab1.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-json

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 45, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 0, "selector": "json"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Step 33: Krona LSU SILVA:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ktImportText  -n 'Root' -o '/tmp/tmps8cm08gj/job_working_directory/000/42/outputs/dataset_325c938e-92d4-406d-858b-7919205becbf.dat'  '/tmp/tmps8cm08gj/files/a/f/d/dataset_afd208bd-5aa1-442c-b640-815e18132983.dat,DRR010481_FASTQ_fasta' && if [ -d '/tmp/tmps8cm08gj/job_working_directory/000/42/outputs/dataset_325c938e-92d4-406d-858b-7919205becbf.dat.files' ] ; then mkdir '/tmp/tmps8cm08gj/job_working_directory/000/42/outputs/dataset_325c938e-92d4-406d-858b-7919205becbf_files' && mv '/tmp/tmps8cm08gj/job_working_directory/000/42/outputs/dataset_325c938e-92d4-406d-858b-7919205becbf.dat.files' '/tmp/tmps8cm08gj/job_working_directory/000/42/outputs/dataset_325c938e-92d4-406d-858b-7919205becbf_files' ; fi

Exit Code:

```
0
```

Standard Output:

Writing /tmp/tmps8cm08gj/job_working_directory/000/42/outputs/dataset_325c938e-92d4-406d-858b-7919205becbf.dat...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 31, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_unite_from_2023-09-26'/*.fasta db.fasta && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_unite_from_2023-09-26'/*.txt taxonomy.txt && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_unite_from_2023-09-26'/*.mscluster db.fasta.mscluster && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_unite_from_2023-09-26'/*.otu db.otu &&    mapseq -nthreads ${GALAXY_SLOTS:-8} -tophits '80' -topotus '40' -minscore '30' -minid1 '1' -minid2 '1' -otulim '50' -outfmt 'simple' '/tmp/tmps8cm08gj/files/1/5/7/dataset_1576ad91-714e-4785-a274-6cff4525c63e.dat' db.fasta taxonomy.txt > '/tmp/tmps8cm08gj/job_working_directory/000/46/outputs/dataset_1978fdc2-267c-4dad-b3db-cf76891f9643.dat'  && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl' --otuTable db.otu --query '/tmp/tmps8cm08gj/job_working_directory/000/46/outputs/dataset_1978fdc2-267c-4dad-b3db-cf76891f9643.dat' --outfile '/tmp/tmps8cm08gj/job_working_directory/000/46/outputs/dataset_8a0089a8-5ae3-41ff-b528-6f2d3dfa3b9d.dat' --taxid --notaxidfile '/tmp/tmps8cm08gj/job_working_directory/000/46/outputs/dataset_75910236-1a24-4a8d-8364-ba83a3d67b37.dat' --krona '/tmp/tmps8cm08gj/job_working_directory/000/46/outputs/dataset_f9bbe80f-24f1-450d-ad0d-ef756b86c671.dat'

Exit Code:

```
0
```

Standard Error:

# loaded 1204050 sequences
# loading taxonomy file: taxonomy.txt
# taxonomies: 1
# tax levels: 8
# tax: 0 level: 0 (1)
# tax: 0 level: 1 (24)
# tax: 0 level: 2 (101)
# tax: 0 level: 3 (268)
# tax: 0 level: 4 (920)
# tax: 0 level: 5 (3268)
# tax: 0 level: 6 (21374)
# tax: 0 level: 7 (124322)
# fcount: 4 otukmercount: 262134
# processing input... 
# processing input... 25
# done processing 25 seqs (0.16284s)
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
minid1	`"1"`
minid2	`"1"`
minscore	`"30"`
otulim	`"50"`
outfmt	`"simple"`
ref_db	`{"__current_case__": 0, "db_cached": "mgnify_its_unite_from_2023-09-26", "db_source": "cached", "mapseq2biom": {"__current_case__": 0, "krona_input": true, "mapseq2biom": "yes"}}`
tophits	`"80"`
topotus	`"40"`

Job 2:

Job state is ok

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_unite_from_2023-09-26'/*.fasta db.fasta && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_unite_from_2023-09-26'/*.txt taxonomy.txt && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_unite_from_2023-09-26'/*.mscluster db.fasta.mscluster && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_unite_from_2023-09-26'/*.otu db.otu &&    mapseq -nthreads ${GALAXY_SLOTS:-8} -tophits '80' -topotus '40' -minscore '30' -minid1 '1' -minid2 '1' -otulim '50' -outfmt 'simple' '/tmp/tmps8cm08gj/files/a/f/0/dataset_af0f2608-e90a-421a-8212-77ec2ad2f432.dat' db.fasta taxonomy.txt > '/tmp/tmps8cm08gj/job_working_directory/000/47/outputs/dataset_93ffb5f9-5f83-4d5d-9ab5-d2b51a6e5bb4.dat'  && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl' --otuTable db.otu --query '/tmp/tmps8cm08gj/job_working_directory/000/47/outputs/dataset_93ffb5f9-5f83-4d5d-9ab5-d2b51a6e5bb4.dat' --outfile '/tmp/tmps8cm08gj/job_working_directory/000/47/outputs/dataset_7dce3aa3-98b7-4a3e-a571-18dfcd1a3294.dat' --taxid --notaxidfile '/tmp/tmps8cm08gj/job_working_directory/000/47/outputs/dataset_1ca601d3-d43d-4b80-a8f0-f13ad31e5a63.dat' --krona '/tmp/tmps8cm08gj/job_working_directory/000/47/outputs/dataset_8e482123-a6cf-4133-8c78-a3bd6a12c3a4.dat'

Exit Code:

```
0
```

Standard Error:

# loaded 1204050 sequences
# loading taxonomy file: taxonomy.txt
# taxonomies: 1
# tax levels: 8
# tax: 0 level: 0 (1)
# tax: 0 level: 1 (24)
# tax: 0 level: 2 (101)
# tax: 0 level: 3 (268)
# tax: 0 level: 4 (920)
# tax: 0 level: 5 (3268)
# tax: 0 level: 6 (21374)
# tax: 0 level: 7 (124322)
# fcount: 4 otukmercount: 262134
# processing input... 
# processing input... 2208
# done processing 2208 seqs (10.247s)
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.
Use of uninitialized value in concatenation (.) or string at /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl line 139.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
minid1	`"1"`
minid2	`"1"`
minscore	`"30"`
otulim	`"50"`
outfmt	`"simple"`
ref_db	`{"__current_case__": 0, "db_cached": "mgnify_its_unite_from_2023-09-26", "db_source": "cached", "mapseq2biom": {"__current_case__": 0, "krona_input": true, "mapseq2biom": "yes"}}`
tophits	`"80"`
topotus	`"40"`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_itsonedb_from_2023-09-26'/*.fasta db.fasta && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_itsonedb_from_2023-09-26'/*.txt taxonomy.txt && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_itsonedb_from_2023-09-26'/*.mscluster db.fasta.mscluster && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_itsonedb_from_2023-09-26'/*.otu db.otu &&    mapseq -nthreads ${GALAXY_SLOTS:-8} -tophits '80' -topotus '40' -minscore '30' -minid1 '1' -minid2 '1' -otulim '50' -outfmt 'simple' '/tmp/tmps8cm08gj/files/1/5/7/dataset_1576ad91-714e-4785-a274-6cff4525c63e.dat' db.fasta taxonomy.txt > '/tmp/tmps8cm08gj/job_working_directory/000/48/outputs/dataset_65957033-e86d-4492-bb93-f6c0101492fb.dat'  && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl' --otuTable db.otu --query '/tmp/tmps8cm08gj/job_working_directory/000/48/outputs/dataset_65957033-e86d-4492-bb93-f6c0101492fb.dat' --outfile '/tmp/tmps8cm08gj/job_working_directory/000/48/outputs/dataset_5a6869be-3759-4847-99ac-aed7c6b536b0.dat' --taxid --notaxidfile '/tmp/tmps8cm08gj/job_working_directory/000/48/outputs/dataset_3aec813f-d780-4083-831d-ac349db8537b.dat' --krona '/tmp/tmps8cm08gj/job_working_directory/000/48/outputs/dataset_169f5310-1f47-4866-b3ac-8e33ed62b25f.dat'

Exit Code:

```
0
```

Standard Error:

# loaded 884783 sequences
# loading taxonomy file: taxonomy.txt
�[1;33m!! Wed Mar 20 11:43:29 2024 [] mapseq.cpp:3614 void load_taxa(const estr&, eseqdb&): loading taxonomy, 1 sequences not found in sequence database�[0m
# taxonomies: 1
# tax levels: 8
# tax: 0 level: 0 (1)
# tax: 0 level: 1 (4)
# tax: 0 level: 2 (44)
# tax: 0 level: 3 (191)
# tax: 0 level: 4 (763)
# tax: 0 level: 5 (2590)
# tax: 0 level: 6 (17578)
# tax: 0 level: 7 (154892)
# fcount: 17 otukmercount: 258848
# processing input... 
# processing input... 25
# done processing 25 seqs (0.108155s)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
minid1	`"1"`
minid2	`"1"`
minscore	`"30"`
otulim	`"50"`
outfmt	`"simple"`
ref_db	`{"__current_case__": 0, "db_cached": "mgnify_its_itsonedb_from_2023-09-26", "db_source": "cached", "mapseq2biom": {"__current_case__": 0, "krona_input": true, "mapseq2biom": "yes"}}`
tophits	`"80"`
topotus	`"40"`

Job 2:

Job state is ok

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_itsonedb_from_2023-09-26'/*.fasta db.fasta && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_itsonedb_from_2023-09-26'/*.txt taxonomy.txt && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_itsonedb_from_2023-09-26'/*.mscluster db.fasta.mscluster && ln -s '/cvmfs/data.galaxyproject.org/byhand/mapseq/mgnify_its_itsonedb_from_2023-09-26'/*.otu db.otu &&    mapseq -nthreads ${GALAXY_SLOTS:-8} -tophits '80' -topotus '40' -minscore '30' -minid1 '1' -minid2 '1' -otulim '50' -outfmt 'simple' '/tmp/tmps8cm08gj/files/a/f/0/dataset_af0f2608-e90a-421a-8212-77ec2ad2f432.dat' db.fasta taxonomy.txt > '/tmp/tmps8cm08gj/job_working_directory/000/49/outputs/dataset_11282a52-41ce-463c-a6db-d1ef337c4034.dat'  && perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/mapseq/f1d1dafc836d/mapseq/mapseq2biom.pl' --otuTable db.otu --query '/tmp/tmps8cm08gj/job_working_directory/000/49/outputs/dataset_11282a52-41ce-463c-a6db-d1ef337c4034.dat' --outfile '/tmp/tmps8cm08gj/job_working_directory/000/49/outputs/dataset_dd4ac833-6491-4280-94aa-edb2f8420009.dat' --taxid --notaxidfile '/tmp/tmps8cm08gj/job_working_directory/000/49/outputs/dataset_7f84b376-5308-448c-81c7-4c6548bd81fe.dat' --krona '/tmp/tmps8cm08gj/job_working_directory/000/49/outputs/dataset_593e131e-a03f-406e-a608-af95833c0f04.dat'

Exit Code:

```
0
```

Standard Error:

# loaded 884783 sequences
# loading taxonomy file: taxonomy.txt
�[1;33m!! Wed Mar 20 11:43:29 2024 [] mapseq.cpp:3614 void load_taxa(const estr&, eseqdb&): loading taxonomy, 1 sequences not found in sequence database�[0m
# taxonomies: 1
# tax levels: 8
# tax: 0 level: 0 (1)
# tax: 0 level: 1 (4)
# tax: 0 level: 2 (44)
# tax: 0 level: 3 (191)
# tax: 0 level: 4 (763)
# tax: 0 level: 5 (2590)
# tax: 0 level: 6 (17578)
# tax: 0 level: 7 (154892)
# fcount: 17 otukmercount: 258848
# processing input... 
# processing input... 2208
# done processing 2208 seqs (7.71038s)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
minid1	`"1"`
minid2	`"1"`
minscore	`"30"`
otulim	`"50"`
outfmt	`"simple"`
ref_db	`{"__current_case__": 0, "db_cached": "mgnify_its_itsonedb_from_2023-09-26", "db_source": "cached", "mapseq2biom": {"__current_case__": 0, "krona_input": true, "mapseq2biom": "yes"}}`
tophits	`"80"`
topotus	`"40"`

Step 36: HDF5 ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/7/5/9/dataset_75910236-1a24-4a8d-8364-ba83a3d67b37.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/50/outputs/dataset_35e5458f-96c3-44df-97ba-1d06171fa761.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-hdf5

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 59, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 1, "collapsed_observations": false, "collapsed_samples": false, "selector": "hdf5"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Job 2:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/1/c/a/dataset_1ca601d3-d43d-4b80-a8f0-f13ad31e5a63.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/51/outputs/dataset_4ceed2da-755c-490c-a532-6dc8ca94049c.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-hdf5

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 60, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 1, "collapsed_observations": false, "collapsed_samples": false, "selector": "hdf5"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Step 37: JSON ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/7/5/9/dataset_75910236-1a24-4a8d-8364-ba83a3d67b37.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/52/outputs/dataset_99ef8dff-038c-44ae-b674-1dc929284146.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-json

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 59, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 0, "selector": "json"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Job 2:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/1/c/a/dataset_1ca601d3-d43d-4b80-a8f0-f13ad31e5a63.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/53/outputs/dataset_0e715499-cdc4-4064-9a45-610f16a5c7d7.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-json

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 60, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 0, "selector": "json"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Step 38: Krona ITSonedb:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ktImportText  -n 'Root' -o '/tmp/tmps8cm08gj/job_working_directory/000/54/outputs/dataset_550b4fd2-2d2a-446b-ad8b-09d332ec44aa.dat'  '/tmp/tmps8cm08gj/files/f/9/b/dataset_f9bbe80f-24f1-450d-ad0d-ef756b86c671.dat,DRR010481_FASTQ_fasta' '/tmp/tmps8cm08gj/files/8/e/4/dataset_8e482123-a6cf-4133-8c78-a3bd6a12c3a4.dat,ERR2715528_MERGED_FASTQ_fasta' && if [ -d '/tmp/tmps8cm08gj/job_working_directory/000/54/outputs/dataset_550b4fd2-2d2a-446b-ad8b-09d332ec44aa.dat.files' ] ; then mkdir '/tmp/tmps8cm08gj/job_working_directory/000/54/outputs/dataset_550b4fd2-2d2a-446b-ad8b-09d332ec44aa_files' && mv '/tmp/tmps8cm08gj/job_working_directory/000/54/outputs/dataset_550b4fd2-2d2a-446b-ad8b-09d332ec44aa.dat.files' '/tmp/tmps8cm08gj/job_working_directory/000/54/outputs/dataset_550b4fd2-2d2a-446b-ad8b-09d332ec44aa_files' ; fi

Exit Code:

```
0
```

Standard Output:

Writing /tmp/tmps8cm08gj/job_working_directory/000/54/outputs/dataset_550b4fd2-2d2a-446b-ad8b-09d332ec44aa.dat...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 39: HDF5 ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/3/a/e/dataset_3aec813f-d780-4083-831d-ac349db8537b.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/55/outputs/dataset_14aba8c6-09c9-409a-b99c-41c87bb22be6.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-hdf5

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 67, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 1, "collapsed_observations": false, "collapsed_samples": false, "selector": "hdf5"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Job 2:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/7/f/8/dataset_7f84b376-5308-448c-81c7-4c6548bd81fe.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/56/outputs/dataset_beda5164-58e5-4386-96fd-666ab5403f6d.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-hdf5

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 68, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 1, "collapsed_observations": false, "collapsed_samples": false, "selector": "hdf5"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Step 40: JSON ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/3/a/e/dataset_3aec813f-d780-4083-831d-ac349db8537b.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/57/outputs/dataset_f5f797a7-2a24-4c13-bcb4-c3cc90bf288c.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-json

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 67, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 0, "selector": "json"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Job 2:

Job state is ok

Command Line:

sed '1s/^\([^#].*\)/#\1/' '/tmp/tmps8cm08gj/files/7/f/8/dataset_7f84b376-5308-448c-81c7-4c6548bd81fe.dat' > input && biom convert --input-fp input --output-fp '/tmp/tmps8cm08gj/job_working_directory/000/58/outputs/dataset_a5a49d8c-ee47-460f-a6b4-5eb6c376f51e.dat' --process-obs-metadata 'taxonomy' --table-type 'OTU table' --to-json

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "input_fp": {"values": [{"id": 68, "src": "dce"}]}, "process_obs_metadata": "taxonomy", "type_selector": "tsv"}`
output	`{"__current_case__": 1, "biom_type": {"__current_case__": 0, "selector": "json"}, "observation_metadata_fp": null, "sample_metadata_fp": null, "table_type": "OTU table", "type_selector": "biom"}`

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmps8cm08gj/files/d/b/3/dataset_db3b01b3-bd6d-4b06-b4c1-8a074a8d63eb.dat' clan_info && ln -s '/tmp/tmps8cm08gj/files/4/c/0/dataset_4c015fb4-bf94-435d-b20e-9cbc636fe271.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/874ad23526a0/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && sed "s/[[:blank:]]\+/\t/g" cmsearch_matches.deoverlapped > cmsearch_matches.deoverlapped.tabular && mv cmsearch_matches.deoverlapped.tabular '/tmp/tmps8cm08gj/job_working_directory/000/7/outputs/dataset_d7b64429-0181-4880-93cd-05c532541ed0.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmps8cm08gj/files/d/b/3/dataset_db3b01b3-bd6d-4b06-b4c1-8a074a8d63eb.dat' clan_info && ln -s '/tmp/tmps8cm08gj/files/f/b/a/dataset_fba04728-a570-4c03-808a-55ff9b0094be.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/874ad23526a0/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && sed "s/[[:blank:]]\+/\t/g" cmsearch_matches.deoverlapped > cmsearch_matches.deoverlapped.tabular && mv cmsearch_matches.deoverlapped.tabular '/tmp/tmps8cm08gj/job_working_directory/000/8/outputs/dataset_573e6126-0b67-4449-a695-fa9ae9a166c5.dat'

Exit Code:

```
0
```

Standard Output:

Saved  4406 hits ( 6623 removed) to cmsearch_matches.deoverlapped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Step 41: Krona ITS UNITE:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ktImportText  -n 'Root' -o '/tmp/tmps8cm08gj/job_working_directory/000/59/outputs/dataset_83a95cd1-7333-465e-9544-548398a21bb0.dat'  '/tmp/tmps8cm08gj/files/1/6/9/dataset_169f5310-1f47-4866-b3ac-8e33ed62b25f.dat,DRR010481_FASTQ_fasta' '/tmp/tmps8cm08gj/files/5/9/3/dataset_593e131e-a03f-406e-a608-af95833c0f04.dat,ERR2715528_MERGED_FASTQ_fasta' && if [ -d '/tmp/tmps8cm08gj/job_working_directory/000/59/outputs/dataset_83a95cd1-7333-465e-9544-548398a21bb0.dat.files' ] ; then mkdir '/tmp/tmps8cm08gj/job_working_directory/000/59/outputs/dataset_83a95cd1-7333-465e-9544-548398a21bb0_files' && mv '/tmp/tmps8cm08gj/job_working_directory/000/59/outputs/dataset_83a95cd1-7333-465e-9544-548398a21bb0.dat.files' '/tmp/tmps8cm08gj/job_working_directory/000/59/outputs/dataset_83a95cd1-7333-465e-9544-548398a21bb0_files' ; fi

Exit Code:

```
0
```

Standard Output:

Writing /tmp/tmps8cm08gj/job_working_directory/000/59/outputs/dataset_83a95cd1-7333-465e-9544-548398a21bb0.dat...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 46, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmps8cm08gj/job_working_directory/000/9/configs/tmpdk9w0v17' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmps8cm08gj/job_working_directory/000/9/configs/tmp2a88xy1w' -Q '/tmp/tmps8cm08gj/job_working_directory/000/9/configs/tmpdk9w0v17'   --no_header   -o '/tmp/tmps8cm08gj/job_working_directory/000/9/outputs/dataset_e23a88f1-ffa4-4c3e-b41b-833cc93b59c5.dat'

Exit Code:

```
0
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmps8cm08gj/files/d/7/b/dataset_d7b64429-0181-4880-93cd-05c532541ed0.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}

SQL: select c1, c9, c8
from t1
where c3 like 'SSU%' and c8 > c9;  
rowcount: None

SQL: select c1, c8, c9
from t1
where c3 like 'LSU%' and c8 <= c9;  
rowcount: None

SQL: select c1, c9, c8
from t1
where c3 like 'LSU%' and c8 > c9;  
rowcount: None

SQL: 
select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;
          
rowcount: None

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 5, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Job 2:

Job state is ok

Command Line:

cat '/tmp/tmps8cm08gj/job_working_directory/000/10/configs/tmpma1z_vv5' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/3a6b78c39dca/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/tmp/tmps8cm08gj/job_working_directory/000/10/configs/tmp7naljeax' -Q '/tmp/tmps8cm08gj/job_working_directory/000/10/configs/tmpma1z_vv5'   --no_header   -o '/tmp/tmps8cm08gj/job_working_directory/000/10/outputs/dataset_9322da78-a69b-4999-b710-91d90458bc11.dat'

Exit Code:

```
0
```

Standard Error:

JSON: {'tables': [{'file_path': '/tmp/tmps8cm08gj/files/5/7/3/dataset_573e6126-0b67-4449-a695-fa9ae9a166c5.dat', 'table_name': 't1', 'column_names': ''}], 'queries': [{'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;", 'result_file': 'results0.tsv'}, {'query': "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;", 'result_file': 'results1.tsv'}, {'query': "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;", 'result_file': 'results2.tsv'}]}

SQL: select c1, c9, c8
from t1
where c3 like 'SSU%' and c8 > c9;  
rowcount: None

SQL: select c1, c8, c9
from t1
where c3 like 'LSU%' and c8 <= c9;  
rowcount: None

SQL: select c1, c9, c8
from t1
where c3 like 'LSU%' and c8 > c9;  
rowcount: None

SQL: 
select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;
          
rowcount: None

Standard Output:

select c1, c8, c9
from t1
where c3 like 'SSU%' and c8 <= c9;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": [{"__index__": 0, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'SSU%' and c8 > c9;"}, {"__index__": 1, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c8, c9\nfrom t1\nwhere c3 like 'LSU%' and c8 <= c9;"}, {"__index__": 2, "query_result": {"__current_case__": 1, "header": "no"}, "sqlquery": "select c1, c9, c8\nfrom t1\nwhere c3 like 'LSU%' and c8 > c9;"}]}`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"select c1, c8, c9\nfrom t1\nwhere c3 like 'SSU%' and c8 <= c9;"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": []}, "table": {"values": [{"id": 6, "src": "dce"}]}, "tbl_opts": {"col_names": "", "column_names_from_first_line": false, "indexes": [], "load_named_columns": false, "pkey_autoincr": "", "table_name": ""}}]`
workdb	`"workdb.sqlite"`

Step 7: SSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmps8cm08gj/job_working_directory/000/11/configs/tmp7ny1jzvj' '/tmp/tmps8cm08gj/files/e/2/3/dataset_e23a88f1-ffa4-4c3e-b41b-833cc93b59c5.dat' > '/tmp/tmps8cm08gj/job_working_directory/000/11/outputs/dataset_d71e8fa1-70bb-4fd4-9f1a-54574a6b4b2d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmps8cm08gj/job_working_directory/000/12/configs/tmpxp74woxt' '/tmp/tmps8cm08gj/files/9/3/2/dataset_9322da78-a69b-4999-b710-91d90458bc11.dat' > '/tmp/tmps8cm08gj/job_working_directory/000/12/outputs/dataset_c392be44-018f-4f30-bbb1-b0216d6cf5bc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 8: SSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmps8cm08gj/job_working_directory/000/13/configs/tmpsp12b80o' '/tmp/tmps8cm08gj/files/e/1/5/dataset_e1509e95-f682-4277-9e39-654f2b7548ea.dat' > '/tmp/tmps8cm08gj/job_working_directory/000/13/outputs/dataset_1cf58a2a-6155-421b-8b5e-1bd831084857.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmps8cm08gj/job_working_directory/000/14/configs/tmp9og44dh5' '/tmp/tmps8cm08gj/files/7/a/e/dataset_7ae21428-1106-4cd9-ac48-58937b1f9b63.dat' > '/tmp/tmps8cm08gj/job_working_directory/000/14/outputs/dataset_2af4c4c9-3f02-4677-8629-6ff870dcb178.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Step 9: LSU BED forward:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmps8cm08gj/job_working_directory/000/15/configs/tmp553z31ia' '/tmp/tmps8cm08gj/files/a/a/4/dataset_aa488fc0-177a-418c-9d6e-d367dc77f867.dat' > '/tmp/tmps8cm08gj/job_working_directory/000/15/outputs/dataset_6e34ae9a-8da1-411b-a67f-257935fce82f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmps8cm08gj/job_working_directory/000/16/configs/tmpt64nf4x_' '/tmp/tmps8cm08gj/files/0/3/3/dataset_0337d924-1c89-4a60-ba01-2cee116a4ff1.dat' > '/tmp/tmps8cm08gj/job_working_directory/000/16/outputs/dataset_3f97edf7-2298-4b48-a07e-e617895b9d77.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"forward\", \"1\", \"+\"}'"`
dbkey	`"?"`

Step 10: LSU BED reverse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmps8cm08gj/job_working_directory/000/17/configs/tmphhfbonxl' '/tmp/tmps8cm08gj/files/6/a/b/dataset_6abff450-75d2-4c33-a3d8-80223e9411c1.dat' > '/tmp/tmps8cm08gj/job_working_directory/000/17/outputs/dataset_4f553136-5bb1-4e1f-8252-9c1613018237.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmps8cm08gj/job_working_directory/000/18/configs/tmpkgicbjng' '/tmp/tmps8cm08gj/files/e/9/c/dataset_e9c4dbad-1520-4fb6-95b8-5df33c93f377.dat' > '/tmp/tmps8cm08gj/job_working_directory/000/18/outputs/dataset_051b2f73-d3b8-4f84-83b0-3c93ff0ba3f6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f5aba53ae6ac11ee8bf6f341fccaebc9"`
chromInfo	`"/tmp/tmps8cm08gj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"'BEGIN {OFS=\"\\t\"} {print $1, $2 - 1, $3, \"reverse\", \"1\", \"-\"}'"`
dbkey	`"?"`

Other invocation details
- history_id
  - 9c0429eb8fdffe01
- history_state
  - ok
- invocation_id
  - 9c0429eb8fdffe01
- invocation_state
  - scheduled
- workflow_id
  - 9c0429eb8fdffe01

❌ testing_query_tabular.ga_0

Problems:

Output with path /tmp/tmpdmq2rhoh/deoverlapped_matches__a51ec103-4839-44c6-861e-ff7330cdbd3b different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/microbiome/testing-query-tabular/test-data/deoverlapped_matches.tabular v. /tmp/tmpohhmjtosdeoverlapped_matches.tabular )
--- local_file
+++ history_data
@@ -1,30 +1,30 @@
-DRR010481.1-HUMWT9A01C6SDL-4	-	LSU_rRNA_eukarya	RF02543	cm	1	180	236	414	+	3'	3	0.49	0.0	123.4	2e-31	!	-
-DRR010481.1-HUMWT9A01C6SDL-4	-	5_8S_rRNA	RF00002	cm	54	154	1	99	+	5'	2	0.51	0.0	76.5	1.2e-21	!	-
-DRR010481.10-HUMWT9A01CLKTT-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.11-HUMWT9A01A55N6-4	-	5_8S_rRNA	RF00002	cm	54	154	1	101	+	5'	2	0.46	0.0	86.6	1.5e-24	!	-
-DRR010481.12-HUMWT9A01DQZ35-4	-	5_8S_rRNA	RF00002	cm	53	154	1	100	+	5'	2	0.51	0.0	76.0	1.6e-21	!	-
-DRR010481.13-HUMWT9A01CWWE7-4	-	LSU_rRNA_eukarya	RF02543	cm	1	173	237	408	+	3'	3	0.48	0.0	122.4	3.6e-31	!	-
-DRR010481.13-HUMWT9A01CWWE7-4	-	5_8S_rRNA	RF00002	cm	53	154	1	100	+	5'	2	0.51	0.0	76.0	1.6e-21	!	-
-DRR010481.14-HUMWT9A01CWM7O-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.15-HUMWT9A01C6KQE-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.15-HUMWT9A01C6KQE-4	-	LSU_rRNA_eukarya	RF02543	cm	1	53	313	365	+	3'	3	0.45	0.0	49.2	2.8e-12	!	-
-DRR010481.16-HUMWT9A01BP5YQ-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.16-HUMWT9A01BP5YQ-4	-	LSU_rRNA_eukarya	RF02543	cm	1	54	313	366	+	3'	3	0.44	0.0	50.9	1e-12	!	-
-DRR010481.17-HUMWT9A01CLKK7-4	-	5_8S_rRNA	RF00002	cm	54	154	1	99	+	5'	2	0.51	0.0	76.5	1.2e-21	!	-
-DRR010481.17-HUMWT9A01CLKK7-4	-	LSU_rRNA_eukarya	RF02543	cm	1	56	236	291	+	3'	3	0.50	0.0	47.1	9.8e-12	!	-
-DRR010481.18-HUMWT9A01ATALC-4	-	5_8S_rRNA	RF00002	cm	54	154	1	101	+	5'	2	0.47	0.0	91.4	6.5e-26	!	-
-DRR010481.2-HUMWT9A01A6FHU-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.47	0.0	91.8	5.1e-26	!	-
-DRR010481.20-HUMWT9A01C8FXI-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.42	0.0	97.8	9.8e-28	!	-
-DRR010481.21-HUMWT9A01A9JR7-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.23-HUMWT9A01AM5Q3-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.24-HUMWT9A01CYLUO-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.25-HUMWT9A01A3MBZ-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
-DRR010481.3-HUMWT9A01CEMJS-4	-	5_8S_rRNA	RF00002	cm	53	154	1	102	+	5'	2	0.46	0.0	92.0	4.5e-26	!	-
********
*SNIP *
********
+DRR010481.13-HUMWT9A01CWWE7-4 - LSU_rRNA_eukarya RF02543 cm 1 173 237 408 + 3' 3 0.48 0.0 122.4 3.6e-31 ! -
+DRR010481.13-HUMWT9A01CWWE7-4 - 5_8S_rRNA RF00002 cm 53 154 1 100 + 5' 2 0.51 0.0 76.0 1.6e-21 ! -
+DRR010481.14-HUMWT9A01CWM7O-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.15-HUMWT9A01C6KQE-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.15-HUMWT9A01C6KQE-4 - LSU_rRNA_eukarya RF02543 cm 1 53 313 365 + 3' 3 0.45 0.0 49.2 2.8e-12 ! -
+DRR010481.16-HUMWT9A01BP5YQ-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.16-HUMWT9A01BP5YQ-4 - LSU_rRNA_eukarya RF02543 cm 1 54 313 366 + 3' 3 0.44 0.0 50.9 1e-12 ! -
+DRR010481.17-HUMWT9A01CLKK7-4 - 5_8S_rRNA RF00002 cm 54 154 1 99 + 5' 2 0.51 0.0 76.5 1.2e-21 ! -
+DRR010481.17-HUMWT9A01CLKK7-4 - LSU_rRNA_eukarya RF02543 cm 1 56 236 291 + 3' 3 0.50 0.0 47.1 9.8e-12 ! -
+DRR010481.18-HUMWT9A01ATALC-4 - 5_8S_rRNA RF00002 cm 54 154 1 101 + 5' 2 0.47 0.0 91.4 6.5e-26 ! -
+DRR010481.2-HUMWT9A01A6FHU-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.47 0.0 91.8 5.1e-26 ! -
+DRR010481.20-HUMWT9A01C8FXI-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.42 0.0 97.8 9.8e-28 ! -
+DRR010481.21-HUMWT9A01A9JR7-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.23-HUMWT9A01AM5Q3-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.24-HUMWT9A01CYLUO-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.25-HUMWT9A01A3MBZ-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.3-HUMWT9A01CEMJS-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.31-HUMWT9A01CFUVG-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.32-HUMWT9A01BTRXI-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.33-HUMWT9A01BUFRP-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.4-HUMWT9A01BRR8F-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.5-HUMWT9A01A29S1-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.6-HUMWT9A01CMBDY-4 - 5_8S_rRNA RF00002 cm 54 154 1 101 + 5' 2 0.47 0.0 91.4 6.5e-26 ! -
+DRR010481.7-HUMWT9A01DMCR3-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -
+DRR010481.8-HUMWT9A01A36AF-4 - 5_8S_rRNA RF00002 cm 53 154 1 102 + 5' 2 0.46 0.0 92.0 4.5e-26 ! -

Workflow invocation details

Invocation Messages

Steps

Step 1: processed seqs:
- step_state: scheduled
Step 2: covariance models:
- step_state: scheduled
Step 3: clan info file:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

temp_tabular_output=$(mktemp) &&  cmsearch --cpu "${GALAXY_SLOTS:-2}" -o /dev/null --tformat fasta        --tblout $temp_tabular_output     --default /tmp/tmpmuexrjyz/files/8/7/1/dataset_8718c233-4847-43a1-a8bd-1ffcfd2bcd86.dat '/tmp/tmpmuexrjyz/files/c/1/7/dataset_c17bfc06-a10f-4afd-bb89-3b7b56ae6e23.dat' 2>&1 && sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' $temp_tabular_output > '/tmp/tmpmuexrjyz/job_working_directory/000/4/outputs/dataset_3431823b-7d50-48a4-a3a5-db33e1d5e3a7.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
A	`false`
Z	`None`
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"cfce552ee6ac11ee808e11946a7ce5fa"`
acceleration_huristics	`{"__current_case__": 3, "acceleration_huristics_selector": "--default"}`
acyk	`false`
anytrunc	`false`
bottomonly	`false`
chromInfo	`"/tmp/tmpmuexrjyz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cm_opts	`{"__current_case__": 1, "cm_opts_selector": "histdb", "cmfile": {"values": [{"id": 3, "src": "hda"}]}}`
cyk	`false`
dbkey	`"?"`
g	`false`
inclusion_thresholds_opts	`{"__current_case__": 0, "inclusion_thresholds_selector": ""}`
model_thresholds	`{"cut_ga": false, "cut_nc": false, "cut_tc": false}`
mxsize	`"128.0"`
noali	`false`
nonull3	`false`
notrunc	`false`
reporting_thresholds_opts	`{"__current_case__": 0, "reporting_thresholds_selector": ""}`
smxsize	`"128.0"`
toponly	`false`
verbose	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpmuexrjyz/files/5/7/4/dataset_574059ad-e306-4766-a677-ae57a23ab7aa.dat' clan_info && ln -s '/tmp/tmpmuexrjyz/files/3/4/3/dataset_3431823b-7d50-48a4-a3a5-db33e1d5e3a7.dat' cmsearch_matches && LC_ALL=C perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/54b16c794341/cmsearch_deoverlap/cmsearch-deoverlap.pl' --clanin clan_info cmsearch_matches && mv *.deoverlapped '/tmp/tmpmuexrjyz/job_working_directory/000/5/outputs/dataset_a51ec103-4839-44c6-861e-ff7330cdbd3b.dat'

Exit Code:

```
0
```

Standard Output:

Saved    30 hits (    5 removed) to cmsearch_matches.deoverlapped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cfce552ee6ac11ee808e11946a7ce5fa"`
chromInfo	`"/tmp/tmpmuexrjyz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
dirty	`false`
maxkeep	`false`

Other invocation details
- history_id
  - eb488226c633e931
- history_state
  - ok
- invocation_id
  - eb488226c633e931
- invocation_state
  - scheduled
- workflow_id
  - eb488226c633e931

Passed Tests

✅ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpce9zas25/job_working_directory/000/1/configs/tmpgzzs3t81' ~/.ncbi/user-settings.mkfg &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-20T11:27:57 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-20T11:27:57 prefetch.3.0.8: 1) Downloading 'DRR218540'...
2024-03-20T11:27:57 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-20T11:27:57 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-20T11:27:58 prefetch.3.0.8:  HTTPS download succeed
2024-03-20T11:27:58 prefetch.3.0.8:  'DRR218540' is valid
2024-03-20T11:27:58 prefetch.3.0.8: 1) 'DRR218540' was downloaded successfully
2024-03-20T11:27:58 prefetch.3.0.8: 'DRR218540' has 0 unresolved dependencies

Standard Output:

Downloading accession: DRR218540...

Read 67485 spots for DRR218540
Written 67485 spots for DRR218540
Done with all accessions.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "d240c094e6ac11eeaf081d204669ce85"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpce9zas25/files/1/5/9/dataset_159f5b7f-3273-4c8a-9559-40ecb0f15466.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmpce9zas25/files/5/d/7/dataset_5d7eb407-30cf-4e8b-88e7-318495bd0392.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmpce9zas25/job_working_directory/000/3/outputs/dataset_1af64920-7b8c-4992-be1b-c70f2cc4cd05.dat' && mv second.fastq.gz '/tmp/tmpce9zas25/job_working_directory/000/3/outputs/dataset_3990e582-4d43-4c71-9fc8-803381c8d435.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 25 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmpce9zas25/files/1/a/f/dataset_1af64920-7b8c-4992-be1b-c70f2cc4cd05.dat' -r '/tmp/tmpce9zas25/files/3/9/9/dataset_3990e582-4d43-4c71-9fc8-803381c8d435.dat' -1 '/tmp/tmpce9zas25/job_working_directory/000/6/outputs/dataset_2d7075ff-9e78-41f8-9e4d-22526130fb92.dat' -2 '/tmp/tmpce9zas25/job_working_directory/000/6/outputs/dataset_1b5d364a-5ccd-4615-bff5-4ce813cd22b4.dat'  -s '/tmp/tmpce9zas25/job_working_directory/000/6/outputs/dataset_d41cebe8-3069-4a64-a488-938035a51f21.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020689

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpce9zas25/files/d/4/1/dataset_d41cebe8-3069-4a64-a488-938035a51f21.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpce9zas25/job_working_directory/000/7/outputs/dataset_8b2a96a0-e7d6-4e87-bad7-3e5219ccd6a8.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 6434 Surviving: 6432 (99.97%) Dropped: 2 (0.03%)
TrimmomaticSE: Completed successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpce9zas25/files/d/4/1/dataset_d41cebe8-3069-4a64-a488-938035a51f21.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpce9zas25/job_working_directory/000/8/outputs/dataset_2f880a63-27b7-4e02-b35d-7d7ddeff631a_files' && fastqc --outdir '/tmp/tmpce9zas25/job_working_directory/000/8/outputs/dataset_2f880a63-27b7-4e02-b35d-7d7ddeff631a_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpce9zas25/job_working_directory/000/8/outputs/dataset_2f880a63-27b7-4e02-b35d-7d7ddeff631a_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpce9zas25/job_working_directory/000/8/outputs/dataset_2f880a63-27b7-4e02-b35d-7d7ddeff631a_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
adapters	`None`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpce9zas25/files/8/b/2/dataset_8b2a96a0-e7d6-4e87-bad7-3e5219ccd6a8.dat' '/tmp/tmpce9zas25/job_working_directory/000/9/configs/tmp8d0w7x1b' '/tmp/tmpce9zas25/job_working_directory/000/9/outputs/dataset_c363ba18-73fc-4bc1-9cb5-5292dbbcc8ab.dat' '/tmp/tmpce9zas25/job_working_directory/000/9/outputs/dataset_c363ba18-73fc-4bc1-9cb5-5292dbbcc8ab_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 6432 of 6432 reads (100.00%).
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpce9zas25/files/8/b/2/dataset_8b2a96a0-e7d6-4e87-bad7-3e5219ccd6a8.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpce9zas25/job_working_directory/000/10/outputs/dataset_7615f70f-f996-46ea-b4be-d303f42c14c3_files' && fastqc --outdir '/tmp/tmpce9zas25/job_working_directory/000/10/outputs/dataset_7615f70f-f996-46ea-b4be-d303f42c14c3_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpce9zas25/job_working_directory/000/10/outputs/dataset_7615f70f-f996-46ea-b4be-d303f42c14c3_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpce9zas25/job_working_directory/000/10/outputs/dataset_7615f70f-f996-46ea-b4be-d303f42c14c3_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
adapters	`None`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpce9zas25/job_working_directory/000/11/outputs/dataset_31bd9dda-81e4-4c17-8570-e29d55e07673.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpce9zas25/files/2/2/e/dataset_22e07ee1-4596-44fd-bda2-17478d57f131.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpce9zas25/files/c/3/6/dataset_c363ba18-73fc-4bc1-9cb5-5292dbbcc8ab.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpce9zas25/job_working_directory/000/12/outputs/dataset_34a4a457-f706-49a8-8170-a1acbc086232_files' && fastqc --outdir '/tmp/tmpce9zas25/job_working_directory/000/12/outputs/dataset_34a4a457-f706-49a8-8170-a1acbc086232_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpce9zas25/job_working_directory/000/12/outputs/dataset_34a4a457-f706-49a8-8170-a1acbc086232_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpce9zas25/job_working_directory/000/12/outputs/dataset_34a4a457-f706-49a8-8170-a1acbc086232_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
adapters	`None`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpce9zas25/files/c/3/6/dataset_c363ba18-73fc-4bc1-9cb5-5292dbbcc8ab.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 6,432
	Input bases: 2,151,394
	Input mean length: 334.48
	Good sequences: 6,432 (100.00%)
	Good bases: 2,151,394
	Good mean length: 334.48
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpce9zas25/job_working_directory/000/14/outputs/dataset_9d52d747-9b05-4879-9515-370a356a5ae5.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpce9zas25/files/4/4/5/dataset_44561b62-1745-4a60-adad-cb3bb427d46f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpce9zas25/job_working_directory/000/15/outputs/dataset_cd22e736-341c-4e48-a15f-7be57c457860.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpce9zas25/files/4/f/3/dataset_4f3b7ba5-6a41-47b6-b2cf-61b0d84070e4.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpce9zas25/files/1/5/5/dataset_155ddea0-7283-43c8-bd31-bedb3b86c6ad.dat' '/tmp/tmpce9zas25/job_working_directory/000/16/outputs/dataset_22a4e905-21c4-4989-acc3-c1795dd07e67.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

6432 FASTQ reads were converted to FASTA.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpce9zas25/files/1/5/5/dataset_155ddea0-7283-43c8-bd31-bedb3b86c6ad.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmpce9zas25/job_working_directory/000/17/outputs/dataset_fe6d1686-9b8d-4321-a167-6153c94cdf4c_files' && fastqc --outdir '/tmp/tmpce9zas25/job_working_directory/000/17/outputs/dataset_fe6d1686-9b8d-4321-a167-6153c94cdf4c_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmpce9zas25/job_working_directory/000/17/outputs/dataset_fe6d1686-9b8d-4321-a167-6153c94cdf4c_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpce9zas25/job_working_directory/000/17/outputs/dataset_fe6d1686-9b8d-4321-a167-6153c94cdf4c_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
adapters	`None`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpce9zas25/files/2/2/a/dataset_22a4e905-21c4-4989-acc3-c1795dd07e67.dat' | fasta_formatter -w 0 -o '/tmp/tmpce9zas25/job_working_directory/000/18/outputs/dataset_9367115e-4ba0-4536-b244-760f56367713.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpce9zas25/job_working_directory/000/19/outputs/dataset_628283dc-eebc-44f3-b21c-842b938b28b2.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpce9zas25/files/2/9/4/dataset_294586a0-157a-469e-881c-ec6b0b6835a0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmpce9zas25/files/3/1/b/dataset_31bd9dda-81e4-4c17-8570-e29d55e07673.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmpce9zas25/files/9/d/5/dataset_9d52d747-9b05-4879-9515-370a356a5ae5.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmpce9zas25/files/c/d/2/dataset_cd22e736-341c-4e48-a15f-7be57c457860.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmpce9zas25/files/6/2/8/dataset_628283dc-eebc-44f3-b21c-842b938b28b2.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpce9zas25/job_working_directory/000/20/working/multiqc_WDir
|            fastqc | Found 4 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d240c094e6ac11eeaf081d204669ce85"`
chromInfo	`"/tmp/tmpce9zas25/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 23, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- history_id
  - 8f3a33490ce83dd5
- history_state
  - ok
- invocation_id
  - 8f3a33490ce83dd5
- invocation_state
  - scheduled
- workflow_id
  - 8f3a33490ce83dd5

github-actions · 2024-03-21T14:39:31Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	3
Passed	2
Error	1
Failure	0
Skipped	0

Errored Tests

❌ mgnify-amplicon-pipeline-after-quality-control.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '40' (Processed sequences) is not optional and no input provided.","err_code":0}

Passed Tests

✅ mgnify-amplicon-pipeline-quality-control-paired-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accession:
- step_state: scheduled
Step 2: fastp - Enable base correction (-c):
- step_state: scheduled
Step 11: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 12: Length filtering - Minimum size:
- step_state: scheduled
Step 13: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmp3g1dmuys/job_working_directory/000/1/configs/tmpwck1v878' ~/.ncbi/user-settings.mkfg &&   echo 'DRR218540' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-21T14:35:55 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-21T14:35:55 prefetch.3.0.8: 1) Downloading 'DRR218540'...
2024-03-21T14:35:55 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-21T14:35:55 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-21T14:35:56 prefetch.3.0.8:  HTTPS download succeed
2024-03-21T14:35:56 prefetch.3.0.8:  'DRR218540' is valid
2024-03-21T14:35:56 prefetch.3.0.8: 1) 'DRR218540' was downloaded successfully
2024-03-21T14:35:56 prefetch.3.0.8: 'DRR218540' has 0 unresolved dependencies

Standard Output:

Downloading accession: DRR218540...

Read 67485 spots for DRR218540
Written 67485 spots for DRR218540
Done with all accessions.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR218540", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "4663ba9ce79011ee9f89037463e90a79"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: fastp filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3g1dmuys/files/f/b/7/dataset_fb77af59-0ffa-467d-a719-a165db4cf9a3.dat' 'DRR218540.fastq.gz' &&  ln -s '/tmp/tmp3g1dmuys/files/d/7/1/dataset_d7104fae-f774-4c03-a2be-de9beba49423.dat' 'DRR218540_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for DRR218540.fastq.gz'   -i 'DRR218540.fastq.gz' -o first.fastq.gz  -I 'DRR218540_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                 -q 20 -u 20      -l 70                     &&  mv first.fastq.gz '/tmp/tmp3g1dmuys/job_working_directory/000/3/outputs/dataset_8c361269-108b-49f8-9fa1-409f61ca267b.dat' && mv second.fastq.gz '/tmp/tmp3g1dmuys/job_working_directory/000/3/outputs/dataset_33cfb898-7496-418f-b822-e7cd9f4251de.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 67485
total bases: 19944885
Q20 bases: 15357309(76.9987%)
Q30 bases: 12717774(63.7646%)

Read2 before filtering:
total reads: 67485
total bases: 20093780
Q20 bases: 13227835(65.8305%)
Q30 bases: 10320534(51.3618%)

Read1 after filtering:
total reads: 6493
total bases: 1924386
Q20 bases: 1750333(90.9554%)
Q30 bases: 1571775(81.6767%)

Read2 after filtering:
total reads: 6493
total bases: 1929099
Q20 bases: 1604538(83.1755%)
Q30 bases: 1348206(69.8879%)

Filtering result:
reads passed filter: 12986
reads failed due to low quality: 120582
reads failed due to too many N: 0
reads failed due to too short: 1402
reads with adapter trimmed: 2588
bases trimmed due to adapters: 38052

Duplication rate: 0.697933%

Insert size peak (evaluated by paired-end reads): 38

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for DRR218540.fastq.gz -i DRR218540.fastq.gz -o first.fastq.gz -I DRR218540_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 20 -u 20 -l 70 
fastp v0.23.2, time used: 25 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "70"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "20", "unqualified_percent_limit": "20"}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 4, "src": "dce"}]}, "in2": {"values": [{"id": 5, "src": "dce"}]}, "single_paired_selector": "paired"}`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

SeqPrep -f '/tmp/tmp3g1dmuys/files/8/c/3/dataset_8c361269-108b-49f8-9fa1-409f61ca267b.dat' -r '/tmp/tmp3g1dmuys/files/3/3/c/dataset_33cfb898-7496-418f-b822-e7cd9f4251de.dat' -1 '/tmp/tmp3g1dmuys/job_working_directory/000/6/outputs/dataset_68736340-5b72-4003-832b-664b8e949041.dat' -2 '/tmp/tmp3g1dmuys/job_working_directory/000/6/outputs/dataset_31551c4a-9e5d-40c4-97ea-4628984b9f06.dat'  -s '/tmp/tmp3g1dmuys/job_working_directory/000/6/outputs/dataset_47d75f60-d495-4ae2-b231-113932ac50b6.dat'  -q '13' -L '30'  -A 'AGATCGGAAGAGCGGTTCAG' -B 'AGATCGGAAGAGCGTCGTGT' -O '10' -M '0.02' -N '0.87' -b '50' -Q '8' -t '2' -e '2' -Z '26' -w '50' -W '26' -p '9' -P '5' -X '0.125'  -o '15' -m '0.02' -n '0.9'

Exit Code:

```
0
```

Standard Error:

Pairs Processed:	0
Pairs Merged:	6434
Pairs With Adapters:	0
Pairs Discarded:	0
CPU Time Used (Minutes):	0.020807

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"first_read_discarded": null, "min_length": "30", "phred64": false, "quality_cutoff": "13", "second_read_discarded": null}`
merge_reads	`true`
merging_options	`{"max_mismatch_fraction": "0.02", "maximum_quality_score": null, "min_base_pair_overlap": "15", "min_match_fraction": "0.9", "print_overhang": false}`
trimming_options	`{"adapter_a": "AGATCGGAAGAGCGGTTCAG", "adapter_b": "AGATCGGAAGAGCGTCGTGT", "adapter_bandwidth": "50", "adapter_overlap": "10", "gap_end": "2", "gap_extend": "2", "gap_open": "8", "local_alignment_score": "26", "max_mismatch_fraction": "0.02", "min_match_fraction": "0.87", "read_alignment_bandwidth": "50", "read_alignment_gap_end": "5", "read_alignment_gap_extend": "9", "read_alignment_gap_open": "26", "read_alignment_max_gap_fraction": "0.125"}`

Step 18: Quality filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmp3g1dmuys/files/4/7/d/dataset_47d75f60-d495-4ae2-b231-113932ac50b6.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmp3g1dmuys/job_working_directory/000/7/outputs/dataset_0f7c1981-be87-4d7a-9676-c5348a1b5bcb.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 6434 Surviving: 6432 (99.97%) Dropped: 2 (0.03%)
TrimmomaticSE: Completed successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 12, "src": "dce"}]}, "single_or_paired": "se"}`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3g1dmuys/files/4/7/d/dataset_47d75f60-d495-4ae2-b231-113932ac50b6.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmp3g1dmuys/job_working_directory/000/8/outputs/dataset_3986f27d-0dc1-4391-bd71-90e361ce8468_files' && fastqc --outdir '/tmp/tmp3g1dmuys/job_working_directory/000/8/outputs/dataset_3986f27d-0dc1-4391-bd71-90e361ce8468_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmp3g1dmuys/job_working_directory/000/8/outputs/dataset_3986f27d-0dc1-4391-bd71-90e361ce8468_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp3g1dmuys/job_working_directory/000/8/outputs/dataset_3986f27d-0dc1-4391-bd71-90e361ce8468_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
adapters	`None`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 20: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmp3g1dmuys/files/0/f/7/dataset_0f7c1981-be87-4d7a-9676-c5348a1b5bcb.dat' '/tmp/tmp3g1dmuys/job_working_directory/000/9/configs/tmpo8m3134p' '/tmp/tmp3g1dmuys/job_working_directory/000/9/outputs/dataset_7839f0ca-fa17-4396-a4d7-948111006834.dat' '/tmp/tmp3g1dmuys/job_working_directory/000/9/outputs/dataset_7839f0ca-fa17-4396-a4d7-948111006834_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 6432 of 6432 reads (100.00%).
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 3: fastp - qualified_phred_quality (-q):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3g1dmuys/files/0/f/7/dataset_0f7c1981-be87-4d7a-9676-c5348a1b5bcb.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmp3g1dmuys/job_working_directory/000/10/outputs/dataset_9154aed5-bca1-4447-909c-a20c91b96bd0_files' && fastqc --outdir '/tmp/tmp3g1dmuys/job_working_directory/000/10/outputs/dataset_9154aed5-bca1-4447-909c-a20c91b96bd0_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmp3g1dmuys/job_working_directory/000/10/outputs/dataset_9154aed5-bca1-4447-909c-a20c91b96bd0_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp3g1dmuys/job_working_directory/000/10/outputs/dataset_9154aed5-bca1-4447-909c-a20c91b96bd0_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
adapters	`None`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 22: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp3g1dmuys/job_working_directory/000/11/outputs/dataset_c50fd89d-aa5e-4a69-86cd-64bff06f71cf.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmp3g1dmuys/files/d/8/e/dataset_d8e4f3c9-2036-4461-82fb-7ddbeea8741a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 23: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3g1dmuys/files/7/8/3/dataset_7839f0ca-fa17-4396-a4d7-948111006834.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmp3g1dmuys/job_working_directory/000/12/outputs/dataset_68738cfd-a7a7-4659-be31-0f94d723025c_files' && fastqc --outdir '/tmp/tmp3g1dmuys/job_working_directory/000/12/outputs/dataset_68738cfd-a7a7-4659-be31-0f94d723025c_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmp3g1dmuys/job_working_directory/000/12/outputs/dataset_68738cfd-a7a7-4659-be31-0f94d723025c_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp3g1dmuys/job_working_directory/000/12/outputs/dataset_68738cfd-a7a7-4659-be31-0f94d723025c_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
adapters	`None`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 24: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmp3g1dmuys/files/7/8/3/dataset_7839f0ca-fa17-4396-a4d7-948111006834.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 6,432
	Input bases: 2,151,394
	Input mean length: 334.48
	Good sequences: 6,432 (100.00%)
	Good bases: 2,151,394
	Good mean length: 334.48
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 16, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp3g1dmuys/job_working_directory/000/14/outputs/dataset_85beb3b7-104c-4e3a-ac88-c30c8da4e506.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmp3g1dmuys/files/0/c/d/dataset_0cd588c9-1232-4211-8e59-9fecebe79745.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp3g1dmuys/job_working_directory/000/15/outputs/dataset_507684c5-b073-44a2-b128-abf8cdee061a.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmp3g1dmuys/files/a/3/e/dataset_a3e724af-ea94-4b87-9b99-f30ea0bf1732.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmp3g1dmuys/files/5/9/1/dataset_591b271a-4fc1-4dc3-a66e-e0bbc58e9ff4.dat' '/tmp/tmp3g1dmuys/job_working_directory/000/16/outputs/dataset_fee7a598-49ac-4775-b20f-9330fd45c939.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

6432 FASTQ reads were converted to FASTA.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3g1dmuys/files/5/9/1/dataset_591b271a-4fc1-4dc3-a66e-e0bbc58e9ff4.dat' 'DRR218540.gz' && mkdir -p '/tmp/tmp3g1dmuys/job_working_directory/000/17/outputs/dataset_5266582d-dc22-4574-af08-7d1734ab2c20_files' && fastqc --outdir '/tmp/tmp3g1dmuys/job_working_directory/000/17/outputs/dataset_5266582d-dc22-4574-af08-7d1734ab2c20_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR218540.gz'  && cp '/tmp/tmp3g1dmuys/job_working_directory/000/17/outputs/dataset_5266582d-dc22-4574-af08-7d1734ab2c20_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp3g1dmuys/job_working_directory/000/17/outputs/dataset_5266582d-dc22-4574-af08-7d1734ab2c20_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
adapters	`None`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp3g1dmuys/files/f/e/e/dataset_fee7a598-49ac-4775-b20f-9330fd45c939.dat' | fasta_formatter -w 0 -o '/tmp/tmp3g1dmuys/job_working_directory/000/18/outputs/dataset_d64448b9-7c57-401e-a35b-06728b6fec59.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp3g1dmuys/job_working_directory/000/19/outputs/dataset_0519e110-a028-40f5-8ef6-190b548977de.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmp3g1dmuys/files/2/0/6/dataset_206a87b9-8f3d-46d3-b4e6-188f478b18ff.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: fastp - unqualified_phred_quality (-u):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmp3g1dmuys/files/c/5/0/dataset_c50fd89d-aa5e-4a69-86cd-64bff06f71cf.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmp3g1dmuys/files/8/5/b/dataset_85beb3b7-104c-4e3a-ac88-c30c8da4e506.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmp3g1dmuys/files/5/0/7/dataset_507684c5-b073-44a2-b128-abf8cdee061a.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmp3g1dmuys/files/0/5/1/dataset_0519e110-a028-40f5-8ef6-190b548977de.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmp3g1dmuys/job_working_directory/000/20/working/multiqc_WDir
|            fastqc | Found 4 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4663ba9ce79011ee9f89037463e90a79"`
chromInfo	`"/tmp/tmp3g1dmuys/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 23, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 24, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 5: fastp - length_required (-l):
- step_state: scheduled
Step 6: Trimmomatic - SLIDINGWINDOW - Number of bases to average across:
- step_state: scheduled
Step 7: Trimmomatic - SLIDINGWINDOW - Average quality required:
- step_state: scheduled
Step 8: Trimmomatic - LEADING:
- step_state: scheduled
Step 9: Trimmomatic - TRAILING:
- step_state: scheduled
Step 10: Trimmomatic - MINLEN:
- step_state: scheduled

Other invocation details
- history_id
  - 97b97bbcb3a4d6b6
- history_state
  - ok
- invocation_id
  - 97b97bbcb3a4d6b6
- invocation_state
  - scheduled
- workflow_id
  - 97b97bbcb3a4d6b6

✅ mgnify-amplicon-pipeline-quality-control-single-end.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Accesion:
- step_state: scheduled
Step 2: Trimmomatic - SLIDING WINDOW - Average quality required:
- step_state: scheduled

Step 11: Trimming:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpzqu291am/files/9/3/2/dataset_932c1fb9-7678-457c-9118-5a27f4c7d900.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpzqu291am/job_working_directory/000/2/outputs/dataset_5443c602-27cc-4e42-8ccc-c3ae6134f7ba.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 196 Surviving: 184 (93.88%) Dropped: 12 (6.12%)
TrimmomaticSE: Completed successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 1, "src": "dce"}]}, "single_or_paired": "se"}`

Job 2:

Job state is ok

Command Line:

if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/tmp/tmpzqu291am/files/6/8/6/dataset_686ce7e6-95cc-42a3-9937-637cc3223aa7.dat' fastq_in.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger.gz' fastq_out.'fastqsanger.gz' SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz' '/tmp/tmpzqu291am/job_working_directory/000/3/outputs/dataset_a9809344-1172-4dd0-bbe5-4910be8e7356.dat'

Exit Code:

```
0
```

Standard Output:

TrimmomaticSE: Started with arguments:
 -threads 1 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:100 -phred33
Input Reads: 90 Surviving: 90 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
illuminaclip	`{"__current_case__": 1, "do_illuminaclip": "no"}`
operations	`[{"__index__": 0, "operation": {"__current_case__": 0, "name": "SLIDINGWINDOW", "required_quality": "15", "window_size": "4"}}, {"__index__": 1, "operation": {"__current_case__": 2, "leading": "3", "name": "LEADING"}}, {"__index__": 2, "operation": {"__current_case__": 3, "name": "TRAILING", "trailing": "3"}}, {"__index__": 3, "operation": {"__current_case__": 1, "minlen": "100", "name": "MINLEN"}}]`
output_err	`false`
output_logs	`false`
quality_score	`"-phred33"`
readtype	`{"__current_case__": 0, "fastq_in": {"values": [{"id": 2, "src": "dce"}]}, "single_or_paired": "se"}`

Step 12: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpzqu291am/files/9/3/2/dataset_932c1fb9-7678-457c-9118-5a27f4c7d900.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpzqu291am/job_working_directory/000/4/outputs/dataset_55849d26-780f-4493-b3ac-78b0b93afd2f_files' && fastqc --outdir '/tmp/tmpzqu291am/job_working_directory/000/4/outputs/dataset_55849d26-780f-4493-b3ac-78b0b93afd2f_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpzqu291am/job_working_directory/000/4/outputs/dataset_55849d26-780f-4493-b3ac-78b0b93afd2f_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpzqu291am/job_working_directory/000/4/outputs/dataset_55849d26-780f-4493-b3ac-78b0b93afd2f_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adapters	`None`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpzqu291am/files/6/8/6/dataset_686ce7e6-95cc-42a3-9937-637cc3223aa7.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpzqu291am/job_working_directory/000/5/outputs/dataset_7c8be726-ce1e-4f4e-b0d4-6ebc6cc0c27d_files' && fastqc --outdir '/tmp/tmpzqu291am/job_working_directory/000/5/outputs/dataset_7c8be726-ce1e-4f4e-b0d4-6ebc6cc0c27d_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpzqu291am/job_working_directory/000/5/outputs/dataset_7c8be726-ce1e-4f4e-b0d4-6ebc6cc0c27d_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpzqu291am/job_working_directory/000/5/outputs/dataset_7c8be726-ce1e-4f4e-b0d4-6ebc6cc0c27d_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adapters	`None`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 13: Length filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpzqu291am/files/5/4/4/dataset_5443c602-27cc-4e42-8ccc-c3ae6134f7ba.dat' '/tmp/tmpzqu291am/job_working_directory/000/6/configs/tmpp80x7ovh' '/tmp/tmpzqu291am/job_working_directory/000/6/outputs/dataset_d81fdbdd-d89d-4ce4-a8bd-e71e41b17f32.dat' '/tmp/tmpzqu291am/job_working_directory/000/6/outputs/dataset_d81fdbdd-d89d-4ce4-a8bd-e71e41b17f32_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 184 of 184 reads (100.00%).
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Job 2:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpzqu291am/files/a/9/8/dataset_a9809344-1172-4dd0-bbe5-4910be8e7356.dat' '/tmp/tmpzqu291am/job_working_directory/000/7/configs/tmpyop8xsqk' '/tmp/tmpzqu291am/job_working_directory/000/7/outputs/dataset_91d7d969-61e7-403e-955c-cb7a9a948947.dat' '/tmp/tmpzqu291am/job_working_directory/000/7/outputs/dataset_91d7d969-61e7-403e-955c-cb7a9a948947_files' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

```
Kept 90 of 90 reads (100.00%).
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"100"`
paired_end	`false`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpzqu291am/files/5/4/4/dataset_5443c602-27cc-4e42-8ccc-c3ae6134f7ba.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpzqu291am/job_working_directory/000/8/outputs/dataset_677e19f5-529c-409f-b603-90335f5d5097_files' && fastqc --outdir '/tmp/tmpzqu291am/job_working_directory/000/8/outputs/dataset_677e19f5-529c-409f-b603-90335f5d5097_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpzqu291am/job_working_directory/000/8/outputs/dataset_677e19f5-529c-409f-b603-90335f5d5097_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpzqu291am/job_working_directory/000/8/outputs/dataset_677e19f5-529c-409f-b603-90335f5d5097_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adapters	`None`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpzqu291am/files/a/9/8/dataset_a9809344-1172-4dd0-bbe5-4910be8e7356.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpzqu291am/job_working_directory/000/9/outputs/dataset_d79164c5-2234-49c3-b9c9-b4e812b32ef4_files' && fastqc --outdir '/tmp/tmpzqu291am/job_working_directory/000/9/outputs/dataset_d79164c5-2234-49c3-b9c9-b4e812b32ef4_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpzqu291am/job_working_directory/000/9/outputs/dataset_d79164c5-2234-49c3-b9c9-b4e812b32ef4_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpzqu291am/job_working_directory/000/9/outputs/dataset_d79164c5-2234-49c3-b9c9-b4e812b32ef4_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adapters	`None`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpzqu291am/job_working_directory/000/10/outputs/dataset_ddb0d38a-658c-4f08-b9bc-b3292a9e37d7.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpzqu291am/files/1/4/5/dataset_1455be9d-a0dd-41bc-a492-146cdcdba9da.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpzqu291am/job_working_directory/000/11/outputs/dataset_47775019-1c05-4018-8d3e-0184f81de9e9.dat' -g    -r '\t(.*?)\.gz' '\t$1_initial_reads' '/tmp/tmpzqu291am/files/a/2/6/dataset_a2652fcd-3565-4d05-919f-d826f9bb072d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_initial_reads", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 16: Ambiguity filtering:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpzqu291am/files/d/8/1/dataset_d81fdbdd-d89d-4ce4-a8bd-e71e41b17f32.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 184
	Input bases: 46,942
	Input mean length: 255.12
	Good sequences: 184 (100.00%)
	Good bases: 46,942
	Good mean length: 255.12
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 9, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Job 2:

Job state is ok

Command Line:

mkdir tmp/ &&    gunzip -c '/tmp/tmpzqu291am/files/9/1/d/dataset_91d7d969-61e7-403e-955c-cb7a9a948947.dat' > fwd.fastq &&   touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&   prinseq-lite.pl -fastq fwd.fastq -out_good "tmp/good_sequences" -out_bad "tmp/rejected_sequences"      -ns_max_p 10  -noniupac      && for f in tmp/*.fastq; do gzip -c $f > tmp_file && mv tmp_file $f; done

Exit Code:

```
0
```

Standard Error:

Input and filter stats:
	Input sequences: 90
	Input bases: 31,735
	Input mean length: 352.61
	Good sequences: 90 (100.00%)
	Good bases: 31,735
	Good mean length: 352.61
	Bad sequences: 0 (0.00%)
	Sequences filtered by specified parameters:
	none

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_treatments	{"__current_case__": 0, "apply_filter_treatments": "true", "base_content_filter_treatments": {"GC_perc_content_filter_treatments": {"__current_case__": 1, "apply_GC_perc_content_filter_treatments": "false"}, "N_number_content_filter_treatments": {"__current_case__": 1, "apply_N_number_content_filter_treatments": "false"}, "N_percentage_content_filter_treatments": {"N_percentage_content_filter_treatment_value": "10", "__current_case__": 0, "apply_N_percentage_content_filter_treatments": "true"}, "__current_case__": 0, "apply_base_content_filter_treatments": "true", "apply_other_base_content_filter_treatments": true}, "complexity_filter_treatments": {"__current_case__": 1, "apply_complexity_filter_treatments": "false"}, "length_filter_treatments": {"__current_case__": 1, "apply_length_filter_treatments": "false"}, "quality_filter_treatments": {"__current_case__": 1, "apply_quality_filter_treatments": "false"}}
seq_type	`{"__current_case__": 0, "input_singles": {"values": [{"id": 10, "src": "dce"}]}, "seq_type_opt": "single"}`
trimming_treatments	`{"__current_case__": 1, "apply_trimming_treatments": "false"}`

Step 17: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpzqu291am/files/d/8/1/dataset_d81fdbdd-d89d-4ce4-a8bd-e71e41b17f32.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpzqu291am/job_working_directory/000/14/outputs/dataset_f2dcaa51-aa37-4a10-8075-6bb60054fb9c_files' && fastqc --outdir '/tmp/tmpzqu291am/job_working_directory/000/14/outputs/dataset_f2dcaa51-aa37-4a10-8075-6bb60054fb9c_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpzqu291am/job_working_directory/000/14/outputs/dataset_f2dcaa51-aa37-4a10-8075-6bb60054fb9c_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpzqu291am/job_working_directory/000/14/outputs/dataset_f2dcaa51-aa37-4a10-8075-6bb60054fb9c_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adapters	`None`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpzqu291am/files/9/1/d/dataset_91d7d969-61e7-403e-955c-cb7a9a948947.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpzqu291am/job_working_directory/000/15/outputs/dataset_0e29707c-b148-41f1-b7b7-f14473124808_files' && fastqc --outdir '/tmp/tmpzqu291am/job_working_directory/000/15/outputs/dataset_0e29707c-b148-41f1-b7b7-f14473124808_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpzqu291am/job_working_directory/000/15/outputs/dataset_0e29707c-b148-41f1-b7b7-f14473124808_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpzqu291am/job_working_directory/000/15/outputs/dataset_0e29707c-b148-41f1-b7b7-f14473124808_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adapters	`None`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpzqu291am/job_working_directory/000/16/outputs/dataset_d6d54161-487f-4595-b85c-01fcdf03e24d.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpzqu291am/files/8/8/6/dataset_8866df90-31dc-45d7-97ce-ad6ae0212450.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpzqu291am/job_working_directory/000/17/outputs/dataset_8fe5174e-342d-467e-85e8-ae37be283512.dat' -g    -r '\t(.*?)\.gz' '\t$1_trimming' '/tmp/tmpzqu291am/files/d/d/f/dataset_ddff9cf4-a7f9-4113-9074-5b1d448a9610.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_trimming", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpzqu291am/files/c/1/6/dataset_c167cca1-09fb-4aa1-a4ce-613748dda937.dat' '/tmp/tmpzqu291am/job_working_directory/000/18/outputs/dataset_6c854edb-a8f1-4fa5-9017-5e1799d378aa.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

184 FASTQ reads were converted to FASTA.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

gx-fastq-to-fasta '/tmp/tmpzqu291am/files/b/3/4/dataset_b34cb6aa-65d1-482f-8e49-8368758223f8.dat' '/tmp/tmpzqu291am/job_working_directory/000/19/outputs/dataset_1d2e2670-2f42-4c7a-a3b5-97a8cef12f05.dat' 'sanger.gz'

Exit Code:

```
0
```

Standard Output:

90 FASTQ reads were converted to FASTA.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpzqu291am/files/c/1/6/dataset_c167cca1-09fb-4aa1-a4ce-613748dda937.dat' 'DRR010705.gz' && mkdir -p '/tmp/tmpzqu291am/job_working_directory/000/20/outputs/dataset_fa089cc9-928f-4313-87a5-5623184fd551_files' && fastqc --outdir '/tmp/tmpzqu291am/job_working_directory/000/20/outputs/dataset_fa089cc9-928f-4313-87a5-5623184fd551_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR010705.gz'  && cp '/tmp/tmpzqu291am/job_working_directory/000/20/outputs/dataset_fa089cc9-928f-4313-87a5-5623184fd551_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpzqu291am/job_working_directory/000/20/outputs/dataset_fa089cc9-928f-4313-87a5-5623184fd551_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adapters	`None`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpzqu291am/files/b/3/4/dataset_b34cb6aa-65d1-482f-8e49-8368758223f8.dat' 'DRR011051.gz' && mkdir -p '/tmp/tmpzqu291am/job_working_directory/000/21/outputs/dataset_1049b7cc-fe3c-4568-94ca-28aa60a10ac4_files' && fastqc --outdir '/tmp/tmpzqu291am/job_working_directory/000/21/outputs/dataset_1049b7cc-fe3c-4568-94ca-28aa60a10ac4_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'DRR011051.gz'  && cp '/tmp/tmpzqu291am/job_working_directory/000/21/outputs/dataset_1049b7cc-fe3c-4568-94ca-28aa60a10ac4_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpzqu291am/job_working_directory/000/21/outputs/dataset_1049b7cc-fe3c-4568-94ca-28aa60a10ac4_files'/*\.html output.html

Exit Code:

```
0
```

Standard Error:

Fontconfig error: No writable cache directories

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adapters	`None`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 3: Trimmomatic - LEADING:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpzqu291am/job_working_directory/000/22/outputs/dataset_cd6ba613-1914-40d7-8d92-1993600e23f2.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpzqu291am/files/e/e/c/dataset_eecd7a99-c29f-4b25-99cb-2c7c16211cb3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpzqu291am/job_working_directory/000/23/outputs/dataset_bdfb05df-b054-4d3f-9ec5-b109d77b2170.dat' -g    -r '\t(.*?)\.gz' '\t$1_length_filtering' '/tmp/tmpzqu291am/files/b/9/c/dataset_b9c122de-56f2-41ae-a274-8aa0d3ff5452.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_length_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpzqu291am/files/6/c/8/dataset_6c854edb-a8f1-4fa5-9017-5e1799d378aa.dat' | fasta_formatter -w 60 -o '/tmp/tmpzqu291am/job_working_directory/000/24/outputs/dataset_353382e2-e34e-4357-84ef-a48fc9f3f1ee.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Job 2:

Job state is ok

Command Line:

cat '/tmp/tmpzqu291am/files/1/d/2/dataset_1d2e2670-2f42-4c7a-a3b5-97a8cef12f05.dat' | fasta_formatter -w 60 -o '/tmp/tmpzqu291am/job_working_directory/000/25/outputs/dataset_8c8decd7-bd30-4bb8-8523-7d028f6cbdf9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
width	`"60"`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpzqu291am/job_working_directory/000/26/outputs/dataset_e39cd039-183b-4f93-b324-86625bfbe606.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpzqu291am/files/c/5/c/dataset_c5c754de-5166-4923-8be3-0c98418ec798.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Job 2:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmpzqu291am/job_working_directory/000/27/outputs/dataset_5e83b227-9156-4dc0-a769-ab1ce733909c.dat' -g    -r '\t(.*?)\.gz' '\t$1_ambiguous_base_filtering' '/tmp/tmpzqu291am/files/9/6/2/dataset_96215508-daba-49ee-be4c-9ae0be50dfa3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "\\t(.*?)\\.gz", "global": true, "is_regex": true, "replace_pattern": "\\t$1_ambiguous_base_filtering", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/tmp/tmpzqu291am/files/d/d/b/dataset_ddb0d38a-658c-4f08-b9bc-b3292a9e37d7.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/tmp/tmpzqu291am/files/4/7/7/dataset_47775019-1c05-4018-8d3e-0184f81de9e9.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_1' &&  mkdir 'multiqc_WDir/fastqc_0/data_1/file_0' && ln -s '/tmp/tmpzqu291am/files/d/6/d/dataset_d6d54161-487f-4595-b85c-01fcdf03e24d.dat' 'multiqc_WDir/fastqc_0/data_1/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_1/file_1' && ln -s '/tmp/tmpzqu291am/files/8/f/e/dataset_8fe5174e-342d-467e-85e8-ae37be283512.dat' 'multiqc_WDir/fastqc_0/data_1/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_2' &&  mkdir 'multiqc_WDir/fastqc_0/data_2/file_0' && ln -s '/tmp/tmpzqu291am/files/c/d/6/dataset_cd6ba613-1914-40d7-8d92-1993600e23f2.dat' 'multiqc_WDir/fastqc_0/data_2/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_2/file_1' && ln -s '/tmp/tmpzqu291am/files/b/d/f/dataset_bdfb05df-b054-4d3f-9ec5-b109d77b2170.dat' 'multiqc_WDir/fastqc_0/data_2/file_1/fastqc_data.txt' &&   mkdir 'multiqc_WDir/fastqc_0/data_3' &&  mkdir 'multiqc_WDir/fastqc_0/data_3/file_0' && ln -s '/tmp/tmpzqu291am/files/e/3/9/dataset_e39cd039-183b-4f93-b324-86625bfbe606.dat' 'multiqc_WDir/fastqc_0/data_3/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_3/file_1' && ln -s '/tmp/tmpzqu291am/files/5/e/8/dataset_5e83b227-9156-4dc0-a769-ab1ce733909c.dat' 'multiqc_WDir/fastqc_0/data_3/file_1/fastqc_data.txt' &&   multiqc multiqc_WDir --filename 'report'

Exit Code:

```
0
```

Standard Error:

  /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpzqu291am/job_working_directory/000/28/working/multiqc_WDir
|            fastqc | Found 8 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | MultiQC complete

Standard Output:

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 8/8

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hdca"}]}, "type": "data"}, {"__index__": 2, "input": {"values": [{"id": 18, "src": "hdca"}]}, "type": "data"}, {"__index__": 3, "input": {"values": [{"id": 20, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}]`
saveLog	`false`
title	`""`

Step 4: Trimmomatic - TRAILING:
- step_state: scheduled
Step 5: Trimmomatic - SLIDING WINDOW - Number of bases to average across:
- step_state: scheduled
Step 6: Trimmomatic - MINLEN:
- step_state: scheduled
Step 7: Trimmomatic - Quality score encoding:
- step_state: scheduled
Step 8: Length filtering - Minimum size:
- step_state: scheduled
Step 9: Ambiguity filtering - Maximal N percentage threshold to conserve sequences:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.8+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p ~/.ncbi && cp '/tmp/tmpzqu291am/job_working_directory/000/1/configs/tmppinq3i80' ~/.ncbi/user-settings.mkfg &&   echo 'DRR011051,DRR010705' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions && for acc in $(cat ./accessions); do ( echo "Downloading accession: $acc..." &&   prefetch -X 200000000 "$acc" && fastq-dump --accession "$acc" --split-files --defline-seq '@$ac.$si-$sn-$ri' --defline-qual '+'  --split-spot  --skip-technical  --gzip  ;  mkdir -p output && data=($(ls ./*.fast*)); if [ ${#data[@]} -eq 2 ]; then mv "${data[0]}" output/"${data[0]}"_forward.fastqsanger.gz; mv "${data[1]}" output/"${data[1]}"_reverse.fastqsanger.gz; elif [ ${#data[@]} -eq 1 ]; then mv "${data[0]}" output/"${data[0]}"__single.fastqsanger.gz; fi;  ); done; echo "Done with all accessions."

Exit Code:

```
0
```

Standard Error:

2024-03-21T14:35:27 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-21T14:35:27 prefetch.3.0.8: 1) Downloading 'DRR011051'...
2024-03-21T14:35:27 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-21T14:35:27 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-21T14:35:27 prefetch.3.0.8:  HTTPS download succeed
2024-03-21T14:35:27 prefetch.3.0.8:  'DRR011051' is valid
2024-03-21T14:35:27 prefetch.3.0.8: 1) 'DRR011051' was downloaded successfully
2024-03-21T14:35:28 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-21T14:35:28 prefetch.3.0.8: 1) Downloading 'DRR010705'...
2024-03-21T14:35:28 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-21T14:35:28 prefetch.3.0.8:  Downloading via HTTPS...
2024-03-21T14:35:28 prefetch.3.0.8:  HTTPS download succeed
2024-03-21T14:35:28 prefetch.3.0.8:  'DRR010705' is valid
2024-03-21T14:35:28 prefetch.3.0.8: 1) 'DRR010705' was downloaded successfully

Standard Output:

Downloading accession: DRR011051...

Rejected 270 READS because of filtering out non-biological READS
Read 90 spots for DRR011051
Written 90 spots for DRR011051
Downloading accession: DRR010705...

Rejected 588 READS because of filtering out non-biological READS
Read 196 spots for DRR010705
Written 196 spots for DRR010705
Done with all accessions.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37958aa4e79011ee99b499387440d20a"`
adv	`{"alignments": "both", "clip": false, "defline_seq": "@$ac.$si-$sn-$ri", "matepairDist": null, "maxID": null, "minID": null, "minlen": null, "readfilter": "", "region": null, "skip_technical": true, "split": true, "spotgroups": null, "table": ""}`
chromInfo	`"/tmp/tmpzqu291am/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"__current_case__": 0, "accession": "DRR011051, DRR010705", "input_select": "accession_number"}`
outputformat	`"fastqsanger.gz"`

Other invocation details
- history_id
  - ecec821c7f0be67a
- history_state
  - ok
- invocation_id
  - ecec821c7f0be67a
- invocation_state
  - scheduled
- workflow_id
  - ecec821c7f0be67a

paulzierep · 2024-06-19T12:48:59Z

I will try to review asap !

paulzierep · 2024-07-18T09:16:41Z

workflows/microbiome/mgnify-amplicon-pipeline-v5-complete/README.md

@@ -0,0 +1,17 @@
+# MGnify's amplicon pipeline (v5.0)


I assume this is the main entry point for the user (or can there be a README for all workflows ? - then this would probably be better !)
Can we add:

What it this? Can you add a few lines of explanation (what is MGnify, what is the amplicon pipeline, what is the advantage of this port, what do the individual workflows do ... )

How can one test the workflow and see that the results are the same.

Explain that the classification part is not the same due to mapseq (show example)

Maybe we should place this into the amplicon folder after all.

And can you describe briefly how to only use parts of the workflow (just in short, the details come in the GTN)

paulzierep

Apart from minor readme changes I think this is good to go. And failing tests ...

workflows/microbiome/mgnify-amplicon-taxonomic-summary-tables/README.md

paulzierep · 2024-07-30T09:02:54Z

workflows/microbiome/mgnify-amplicon-pipeline-v5-complete/README.md

@@ -0,0 +1,17 @@
+# MGnify's amplicon pipeline (v5.0)


And can you describe briefly how to only use parts of the workflow (just in short, the details come in the GTN)

paulzierep · 2024-08-15T10:40:43Z

If the tests work it can be merged from my side, then we can make updates in a new PR, for this huge PR the GitHub rendering often fails.

mvdbeek · 2024-08-15T11:32:44Z

If the tests work it can be merged from my side, then we can make updates in a new PR, for this huge PR the GitHub rendering often fails.

The test data files should go to zenodo.

RZ9082 · 2024-10-21T15:15:15Z

Hey @mvdbeek,
@paulzierep approves the changes and this PR to be merged. He asked me to notify you, since the PR is not loading for him!

mvdbeek · 2024-10-21T17:54:12Z

I have a bunch of pending comments, there are a few changes still necessary. I'll get those submitted when I'm back at my computer

workflows/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga

workflows/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2-tests.yml

workflows/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga

workflows/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2-tests.yml

workflows/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga

...amplicon-mgnify/mgnify-amplicon-pipeline-v5-complete/mgnify-amplicon-pipeline-v5-complete.ga

mvdbeek · 2024-09-27T15:18:56Z

...amplicon-mgnify/mgnify-amplicon-pipeline-v5-complete/mgnify-amplicon-pipeline-v5-complete.ga

+                    "name": "SE Trimmomatic - LEADING"
+                }
+            ],
+            "label": "SE Trimmomatic - LEADING",


This parameter is also optional, is that correct ?

In the case of the tool itself you are right, it is optional. Here it is actually set to a default value, because this is the pipeline default value..

mvdbeek · 2024-09-27T15:19:25Z

...amplicon-mgnify/mgnify-amplicon-pipeline-v5-complete/mgnify-amplicon-pipeline-v5-complete.ga

+                    "name": "SE Trimmomatic - TRAILING"
+                }
+            ],
+            "label": "SE Trimmomatic - TRAILING",


This is also optional

...amplicon-mgnify/mgnify-amplicon-pipeline-v5-complete/mgnify-amplicon-pipeline-v5-complete.ga

mvdbeek · 2024-10-28T13:29:53Z

You're missing the release field in the workflows now:
https://github.com/galaxyproject/iwc/actions/runs/11550127632/job/32144507467?pr=343#step:6:776

RZ9082 · 2024-11-07T16:34:22Z

@mvdbeek is it possible to add the infernal indexes to the CVMFS? I think this is the reason why cmsearch is failing..

mvdbeek · 2024-11-15T17:40:20Z

Sure, I'll copy that from .eu

RZ9082 added 2 commits February 25, 2024 23:20

amplicon subworkflows

5292081

add .dockstore.yml

8fbf0ac

update trimmomatic suffix

8b37b93

RZ9082 added 2 commits February 28, 2024 12:54

update trimmomatic revision

aeccaa9

update workflows

b1ba46f

RZ9082 added 2 commits March 1, 2024 10:59

updated PE and SE tests

48191eb

updated PE and SE tests

fcf4550

RZ9082 added 3 commits March 1, 2024 16:11

add workflow to test query_tabular input

195028a

add workflow to test query_tabular input

5702b8d

add workflow to test query_tabular input

a33ac5d

update test query_tabular

5459484

update test query_tabular

159ad05

updated cmsearch-deoverlap

216d0e4

update cmsearch-deoverlap

69c84c0

RZ9082 added 4 commits March 20, 2024 12:49

remove testing-query-tabular

d7d913e

update after-quality-control tests

8b64392

update after-quality-control tests

79ee75b

add annotations to the post-QC sub-WF

6c38879

RZ9082 added 2 commits March 21, 2024 15:41

updated input names

b6b6472

add annotations

cd67328

RZ9082 added 7 commits May 29, 2024 14:28

has_n_lines

edfe16b

first line in summary tables was missing

ffb7642

add mapseq-to-ampvis2 WF

bda2fb7

filter empty datasets

b63223f

update mapseq-to-ampvis2/.dockstore.yml

1c4085b

update QC tests

6ad41d9

update ampvis test

57c81df

RZ9082 added 3 commits June 26, 2024 17:32

update WF-names & add conditions for col-join, krona, and biom-convert

1b4d037

del old WFs

85bcec4

adjust ssu summ test

901d05c

paulzierep reviewed Jul 18, 2024

View reviewed changes

RZ9082 added 2 commits July 29, 2024 14:13

set fasta width to 60 in PE sub-WF

4bb715b

update PE QC processed fasta test-file

0085af6

paulzierep reviewed Jul 30, 2024

View reviewed changes

RZ9082 and others added 4 commits September 26, 2024 10:58

Merge branch 'galaxyproject:main' into mgnify_amplicon_pipeline

69a9fe8

add zenodo link & remove test files

05af05a

move workflows to dedicated folder

aec58c6

add taxonomic rank abundane summary table workflow

80ace02

mvdbeek reviewed Oct 21, 2024

View reviewed changes

apply review suggestions

a5ec087

RZ9082 added 2 commits October 28, 2024 14:50

add release to WFs

04d9015

add missing quotation mark

798153a

Add MGnify amplicon pipeline #343

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Add MGnify amplicon pipeline #343

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paulzierep commented Aug 15, 2024

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