Updating workflows/virology/pox-virus-amplicon from 0.2 to 0.3 #462

gxydevbot · 2024-06-28T09:46:20Z

Hello! This is an automated update of the following workflow: workflows/virology/pox-virus-amplicon. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0

The workflow release number has been updated from 0.2 to 0.3.

wm75

Sorry, qualimap auto-updates just never work.

bgruening · 2024-07-01T19:01:33Z

What is the problem?

wm75 · 2024-07-01T19:02:47Z

Non-standard versioning makes the bot suggest downgrades. Happening every time.

bgruening · 2024-07-10T10:29:06Z

xref: galaxyproject/tools-iuc#6138

gxydevbot · 2024-09-23T14:59:00Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-23T15:20:27Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ pox-virus-half-genome.ga_0

Execution Problem:

Final state of invocation 24c631f4f2bd8751 is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 38 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Reference FASTA:
- step_state: scheduled
Step 2: Primer Scheme:
- step_state: scheduled

Step 11: 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/tmpmj69_rr7/job_working_directory/000/10/configs/tmp3t3qglsj' '/tmp/tmpmj69_rr7/job_working_directory/000/10/outputs/dataset_a20c141e-61e2-4043-a54e-e318f544d53d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 12: fastp: Trimmed Illumina Reads Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -sf '/tmp/tmpmj69_rr7/files/4/4/c/dataset_44c6b172-612c-4576-b546-3e5a1b8075db.dat' '20L70.fastq.gz' && ln -sf '/tmp/tmpmj69_rr7/files/3/2/7/dataset_327a1f6c-4230-4f6c-ab7e-e6b6849d9c15.dat' '20L70_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for 20L70.fastq.gz'   -i '20L70.fastq.gz' -o first.fastq.gz  -I '20L70_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpmj69_rr7/job_working_directory/000/11/outputs/dataset_1db73f55-af73-40f3-83f1-590a259b1815.dat' && mv second.fastq.gz '/tmp/tmpmj69_rr7/job_working_directory/000/11/outputs/dataset_91a2e19e-2416-42e1-9c35-0d070926eddd.dat'

Exit Code:

```
255
```

Standard Error:

ERROR: igzip: Error invalid gzip header found: 20L70.fastq.gz

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "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": null, "unqualified_percent_limit": null}}`
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": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 13: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpmj69_rr7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpmj69_rr7/files/0/6/1/dataset_061bd6f5-22f9-480e-8f14-48122a5ce7aa.dat' 'c2' T '/tmp/tmpmj69_rr7/job_working_directory/000/12/outputs/dataset_7391675c-e160-40ce-bc5d-40e958179dca.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         max 3 < /tmp/tmpmj69_rr7/files/2/e/9/dataset_2e9d1205-0a9b-420d-a291-c8a5fa0f1be1.dat > '/tmp/tmpmj69_rr7/job_working_directory/000/13/outputs/dataset_43fa6c45-0b48-4188-8501-85f4e71fc2ae.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "max"}]`
print_full_line	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         min 2 < /tmp/tmpmj69_rr7/files/d/b/c/dataset_dbc8a3cf-3604-44d1-9cfd-48813d15de77.dat > '/tmp/tmpmj69_rr7/job_working_directory/000/14/outputs/dataset_64c402e5-0ea8-4414-8c4d-5438c9ab86ca.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "2", "op_name": "min"}]`
print_full_line	`false`

Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmpmj69_rr7/files/a/2/0/dataset_a20c141e-61e2-4043-a54e-e318f544d53d.dat' --ftype 'txt' --chunksize 1 --file_names 'pool1_ids' --file_ext 'txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 10, "src": "hda"}]}, "newfilenames": "pool1_ids", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 17: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
input	`{"values": [{"id": 2, "src": "hdca"}]}`
sort_type	`{"__current_case__": 2, "sort_file": {"values": [{"id": 10, "src": "hda"}]}, "sort_type": "file"}`

Step 18: Get end position of sequence:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 19: Get end position of Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 20: Get start position of Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 3: PE Reads Pool1:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 22: fastp: Trimmed Illumina Reads Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -sf '/tmp/tmpmj69_rr7/files/0/d/4/dataset_0d421cdb-a1cb-45c7-bfc6-5eb4a564bc85.dat' '20L70.fastq.gz' && ln -sf '/tmp/tmpmj69_rr7/files/b/3/3/dataset_b334448c-9898-4bf7-b9ee-abd9a485da6b.dat' '20L70_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for 20L70.fastq.gz'   -i '20L70.fastq.gz' -o first.fastq.gz  -I '20L70_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpmj69_rr7/job_working_directory/000/20/outputs/dataset_5144ece2-0d3b-45cf-a741-2864b9227e4a.dat' && mv second.fastq.gz '/tmp/tmpmj69_rr7/job_working_directory/000/20/outputs/dataset_e08d0c00-d70c-4f28-9cbe-426b95b342c6.dat'

Exit Code:

```
255
```

Standard Error:

ERROR: igzip: Error invalid gzip header found: 20L70.fastq.gz

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "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": null, "unqualified_percent_limit": null}}`
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": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 14, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "80202", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "-", "select_param_type": "text"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": "150773", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "1-", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "79081", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "20L70", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "_pool1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "20L70", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "_pool2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 27: Mask Reference for Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

maskseq -sequence '/tmp/tmpmj69_rr7/files/5/8/9/dataset_589b93f1-907b-4026-b03a-5410318ffbc4.dat' -outseq '/tmp/tmpmj69_rr7/job_working_directory/000/27/outputs/dataset_5d14164f-a052-40fd-af86-dc1aa0a052cb.dat' -regions '80202-150773' -tolower no -maskchar 'N' -osformat2 fasta -auto

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
maskchar	`"N"`
out_format1	`"fasta"`
regions	`"80202-150773"`
tolower	`"no"`

Step 28: Mask Reference for Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

maskseq -sequence '/tmp/tmpmj69_rr7/files/5/8/9/dataset_589b93f1-907b-4026-b03a-5410318ffbc4.dat' -outseq '/tmp/tmpmj69_rr7/job_working_directory/000/26/outputs/dataset_7cfa8ccf-58bc-4419-8936-655b8cc9e670.dat' -regions '1-79081' -tolower no -maskchar 'N' -osformat2 fasta -auto

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
maskchar	`"N"`
out_format1	`"fasta"`
regions	`"1-79081"`
tolower	`"no"`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 7, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 32, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": "", "DS": "", "DT": "", "FO": "", "KS": "", "PG": "", "PI": null, "PL": "ILLUMINA", "PU": "", "__current_case__": 1, "read_group_id_conditional": {"ID": "20L70_pool1", "__current_case__": 1, "do_auto_name": false}, "read_group_lb_conditional": {"LB": "", "__current_case__": 1, "do_auto_name": false}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"}`

Step 30: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 15, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 31, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": "", "DS": "", "DT": "", "FO": "", "KS": "", "PG": "", "PI": null, "PL": "ILLUMINA", "PU": "", "__current_case__": 1, "read_group_id_conditional": {"ID": "20L70_pool2", "__current_case__": 1, "do_auto_name": false}, "read_group_lb_conditional": {"LB": "", "__current_case__": 1, "do_auto_name": false}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"}`

Step 4: PE Reads Pool2:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "20", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 32: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "20", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 34: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 5, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 19, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}]`
saveLog	`"false"`
title	`""`

Step 36: __ZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "0014aa7679bf11efb5ada7aefcbcb04f"

Step 37: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 10, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 16, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}]`
saveLog	`"false"`
title	`""`

Step 38: __APPLY_RULES__:

step_state: new

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
input	`{"values": [{"id": 20, "src": "hdca"}]}`
rules	{"mapping": [{"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [0, 1], "connectable": true, "editing": false, "is_workflow": false, "type": "list_identifiers"}], "rules": [{"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier1", "warn": null}]}

Step 39: Unlabelled step:
- step_state: new
Step 40: Unlabelled step:
- step_state: new
Step 5: Minimum quality score to call base:
- step_state: scheduled
Step 41: Unlabelled step:
- step_state: new
Step 42: Unlabelled step:
- step_state: new
Step 43: Unlabelled step:
- step_state: new
Step 44: Unlabelled step:
- step_state: new
Step 45: Unlabelled step:
- step_state: new
Step 46: Unlabelled step:
- step_state: new
Step 47: Unlabelled step:
- step_state: new
Step 6: Allele frequency to call SNV:
- step_state: scheduled
Step 7: Allele frequency to call indel:
- step_state: scheduled

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/fasta_compute_length/fasta_compute_length.py' '/tmp/tmpmj69_rr7/files/5/8/9/dataset_589b93f1-907b-4026-b03a-5410318ffbc4.dat' '/tmp/tmpmj69_rr7/job_working_directory/000/7/outputs/dataset_061bd6f5-22f9-480e-8f14-48122a5ce7aa.dat' 0 id_and_desc

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref	`{"__current_case__": 0, "input": {"values": [{"id": 1, "src": "hda"}]}, "keep_first": "0", "keep_first_word": false, "ref_source": "history"}`

Step 9: Select pool1 primers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -eo pipefail; cat '/tmp/tmpmj69_rr7/files/a/3/2/dataset_a3292db0-7b62-4e8b-8bbb-8b5a304b91a8.dat' | grep -P -f '/tmp/tmpmj69_rr7/job_working_directory/000/8/configs/tmpo9kl4pnx'  >> '/tmp/tmpmj69_rr7/job_working_directory/000/8/outputs/dataset_2e9d1205-0a9b-420d-a291-c8a5fa0f1be1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	` "[p

Step 10: Select pool2 primers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -eo pipefail; cat '/tmp/tmpmj69_rr7/files/a/3/2/dataset_a3292db0-7b62-4e8b-8bbb-8b5a304b91a8.dat' | grep -P -f '/tmp/tmpmj69_rr7/job_working_directory/000/9/configs/tmpdx4nbzv7'  >> '/tmp/tmpmj69_rr7/job_working_directory/000/9/outputs/dataset_dbc8a3cf-3604-44d1-9cfd-48813d15de77.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0014aa7679bf11efb5ada7aefcbcb04f"`
chromInfo	`"/tmp/tmpmj69_rr7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	` "[p

Other invocation details
- error_message
  - Final state of invocation 24c631f4f2bd8751 is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - 24c631f4f2bd8751
- history_state
  - error
- invocation_id
  - 24c631f4f2bd8751
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': 'f1596aca09dcfcb5', 'reason': 'dataset_failed', 'workflow_step_id': 37}]
- workflow_id
  - 24c631f4f2bd8751

gxydevbot · 2024-09-24T14:35:12Z

There are new updates, they have been integrated to the PR, check the file diff.

gxydevbot · 2024-10-07T05:36:02Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-10-07T05:58:40Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ pox-virus-half-genome.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Reference FASTA:
- step_state: scheduled
Step 2: Primer Scheme:
- step_state: scheduled

Step 11: 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/tmpac8psprr/job_working_directory/000/10/configs/tmp3kyaucy7' '/tmp/tmpac8psprr/job_working_directory/000/10/outputs/dataset_aad6a9d9-520a-4d63-96dd-2a251eaf962a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 12: fastp: Trimmed Illumina Reads Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmpac8psprr/files/3/2/e/dataset_32e64a5c-081e-4e9b-91f7-ec00f40d47a1.dat' '20L70.fastq.gz' && ln -sf '/tmp/tmpac8psprr/files/6/5/8/dataset_658a7fb4-8fc3-4e70-8439-6b4bd766f38e.dat' '20L70_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for 20L70.fastq.gz'   -i '20L70.fastq.gz' -o first.fastq.gz  -I '20L70_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpac8psprr/job_working_directory/000/11/outputs/dataset_9a2f5627-4da0-4ad9-9a58-4c8912e8c085.dat' && mv second.fastq.gz '/tmp/tmpac8psprr/job_working_directory/000/11/outputs/dataset_3b05c54d-596b-48f7-bef8-8d7f8c097e9c.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 431910
total bases: 103339532
Q20 bases: 98448058(95.2666%)
Q30 bases: 90665113(87.7352%)

Read2 before filtering:
total reads: 431910
total bases: 103673219
Q20 bases: 96299323(92.8874%)
Q30 bases: 86164179(83.1113%)

Read1 after filtering:
total reads: 428069
total bases: 101962536
Q20 bases: 97637351(95.7581%)
Q30 bases: 90074901(88.3412%)

Read2 after filtering:
total reads: 428069
total bases: 101579408
Q20 bases: 95413124(93.9296%)
Q30 bases: 85630261(84.2988%)

Filtering result:
reads passed filter: 856138
reads failed due to low quality: 5036
reads failed due to too many N: 2646
reads failed due to too short: 0
reads with adapter trimmed: 45470
bases trimmed due to adapters: 1457892

Duplication rate: 5.81255%

Insert size peak (evaluated by paired-end reads): 243

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

fastp --thread 1 --report_title fastp report for 20L70.fastq.gz -i 20L70.fastq.gz -o first.fastq.gz -I 20L70_R2.fastq.gz -O second.fastq.gz 
fastp v0.23.4, time used: 18 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "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": null, "unqualified_percent_limit": null}}`
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": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 13: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpac8psprr/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpac8psprr/files/9/8/4/dataset_984ac1d5-a0eb-4266-8fdf-0dda81086d3a.dat' 'c2' T '/tmp/tmpac8psprr/job_working_directory/000/12/outputs/dataset_9007f7cf-3ef1-45b3-b760-b1df0e29eb50.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         max 3 < /tmp/tmpac8psprr/files/6/3/4/dataset_634e96b8-e760-4b0a-bda2-0f74f40839f4.dat > '/tmp/tmpac8psprr/job_working_directory/000/13/outputs/dataset_ed182bc8-0ce7-44ac-86d0-7fb7c25ba808.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "max"}]`
print_full_line	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         min 2 < /tmp/tmpac8psprr/files/6/4/5/dataset_645d26aa-52a1-451c-898f-fc73d771da12.dat > '/tmp/tmpac8psprr/job_working_directory/000/14/outputs/dataset_e865c067-92b1-4d64-99dd-76ec867164a3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "2", "op_name": "min"}]`
print_full_line	`false`

Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmpac8psprr/files/a/a/d/dataset_aad6a9d9-520a-4d63-96dd-2a251eaf962a.dat' --ftype 'txt' --chunksize 1 --file_names 'pool1_ids' --file_ext 'txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 10, "src": "hda"}]}, "newfilenames": "pool1_ids", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 17: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
input	`{"values": [{"id": 2, "src": "hdca"}]}`
sort_type	`{"__current_case__": 2, "sort_file": {"values": [{"id": 10, "src": "hda"}]}, "sort_type": "file"}`

Step 18: Get end position of sequence:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 19: Get end position of Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 20: Get start position of Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 3: PE Reads Pool1:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 22: fastp: Trimmed Illumina Reads Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmpac8psprr/files/d/8/9/dataset_d8904a06-42dd-48c7-af84-9d59acbfdd8a.dat' '20L70.fastq.gz' && ln -sf '/tmp/tmpac8psprr/files/9/1/e/dataset_91e1d775-4ba7-45f4-857f-003127e85905.dat' '20L70_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for 20L70.fastq.gz'   -i '20L70.fastq.gz' -o first.fastq.gz  -I '20L70_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpac8psprr/job_working_directory/000/20/outputs/dataset_80d2f41f-caeb-4812-90ac-2c724ac6f809.dat' && mv second.fastq.gz '/tmp/tmpac8psprr/job_working_directory/000/20/outputs/dataset_c61c6f46-75ad-4532-bab7-811e29b85f38.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 431020
total bases: 111607886
Q20 bases: 106858632(95.7447%)
Q30 bases: 98853807(88.5724%)

Read2 before filtering:
total reads: 431020
total bases: 112098904
Q20 bases: 102633048(91.5558%)
Q30 bases: 90203120(80.4674%)

Read1 after filtering:
total reads: 426304
total bases: 110015790
Q20 bases: 105819490(96.1857%)
Q30 bases: 98082203(89.1528%)

Read2 after filtering:
total reads: 426304
total bases: 109849805
Q20 bases: 101643068(92.5291%)
Q30 bases: 89610865(81.5758%)

Filtering result:
reads passed filter: 852608
reads failed due to low quality: 6648
reads failed due to too many N: 2784
reads failed due to too short: 0
reads with adapter trimmed: 42620
bases trimmed due to adapters: 1228807

Duplication rate: 3.87337%

Insert size peak (evaluated by paired-end reads): 300

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

fastp --thread 1 --report_title fastp report for 20L70.fastq.gz -i 20L70.fastq.gz -o first.fastq.gz -I 20L70_R2.fastq.gz -O second.fastq.gz 
fastp v0.23.4, time used: 19 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "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": null, "unqualified_percent_limit": null}}`
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": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 14, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "80202", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "-", "select_param_type": "text"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": "150773", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "1-", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "79081", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "20L70", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "_pool1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "20L70", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "_pool2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 27: Mask Reference for Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

maskseq -sequence '/tmp/tmpac8psprr/files/7/2/1/dataset_72124e4a-5ccf-40fa-b22f-efb0509044fa.dat' -outseq '/tmp/tmpac8psprr/job_working_directory/000/26/outputs/dataset_9610236a-2d35-4443-96c5-2507d46e0dfe.dat' -regions '80202-150773' -tolower no -maskchar 'N' -osformat2 fasta -auto

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
maskchar	`"N"`
out_format1	`"fasta"`
regions	`"80202-150773"`
tolower	`"no"`

Step 28: Mask Reference for Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

maskseq -sequence '/tmp/tmpac8psprr/files/7/2/1/dataset_72124e4a-5ccf-40fa-b22f-efb0509044fa.dat' -outseq '/tmp/tmpac8psprr/job_working_directory/000/27/outputs/dataset_013e69fe-5d29-4e9f-86fa-051f3c35d95c.dat' -regions '1-79081' -tolower no -maskchar 'N' -osformat2 fasta -auto

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
maskchar	`"N"`
out_format1	`"fasta"`
regions	`"1-79081"`
tolower	`"no"`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpac8psprr/files/9/6/1/dataset_9610236a-2d35-4443-96c5-2507d46e0dfe.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1                            -R '@RG\tID:20L70_pool1\tSM:20L70\tPL:ILLUMINA'   'localref.fa' '/tmp/tmpac8psprr/files/9/a/2/dataset_9a2f5627-4da0-4ad9-9a58-4c8912e8c085.dat' '/tmp/tmpac8psprr/files/3/b/0/dataset_3b05c54d-596b-48f7-bef8-8d7f8c097e9c.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpac8psprr/job_working_directory/000/28/outputs/dataset_e5eca77c-32d6-4435-8740-06a1a69157c5.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.03 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 0.048 sec; CPU: 0.041 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 254, 332)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 622)
[M::mem_pestat] mean and std.dev: (264.46, 106.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 767)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 330)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 614)
[M::mem_pestat] mean and std.dev: (263.11, 105.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 756)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 330)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 614)
[M::mem_pestat] mean and std.dev: (263.44, 105.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 756)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 252, 328)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 612)
[M::mem_pestat] mean and std.dev: (262.23, 106.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 754)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 252, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 613)
[M::mem_pestat] mean and std.dev: (263.09, 105.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 755)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 252, 330)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 616)
[M::mem_pestat] mean and std.dev: (262.68, 105.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 759)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 253, 328)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 608)
[M::mem_pestat] mean and std.dev: (262.66, 104.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 748)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 253, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 613)
[M::mem_pestat] mean and std.dev: (262.94, 106.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 755)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 253, 328)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 610)
[M::mem_pestat] mean and std.dev: (262.38, 104.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 751)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 251, 327)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 609)
[M::mem_pestat] mean and std.dev: (261.37, 104.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 750)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 253, 327)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 607)
[M::mem_pestat] mean and std.dev: (262.48, 104.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 747)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 255, 333)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 621)
[M::mem_pestat] mean and std.dev: (266.16, 106.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 765)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 256, 333)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 621)
[M::mem_pestat] mean and std.dev: (265.32, 105.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 765)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 253, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 621)
[M::mem_pestat] mean and std.dev: (264.05, 106.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 766)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 611)
[M::mem_pestat] mean and std.dev: (263.25, 105.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 752)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 617)
[M::mem_pestat] mean and std.dev: (264.45, 106.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 760)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 254, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 613)
[M::mem_pestat] mean and std.dev: (263.17, 105.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 755)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 255, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 615)
[M::mem_pestat] mean and std.dev: (264.95, 106.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 757)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 255, 330)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 612)
[M::mem_pestat] mean and std.dev: (264.09, 104.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 753)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 255, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 611)
[M::mem_pestat] mean and std.dev: (263.74, 104.69)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 752)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 617)
[M::mem_pestat] mean and std.dev: (264.49, 106.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 760)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -R @RG\tID:20L70_pool1\tSM:20L70\tPL:ILLUMINA localref.fa /tmp/tmpac8psprr/files/9/a/2/dataset_9a2f5627-4da0-4ad9-9a58-4c8912e8c085.dat /tmp/tmpac8psprr/files/3/b/0/dataset_3b05c54d-596b-48f7-bef8-8d7f8c097e9c.dat
[main] Real time: 96.583 sec; CPU: 95.454 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 7, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 31, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": "", "DS": "", "DT": "", "FO": "", "KS": "", "PG": "", "PI": null, "PL": "ILLUMINA", "PU": "", "__current_case__": 1, "read_group_id_conditional": {"ID": "20L70_pool1", "__current_case__": 1, "do_auto_name": false}, "read_group_lb_conditional": {"LB": "", "__current_case__": 1, "do_auto_name": false}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"}`

Step 30: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpac8psprr/files/0/1/3/dataset_013e69fe-5d29-4e9f-86fa-051f3c35d95c.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1                            -R '@RG\tID:20L70_pool2\tSM:20L70\tPL:ILLUMINA'   'localref.fa' '/tmp/tmpac8psprr/files/8/0/d/dataset_80d2f41f-caeb-4812-90ac-2c724ac6f809.dat' '/tmp/tmpac8psprr/files/c/6/1/dataset_c61c6f46-75ad-4532-bab7-811e29b85f38.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpac8psprr/job_working_directory/000/29/outputs/dataset_073ef7af-1482-49f6-a91d-211799072d09.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.03 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 0.051 sec; CPU: 0.043 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (224, 297, 381)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 695)
[M::mem_pestat] mean and std.dev: (306.39, 117.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 852)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (227, 298, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 683)
[M::mem_pestat] mean and std.dev: (307.71, 116.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 835)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 296, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (305.31, 116.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 298, 381)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 691)
[M::mem_pestat] mean and std.dev: (307.34, 117.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 846)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 297, 378)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 682)
[M::mem_pestat] mean and std.dev: (306.29, 116.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 834)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 297, 378)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 684)
[M::mem_pestat] mean and std.dev: (305.78, 116.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 837)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 297, 380)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 688)
[M::mem_pestat] mean and std.dev: (307.02, 116.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 842)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 295, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (304.90, 115.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (223, 294, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 685)
[M::mem_pestat] mean and std.dev: (303.81, 116.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 839)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (223, 295, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 691)
[M::mem_pestat] mean and std.dev: (305.70, 116.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 847)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (224, 296, 378)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 686)
[M::mem_pestat] mean and std.dev: (305.05, 115.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 840)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 297, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 687)
[M::mem_pestat] mean and std.dev: (306.81, 117.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 841)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 294, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (305.12, 115.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (227, 298, 380)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 686)
[M::mem_pestat] mean and std.dev: (307.28, 115.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 839)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (223, 296, 380)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 694)
[M::mem_pestat] mean and std.dev: (305.92, 117.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 851)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (224, 296, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 689)
[M::mem_pestat] mean and std.dev: (305.44, 116.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 844)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 296, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (305.37, 115.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 298, 381)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 691)
[M::mem_pestat] mean and std.dev: (307.86, 117.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 846)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (223, 295, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 685)
[M::mem_pestat] mean and std.dev: (304.43, 115.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 839)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (224, 296, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 689)
[M::mem_pestat] mean and std.dev: (305.95, 116.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 844)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 295, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 679)
[M::mem_pestat] mean and std.dev: (305.07, 115.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 830)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (227, 298, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 683)
[M::mem_pestat] mean and std.dev: (306.69, 115.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 835)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -R @RG\tID:20L70_pool2\tSM:20L70\tPL:ILLUMINA localref.fa /tmp/tmpac8psprr/files/8/0/d/dataset_80d2f41f-caeb-4812-90ac-2c724ac6f809.dat /tmp/tmpac8psprr/files/c/6/1/dataset_c61c6f46-75ad-4532-bab7-811e29b85f38.dat
[main] Real time: 107.316 sec; CPU: 106.112 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 15, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 32, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": "", "DS": "", "DT": "", "FO": "", "KS": "", "PG": "", "PI": null, "PL": "ILLUMINA", "PU": "", "__current_case__": 1, "read_group_id_conditional": {"ID": "20L70_pool2", "__current_case__": 1, "do_auto_name": false}, "read_group_lb_conditional": {"LB": "", "__current_case__": 1, "do_auto_name": false}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"}`

Step 4: PE Reads Pool2:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmpac8psprr/files/e/5/e/dataset_e5eca77c-32d6-4435-8740-06a1a69157c5.dat' infile && ln -s '/tmp/tmpac8psprr/files/_metadata_files/6/d/3/metadata_6d320d68-3ff5-4273-9c66-c9f244aa491c.dat' infile.bai &&               samtools view -@ $addthreads -b  -q 20 -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "20", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 32: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmpac8psprr/files/e/5/e/dataset_e5eca77c-32d6-4435-8740-06a1a69157c5.dat' infile && ln -s '/tmp/tmpac8psprr/files/_metadata_files/6/d/3/metadata_6d320d68-3ff5-4273-9c66-c9f244aa491c.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmpac8psprr/job_working_directory/000/31/outputs/dataset_57b2708b-fb3c-45b0-8eb1-87d3a6034296.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmpac8psprr/files/0/7/3/dataset_073ef7af-1482-49f6-a91d-211799072d09.dat' infile && ln -s '/tmp/tmpac8psprr/files/_metadata_files/8/8/1/metadata_8817dd26-9c5a-4a63-9068-fb297a34ad40.dat' infile.bai &&               samtools view -@ $addthreads -b  -q 20 -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "20", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 34: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmpac8psprr/files/0/7/3/dataset_073ef7af-1482-49f6-a91d-211799072d09.dat' infile && ln -s '/tmp/tmpac8psprr/files/_metadata_files/8/8/1/metadata_8817dd26-9c5a-4a63-9068-fb297a34ad40.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmpac8psprr/job_working_directory/000/33/outputs/dataset_901f346d-db4f-4d3a-a51e-27c6043077d6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpac8psprr/files/9/a/6/dataset_9a68621e-50f6-458c-9762-7d016ef391d5.dat' 'multiqc_WDir/fastp_0/20L70fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/20L70fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/samtools_1 &&    mkdir 'multiqc_WDir/samtools_1/stats_0' &&      grep -q 'This file was produced by samtools stats' /tmp/tmpac8psprr/files/5/7/b/dataset_57b2708b-fb3c-45b0-8eb1-87d3a6034296.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file '20L70'" && ln -s '/tmp/tmpac8psprr/files/5/7/b/dataset_57b2708b-fb3c-45b0-8eb1-87d3a6034296.dat' 'multiqc_WDir/samtools_1/stats_0/20L70'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25.1 now available!
       file_search | Search path: /tmp/tmpac8psprr/job_working_directory/000/34/working/multiqc_WDir

          samtools | Found 1 stats reports
             fastp | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1804
-rw-r--r-- 1 1001 127    8795 Oct  7 05:55 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 127    6804 Oct  7 05:55 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    6887 Oct  7 05:55 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    6689 Oct  7 05:55 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    6707 Oct  7 05:55 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127    4681 Oct  7 05:55 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    6283 Oct  7 05:55 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    4569 Oct  7 05:55 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    6096 Oct  7 05:55 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127    5488 Oct  7 05:55 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    5482 Oct  7 05:55 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    5477 Oct  7 05:55 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    5486 Oct  7 05:55 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127      67 Oct  7 05:55 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 127     183 Oct  7 05:55 multiqc_citations.txt
-rw-r--r-- 1 1001 127 1504400 Oct  7 05:55 multiqc_data.json
-rw-r--r-- 1 1001 127  193297 Oct  7 05:55 multiqc_fastp.txt
-rw-r--r-- 1 1001 127    1018 Oct  7 05:55 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    1360 Oct  7 05:55 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 127      51 Oct  7 05:55 multiqc_software_versions.txt
-rw-r--r-- 1 1001 127     263 Oct  7 05:55 multiqc_sources.txt
-rw-r--r-- 1 1001 127     313 Oct  7 05:55 samtools-stats-dp.txt
-rw-r--r-- 1 1001 127      53 Oct  7 05:55 samtools_alignment_plot.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 5, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 17, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}]`
saveLog	`"false"`
title	`""`

Step 36: __ZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "ef1e6020846f11ef97e37748175b9ce0"

Step 37: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpac8psprr/files/3/5/1/dataset_35103980-49cd-4025-9958-3ce184ea648f.dat' 'multiqc_WDir/fastp_0/20L70fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/20L70fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/samtools_1 &&    mkdir 'multiqc_WDir/samtools_1/stats_0' &&      grep -q 'This file was produced by samtools stats' /tmp/tmpac8psprr/files/9/0/1/dataset_901f346d-db4f-4d3a-a51e-27c6043077d6.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file '20L70'" && ln -s '/tmp/tmpac8psprr/files/9/0/1/dataset_901f346d-db4f-4d3a-a51e-27c6043077d6.dat' 'multiqc_WDir/samtools_1/stats_0/20L70'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25.1 now available!
       file_search | Search path: /tmp/tmpac8psprr/job_working_directory/000/36/working/multiqc_WDir

          samtools | Found 1 stats reports
             fastp | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1804
-rw-r--r-- 1 1001 127    8772 Oct  7 05:55 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 127    6871 Oct  7 05:55 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    6788 Oct  7 05:55 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    6854 Oct  7 05:55 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    6887 Oct  7 05:55 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127    4679 Oct  7 05:55 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    6226 Oct  7 05:55 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    4520 Oct  7 05:55 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    6173 Oct  7 05:55 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127    5475 Oct  7 05:55 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    5485 Oct  7 05:55 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    5488 Oct  7 05:55 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    5482 Oct  7 05:55 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127      67 Oct  7 05:55 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 127     183 Oct  7 05:55 multiqc_citations.txt
-rw-r--r-- 1 1001 127 1505724 Oct  7 05:55 multiqc_data.json
-rw-r--r-- 1 1001 127  193447 Oct  7 05:55 multiqc_fastp.txt
-rw-r--r-- 1 1001 127    1065 Oct  7 05:55 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    1380 Oct  7 05:55 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 127      51 Oct  7 05:55 multiqc_software_versions.txt
-rw-r--r-- 1 1001 127     263 Oct  7 05:55 multiqc_sources.txt
-rw-r--r-- 1 1001 127     328 Oct  7 05:55 samtools-stats-dp.txt
-rw-r--r-- 1 1001 127      60 Oct  7 05:55 samtools_alignment_plot.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 10, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 19, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}]`
saveLog	`"false"`
title	`""`

Step 38: __APPLY_RULES__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
input	`{"values": [{"id": 20, "src": "hdca"}]}`
rules	{"mapping": [{"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [0, 1], "connectable": true, "editing": false, "is_workflow": false, "type": "list_identifiers"}], "rules": [{"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier1", "warn": null}]}

Step 39: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&  ln -s '/tmp/tmpac8psprr/files/8/7/a/dataset_87a91260-1fc9-4099-b25b-51d8a0f4009b.dat' 0.sam && ln -s '/tmp/tmpac8psprr/files/0/5/2/dataset_0527d826-2aee-4ac5-8a03-4a80986d9145.dat' 1.sam && samtools merge -@ $addthreads -s 1 -f  -p /tmp/tmpac8psprr/job_working_directory/000/38/outputs/dataset_57fadcd5-988b-48a9-8f30-8c7f2f29f443.dat 0.sam 1.sam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
bed_file	`None`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
headerbam	`None`
idpg	`true`
idrg	`false`
region	`""`
seed	`"1"`

Step 40: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

export JAVA_OPTS="-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m" &&    ln -s '/tmp/tmpac8psprr/files/5/7/f/dataset_57fadcd5-988b-48a9-8f30-8c7f2f29f443.dat' '20L70' &&  qualimap bamqc -bam '20L70' -outdir results -outformat html --collect-overlap-pairs -nw 400 --paint-chromosome-limits -hm 3  --skip-duplicated --skip-dup-mode 0 -nt ${GALAXY_SLOTS:-1} &&   sed 's|images_qualimapReport/||g;s|css/||g' results/qualimapReport.html > '/tmp/tmpac8psprr/job_working_directory/000/39/outputs/dataset_cc6db014-4190-4ed4-abb0-011bfb598fdf.dat' && mkdir '/tmp/tmpac8psprr/job_working_directory/000/39/outputs/dataset_cc6db014-4190-4ed4-abb0-011bfb598fdf_files' && mv results/css/*.css '/tmp/tmpac8psprr/job_working_directory/000/39/outputs/dataset_cc6db014-4190-4ed4-abb0-011bfb598fdf_files' && mv results/css/*.png '/tmp/tmpac8psprr/job_working_directory/000/39/outputs/dataset_cc6db014-4190-4ed4-abb0-011bfb598fdf_files' && if [ -d results/images_qualimapReport ]; then mv results/images_qualimapReport/* '/tmp/tmpac8psprr/job_working_directory/000/39/outputs/dataset_cc6db014-4190-4ed4-abb0-011bfb598fdf_files' && for file in $(ls -A results/raw_data_qualimapReport); do mv "results/raw_data_qualimapReport/$file" `echo "results/$file" | sed 's/(//;s/)//'`; done fi && mv results/genome_results.txt results/summary_report.txt

Exit Code:

```
0
```

Standard Output:

Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx1024m
QualiMap v.2.3
Built on 2023-05-19 16:57

Selected tool: bamqc
Available memory (Mb): 253
Max memory (Mb): 1037
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 400
Chunk of reads size: 1000
Number of threads: 1
Processed 50 out of 400 windows...
Processed 100 out of 400 windows...
Processed 150 out of 400 windows...
Processed 200 out of 400 windows...
Processed 250 out of 400 windows...
Processed 300 out of 400 windows...
Processed 350 out of 400 windows...
Processed 400 out of 400 windows...
Total processed windows:400
Number of reads: 1652137
Number of valid reads: 1652591
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 1652137
Num mapped first of pair: 826067
Num mapped second of pair: 826070
Num singletons: 0
Time taken to analyze reads: 49
Computing descriptors...
numberOfMappedBases: 407862885
referenceSize: 150773
numberOfSequencedBases: 407679920
numberOfAs: 144219774
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 51
end of bam qc
Computing report...
Writing HTML report...
HTML report created successfully

Finished

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicate_skipping	`["0"]`
per_base_coverage	`false`
plot_specific	`{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": true}`
stats_regions	`{"__current_case__": 0, "region_select": "all"}`

Step 5: Minimum quality score to call base:
- step_state: scheduled

Step 41: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpac8psprr/files/6/3/6/dataset_6368f117-d379-4387-beb6-482d0576ba0a.dat' bed.bed && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/sanitize_bed.py' bed.bed && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/write_amplicon_info_file.py' bed.bed amplicon_info_raw.tsv && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/prepare_amplicon_info.py' bed.bed amplicon_info_raw.tsv amplicon_info.tsv && ln -s '/tmp/tmpac8psprr/files/5/7/f/dataset_57fadcd5-988b-48a9-8f30-8c7f2f29f443.dat' sorted.bam && ln -s '/tmp/tmpac8psprr/files/_metadata_files/a/8/9/metadata_a89a7388-e36b-4932-a7ec-7add141dcf8c.dat' sorted.bam.bai &&  ivar trim -i sorted.bam -b bed.bed -f amplicon_info.tsv -x 0 -e -m -1 -q 20 -s 4 | samtools sort -@ ${GALAXY_SLOTS:-1} -T "${TMPDIR:-.}" -o trimmed.sorted.bam -

Exit Code:

```
0
```

Standard Error:

Found 46 primers in BED file
Amplicons detected: 
[235, 7801] max = 150538
[6789, 14482] max = 150538
[13515, 21229] max = 150538
[20192, 27814] max = 150538
[26787, 34395] max = 150538
[33277, 40897] max = 150538
[39894, 47453] max = 150538
[46393, 54069] max = 150538
[52864, 60559] max = 150538
[59439, 66989] max = 150538
[66008, 73601] max = 150538
[72534, 80202] max = 150538
[79081, 86781] max = 150538
[85743, 93351] max = 150538
[92208, 100000] max = 150538
[98974, 106612] max = 150538
[105634, 113144] max = 150538
[112082, 119675] max = 150538
[118617, 126328] max = 150538
[125361, 132988] max = 150538
[131713, 139365] max = 150538
[138437, 146219] max = 150538
[143117, 150538] max = 150538
Reading from sorted.bam
Minimum Read Length based on 1000 reads: 124
Processed 1000000 reads ... 

-------
Results: 
Primer Name	Read Count
CaPV-V1_1_LEFT	164
CaPV-V1_2_LEFT	538
CaPV-V1_1_RIGHT	1656
CaPV-V1_3_LEFT	148
CaPV-V1_2_RIGHT	1971
CaPV-V1_4_LEFT	294
CaPV-V1_3_RIGHT	1951
CaPV-V1_5_LEFT	166
CaPV-V1_4_RIGHT	1856
CaPV-V1_6_LEFT	3453
CaPV-V1_5_RIGHT	224
CaPV-V1_7_LEFT	507
CaPV-V1_6_RIGHT	222
CaPV-V1_8_LEFT	396
CaPV-V1_7_RIGHT	91
CaPV-V1_9_LEFT	80
CaPV-V1_8_RIGHT	461
CaPV-V1_10_LEFT	88
CaPV-V1_9_RIGHT	373
CaPV-V1_11_LEFT	478
CaPV-V1_10_RIGHT	132
CaPV-V1_12_LEFT	1210
CaPV-V1_11_RIGHT	442
CaPV-V1_13_LEFT	1247
CaPV-V1_12_RIGHT	671
CaPV-V1_14_LEFT	375
CaPV-V1_13_RIGHT	187
CaPV-V1_15_LEFT	313
CaPV-V1_14_RIGHT	105
CaPV-V1_16_LEFT	83
CaPV-V1_15_RIGHT	401
CaPV-V1_17_LEFT	85
CaPV-V1_16_RIGHT	131
CaPV-V1_18_LEFT	473
CaPV-V1_17_RIGHT	3575
CaPV-V1a_19_LEFT	518
CaPV-V1_18_RIGHT	97
CaPV-V1_20_LEFT	1659
CaPV-V1_19_RIGHT	2221
CaPV-V1_21_LEFT	297
CaPV-V1_20_RIGHT	278
CaPV-V1_22_LEFT	590
CaPV-V1_21_RIGHT	297
CaPV-V1_23_LEFT	237
CaPV-V1_22_RIGHT	731
CaPV-V1_23_RIGHT	277

Trimmed primers from 1.92% (31749) of reads.
12.02% (198671) of reads were quality trimmed below the minimum length of 124 bp and were not written to file.
86.36% (1427241) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.
0% (12) reads were ignored because they did not fall within an amplicon
57.87% (956350) of reads had their insert size smaller than their read length

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
amplicons	`{"__current_case__": 0, "filter_by": "yes_compute"}`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inc_primers	`true`
min_len	`"30"`
min_qual	`"20"`
primer	`{"__current_case__": 0, "input_bed": {"values": [{"id": 2, "src": "hda"}]}, "source": "history"}`
primer_pos_wiggle	`"0"`
trimmed_length	`{"__current_case__": 1, "filter": "auto"}`
window_width	`"4"`

Step 42: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "ef1e6020846f11ef97e37748175b9ce0"
      
      input {"values": [{"id": 37, "src": "dce"}]}

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpac8psprr/files/f/d/2/dataset_fd2bfca5-0c6d-4af3-8f56-7bfd760297e2.dat' sorted.bam && samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus -p consensus -q 20 -t 0.7 -c 0.8 -m 50 -n N && sed -i "s|consensus|20L70|" consensus.fa

Exit Code:

```
0
```

Standard Error:

[mpileup] 1 samples in 1 input files
[mpileup] Max depth set to maximum value (2147483647)

Standard Output:

Minimum Quality: 20
Threshold: 0.7
Minimum depth: 50
Minimum Insert Threshold: 0.8
Regions with depth less than minimum depth covered by: N
Reference length: 150773
Positions with 0 depth: 532
Positions with depth below 50: 532

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
depth_action	`"-n N"`
min_depth	`"50"`
min_freq	`"0.7"`
min_indel_freq	`"0.8"`
min_qual	`"20"`

Step 44: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "ef1e6020846f11ef97e37748175b9ce0"
      
      input {"values": [{"id": 28, "src": "hdca"}]}
      
      join_identifier "_"

Step 45: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmpac8psprr/job_working_directory/000/42/configs/tmp2ifk24e9' '/tmp/tmpac8psprr/files/e/f/b/dataset_efb9fe32-8e8e-4b4f-9e8b-7729acfda541.dat' > '/tmp/tmpac8psprr/job_working_directory/000/42/outputs/dataset_8b607dad-9cb2-40fd-980f-07e74540a177.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^>/s/Consensus_(.)_threshold_./\\1/"`
dbkey	`"?"`

Step 46: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/qualimap_0 &&  sample="$(grep 'bam file = ' /tmp/tmpac8psprr/files/3/2/3/dataset_3239a30b-4ef5-4eb5-8db6-216a19804c3d.dat | sed 's/bam file = //g' | sed 's: ::g')" && dir_name="multiqc_WDir/qualimap_0/${sample}" && mkdir -p ${dir_name} && filepath_1="${dir_name}/genome_results.txt" && ln -sf '/tmp/tmpac8psprr/files/3/2/3/dataset_3239a30b-4ef5-4eb5-8db6-216a19804c3d.dat' ${filepath_1} && nested_dir_name="${dir_name}/raw_data_qualimapReport/" && mkdir -p ${nested_dir_name} && filepath_2="${nested_dir_name}/coverage_histogram.txt" && ln -sf '/tmp/tmpac8psprr/files/0/e/6/dataset_0e656a91-c49e-460d-80b2-5def0be3b4d9.dat' ${filepath_2} && nested_dir_name="${dir_name}/raw_data_qualimapReport/" && mkdir -p ${nested_dir_name} && filepath_3="${nested_dir_name}/mapped_reads_gc-content_distribution.txt" && ln -sf '/tmp/tmpac8psprr/files/7/b/7/dataset_7b74a9d0-3b0a-4863-9b32-cc5b3ac18b3a.dat' ${filepath_3} &&   multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25.1 now available!
       file_search | Search path: /tmp/tmpac8psprr/job_working_directory/000/46/working/multiqc_WDir

          qualimap | Found 1 BamQC reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete
cp: cannot stat './report_data/*plot*.txt': No such file or directory

Standard Output:

total 284
-rw-r--r-- 1 1001 127    186 Oct  7 05:56 multiqc_citations.txt
-rw-r--r-- 1 1001 127 247688 Oct  7 05:56 multiqc_data.json
-rw-r--r-- 1 1001 127    900 Oct  7 05:56 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    324 Oct  7 05:56 multiqc_qualimap_bamqc_genome_results.txt
-rw-r--r-- 1 1001 127    519 Oct  7 05:56 multiqc_sources.txt
-rw-r--r-- 1 1001 127   8119 Oct  7 05:56 qualimap_coverage_histogram.txt
-rw-r--r-- 1 1001 127   1962 Oct  7 05:56 qualimap_gc_content.txt
-rw-r--r-- 1 1001 127  12175 Oct  7 05:56 qualimap_genome_fraction.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 20, "input": {"values": [{"id": 29, "src": "hdca"}]}, "software": "qualimap"}}]`
saveLog	`"false"`
title	`""`

Step 47: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpac8psprr/files/8/b/6/dataset_8b607dad-9cb2-40fd-980f-07e74540a177.dat' >> '/tmp/tmpac8psprr/job_working_directory/000/43/outputs/dataset_1007a2c2-7fb3-4ff5-ab03-eba044d22450.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

Step 6: Allele frequency to call SNV:
- step_state: scheduled
Step 7: Allele frequency to call indel:
- step_state: scheduled

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/5cbde03c1103/fasta_compute_length/fasta_compute_length.py' '/tmp/tmpac8psprr/files/7/2/1/dataset_72124e4a-5ccf-40fa-b22f-efb0509044fa.dat' '/tmp/tmpac8psprr/job_working_directory/000/7/outputs/dataset_984ac1d5-a0eb-4266-8fdf-0dda81086d3a.dat' 0 id_and_desc

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref	`{"__current_case__": 0, "input": {"values": [{"id": 1, "src": "hda"}]}, "keep_first": "0", "keep_first_word": false, "ref_source": "history"}`

Step 9: Select pool1 primers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -eo pipefail; cat '/tmp/tmpac8psprr/files/6/3/6/dataset_6368f117-d379-4387-beb6-482d0576ba0a.dat' | grep -P -f '/tmp/tmpac8psprr/job_working_directory/000/8/configs/tmpj56l3g_k'  >> '/tmp/tmpac8psprr/job_working_directory/000/8/outputs/dataset_634e96b8-e760-4b0a-bda2-0f74f40839f4.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	` "[p

Step 10: Select pool2 primers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -eo pipefail; cat '/tmp/tmpac8psprr/files/6/3/6/dataset_6368f117-d379-4387-beb6-482d0576ba0a.dat' | grep -P -f '/tmp/tmpac8psprr/job_working_directory/000/9/configs/tmp4crqmxxa'  >> '/tmp/tmpac8psprr/job_working_directory/000/9/outputs/dataset_645d26aa-52a1-451c-898f-fc73d771da12.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ef1e6020846f11ef97e37748175b9ce0"`
chromInfo	`"/tmp/tmpac8psprr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	` "[p

Other invocation details
- history_id
  - f435fb66d097b1a9
- history_state
  - ok
- invocation_id
  - f435fb66d097b1a9
- invocation_state
  - scheduled
- workflow_id
  - f435fb66d097b1a9

gxydevbot · 2024-10-21T05:24:10Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-10-21T05:42:50Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ pox-virus-half-genome.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Reference FASTA:
- step_state: scheduled
Step 2: Primer Scheme:
- step_state: scheduled

Step 11: 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/tmpt3zbjqgd/job_working_directory/000/10/configs/tmpyw497ruo' '/tmp/tmpt3zbjqgd/job_working_directory/000/10/outputs/dataset_479c42b9-5c1b-46f0-8cc7-ddea1fb8f7f3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 12: fastp: Trimmed Illumina Reads Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmpt3zbjqgd/files/7/b/e/dataset_7bedec47-5a7a-4b83-83eb-144d7b0757a1.dat' '20L70.fastqsanger.gz' && ln -sf '/tmp/tmpt3zbjqgd/files/d/5/0/dataset_d503d791-52c6-4087-bcf3-168410daa24f.dat' '20L70_R2.fastqsanger.gz' &&  cp '/tmp/tmpt3zbjqgd/job_working_directory/000/11/configs/tmp19rvw9n6' galaxy.json &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for 20L70.fastqsanger.gz'   -i '20L70.fastqsanger.gz'   -I '20L70_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmpt3zbjqgd/job_working_directory/000/11/outputs/dataset_8315942c-d63a-47d9-a6bb-4c153910b5e3.dat' && mv second.fastqsanger.gz '/tmp/tmpt3zbjqgd/job_working_directory/000/11/outputs/dataset_a69129d2-d92f-408a-9631-c64ad0651844.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 431910
total bases: 103339532
Q20 bases: 98448058(95.2666%)
Q30 bases: 90665113(87.7352%)

Read2 before filtering:
total reads: 431910
total bases: 103673219
Q20 bases: 96299323(92.8874%)
Q30 bases: 86164179(83.1113%)

Read1 after filtering:
total reads: 428069
total bases: 101962536
Q20 bases: 97637351(95.7581%)
Q30 bases: 90074901(88.3412%)

Read2 after filtering:
total reads: 428069
total bases: 101579408
Q20 bases: 95413124(93.9296%)
Q30 bases: 85630261(84.2988%)

Filtering result:
reads passed filter: 856138
reads failed due to low quality: 5036
reads failed due to too many N: 2646
reads failed due to too short: 0
reads with adapter trimmed: 45470
bases trimmed due to adapters: 1457892

Duplication rate: 5.81255%

Insert size peak (evaluated by paired-end reads): 243

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

fastp --thread 1 --report_title fastp report for 20L70.fastqsanger.gz -i 20L70.fastqsanger.gz -I 20L70_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz 
fastp v0.23.4, time used: 19 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "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": null, "unqualified_percent_limit": null}}`
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": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 13: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpt3zbjqgd/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpt3zbjqgd/files/0/4/3/dataset_043bf2f2-1c31-42e9-b30a-b4dc3c4a732d.dat' 'c2' T '/tmp/tmpt3zbjqgd/job_working_directory/000/12/outputs/dataset_3fb2be9a-c893-41d3-94c1-999e2d427394.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         max 3 < /tmp/tmpt3zbjqgd/files/d/e/a/dataset_dea12fd7-6b6e-4d46-b201-26e91f3839c0.dat > '/tmp/tmpt3zbjqgd/job_working_directory/000/13/outputs/dataset_614b4bda-3178-48d9-8876-b551d3576425.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "max"}]`
print_full_line	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         min 2 < /tmp/tmpt3zbjqgd/files/3/e/c/dataset_3ec79b76-e566-458e-ab8a-166666d75d67.dat > '/tmp/tmpt3zbjqgd/job_working_directory/000/14/outputs/dataset_df4f4276-4d24-4cb0-ac4c-a038140727d4.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "2", "op_name": "min"}]`
print_full_line	`false`

Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmpt3zbjqgd/files/4/7/9/dataset_479c42b9-5c1b-46f0-8cc7-ddea1fb8f7f3.dat' --ftype 'txt' --chunksize 1 --file_names 'pool1_ids' --file_ext 'txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 10, "src": "hda"}]}, "newfilenames": "pool1_ids", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 17: __SORTLIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
input	`{"values": [{"id": 2, "src": "hdca"}]}`
sort_type	`{"__current_case__": 2, "sort_file": {"values": [{"id": 10, "src": "hda"}]}, "sort_type": "file"}`

Step 18: Get end position of sequence:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 19: Get end position of Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 20: Get start position of Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bed"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 3: PE Reads Pool1:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 22: fastp: Trimmed Illumina Reads Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmpt3zbjqgd/files/d/d/e/dataset_dde698c8-d86f-4273-8c25-6cd844e23d10.dat' '20L70.fastqsanger.gz' && ln -sf '/tmp/tmpt3zbjqgd/files/d/4/9/dataset_d4925a6d-0064-440e-92a7-0d9efa032b85.dat' '20L70_R2.fastqsanger.gz' &&  cp '/tmp/tmpt3zbjqgd/job_working_directory/000/20/configs/tmp2ax5o55a' galaxy.json &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for 20L70.fastqsanger.gz'   -i '20L70.fastqsanger.gz'   -I '20L70_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmpt3zbjqgd/job_working_directory/000/20/outputs/dataset_c667287f-96ee-4140-a2b0-4e2f7cb6c5cd.dat' && mv second.fastqsanger.gz '/tmp/tmpt3zbjqgd/job_working_directory/000/20/outputs/dataset_2218abb5-a1b0-41e2-84ab-d3c75bf1f2e9.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 431020
total bases: 111607886
Q20 bases: 106858632(95.7447%)
Q30 bases: 98853807(88.5724%)

Read2 before filtering:
total reads: 431020
total bases: 112098904
Q20 bases: 102633048(91.5558%)
Q30 bases: 90203120(80.4674%)

Read1 after filtering:
total reads: 426304
total bases: 110015790
Q20 bases: 105819490(96.1857%)
Q30 bases: 98082203(89.1528%)

Read2 after filtering:
total reads: 426304
total bases: 109849805
Q20 bases: 101643068(92.5291%)
Q30 bases: 89610865(81.5758%)

Filtering result:
reads passed filter: 852608
reads failed due to low quality: 6648
reads failed due to too many N: 2784
reads failed due to too short: 0
reads with adapter trimmed: 42620
bases trimmed due to adapters: 1228807

Duplication rate: 3.87337%

Insert size peak (evaluated by paired-end reads): 300

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

fastp --thread 1 --report_title fastp report for 20L70.fastqsanger.gz -i 20L70.fastqsanger.gz -I 20L70_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz 
fastp v0.23.4, time used: 20 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "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": null, "unqualified_percent_limit": null}}`
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": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 14, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "80202", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "-", "select_param_type": "text"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": "150773", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "1-", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "79081", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "20L70", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "_pool1", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "20L70", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "_pool2", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 27: Mask Reference for Pool1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

maskseq -sequence '/tmp/tmpt3zbjqgd/files/1/6/a/dataset_16adfa79-0bae-4550-b9e1-156a0ac99204.dat' -outseq '/tmp/tmpt3zbjqgd/job_working_directory/000/26/outputs/dataset_b6446359-1889-41ae-afff-18e4f602201c.dat' -regions '80202-150773' -tolower no -maskchar 'N' -osformat2 fasta -auto

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
maskchar	`"N"`
out_format1	`"fasta"`
regions	`"80202-150773"`
tolower	`"no"`

Step 28: Mask Reference for Pool2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

maskseq -sequence '/tmp/tmpt3zbjqgd/files/1/6/a/dataset_16adfa79-0bae-4550-b9e1-156a0ac99204.dat' -outseq '/tmp/tmpt3zbjqgd/job_working_directory/000/27/outputs/dataset_cb07840c-a749-46f5-bae9-6a0ee3a50e53.dat' -regions '1-79081' -tolower no -maskchar 'N' -osformat2 fasta -auto

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
maskchar	`"N"`
out_format1	`"fasta"`
regions	`"1-79081"`
tolower	`"no"`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpt3zbjqgd/files/b/6/4/dataset_b6446359-1889-41ae-afff-18e4f602201c.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1                            -R '@RG\tID:20L70_pool1\tSM:20L70\tPL:ILLUMINA'   'localref.fa' '/tmp/tmpt3zbjqgd/files/8/3/1/dataset_8315942c-d63a-47d9-a6bb-4c153910b5e3.dat' '/tmp/tmpt3zbjqgd/files/a/6/9/dataset_a69129d2-d92f-408a-9631-c64ad0651844.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpt3zbjqgd/job_working_directory/000/28/outputs/dataset_164a42bb-d854-43a1-b771-67f355b9f020.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 0.037 sec; CPU: 0.032 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 254, 332)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 622)
[M::mem_pestat] mean and std.dev: (264.46, 106.78)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 767)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 330)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 614)
[M::mem_pestat] mean and std.dev: (263.11, 105.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 756)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 330)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 614)
[M::mem_pestat] mean and std.dev: (263.44, 105.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 756)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 252, 328)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 612)
[M::mem_pestat] mean and std.dev: (262.23, 106.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 754)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 252, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 613)
[M::mem_pestat] mean and std.dev: (263.09, 105.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 755)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 252, 330)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 616)
[M::mem_pestat] mean and std.dev: (262.68, 105.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 759)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 253, 328)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 608)
[M::mem_pestat] mean and std.dev: (262.66, 104.88)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 748)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 253, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 613)
[M::mem_pestat] mean and std.dev: (262.94, 106.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 755)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 253, 328)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 610)
[M::mem_pestat] mean and std.dev: (262.38, 104.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 751)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 251, 327)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 609)
[M::mem_pestat] mean and std.dev: (261.37, 104.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 750)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 253, 327)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 607)
[M::mem_pestat] mean and std.dev: (262.48, 104.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 747)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 255, 333)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 621)
[M::mem_pestat] mean and std.dev: (266.16, 106.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 765)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 256, 333)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 621)
[M::mem_pestat] mean and std.dev: (265.32, 105.81)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 765)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 253, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 621)
[M::mem_pestat] mean and std.dev: (264.05, 106.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 766)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 611)
[M::mem_pestat] mean and std.dev: (263.25, 105.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 752)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 617)
[M::mem_pestat] mean and std.dev: (264.45, 106.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 760)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (187, 254, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 613)
[M::mem_pestat] mean and std.dev: (263.17, 105.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 755)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 255, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 615)
[M::mem_pestat] mean and std.dev: (264.95, 106.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 757)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (189, 255, 330)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 612)
[M::mem_pestat] mean and std.dev: (264.09, 104.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 753)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 255, 329)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 611)
[M::mem_pestat] mean and std.dev: (263.74, 104.69)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 752)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 254, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 617)
[M::mem_pestat] mean and std.dev: (264.49, 106.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 760)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -R @RG\tID:20L70_pool1\tSM:20L70\tPL:ILLUMINA localref.fa /tmp/tmpt3zbjqgd/files/8/3/1/dataset_8315942c-d63a-47d9-a6bb-4c153910b5e3.dat /tmp/tmpt3zbjqgd/files/a/6/9/dataset_a69129d2-d92f-408a-9631-c64ad0651844.dat
[main] Real time: 90.664 sec; CPU: 89.464 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 7, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 31, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": "", "DS": "", "DT": "", "FO": "", "KS": "", "PG": "", "PI": null, "PL": "ILLUMINA", "PU": "", "__current_case__": 1, "read_group_id_conditional": {"ID": "20L70_pool1", "__current_case__": 1, "do_auto_name": false}, "read_group_lb_conditional": {"LB": "", "__current_case__": 1, "do_auto_name": false}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"}`

Step 30: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpt3zbjqgd/files/c/b/0/dataset_cb07840c-a749-46f5-bae9-6a0ee3a50e53.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1                            -R '@RG\tID:20L70_pool2\tSM:20L70\tPL:ILLUMINA'   'localref.fa' '/tmp/tmpt3zbjqgd/files/c/6/6/dataset_c667287f-96ee-4140-a2b0-4e2f7cb6c5cd.dat' '/tmp/tmpt3zbjqgd/files/2/2/1/dataset_2218abb5-a1b0-41e2-84ab-d3c75bf1f2e9.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpt3zbjqgd/job_working_directory/000/29/outputs/dataset_66e0235a-04e4-4d14-9bce-a000bc6cfded.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 0.041 sec; CPU: 0.036 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (224, 297, 381)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 695)
[M::mem_pestat] mean and std.dev: (306.39, 117.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 852)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (227, 298, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 683)
[M::mem_pestat] mean and std.dev: (307.71, 116.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 835)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 296, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (305.31, 116.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 298, 381)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 691)
[M::mem_pestat] mean and std.dev: (307.34, 117.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 846)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 297, 378)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 682)
[M::mem_pestat] mean and std.dev: (306.29, 116.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 834)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 297, 378)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 684)
[M::mem_pestat] mean and std.dev: (305.78, 116.22)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 837)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 297, 380)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 688)
[M::mem_pestat] mean and std.dev: (307.02, 116.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 842)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 295, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (304.90, 115.32)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (223, 294, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 685)
[M::mem_pestat] mean and std.dev: (303.81, 116.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 839)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (223, 295, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 691)
[M::mem_pestat] mean and std.dev: (305.70, 116.14)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 847)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (224, 296, 378)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 686)
[M::mem_pestat] mean and std.dev: (305.05, 115.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 840)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 297, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 687)
[M::mem_pestat] mean and std.dev: (306.81, 117.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 841)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 294, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (305.12, 115.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (227, 298, 380)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 686)
[M::mem_pestat] mean and std.dev: (307.28, 115.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 839)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (223, 296, 380)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 694)
[M::mem_pestat] mean and std.dev: (305.92, 117.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 851)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (224, 296, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 689)
[M::mem_pestat] mean and std.dev: (305.44, 116.27)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 844)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (225, 296, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (305.37, 115.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 298, 381)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 691)
[M::mem_pestat] mean and std.dev: (307.86, 117.75)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 846)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (223, 295, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 685)
[M::mem_pestat] mean and std.dev: (304.43, 115.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 839)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (224, 296, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 689)
[M::mem_pestat] mean and std.dev: (305.95, 116.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 844)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (226, 295, 377)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 679)
[M::mem_pestat] mean and std.dev: (305.07, 115.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 830)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (227, 298, 379)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 683)
[M::mem_pestat] mean and std.dev: (306.69, 115.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 835)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -R @RG\tID:20L70_pool2\tSM:20L70\tPL:ILLUMINA localref.fa /tmp/tmpt3zbjqgd/files/c/6/6/dataset_c667287f-96ee-4140-a2b0-4e2f7cb6c5cd.dat /tmp/tmpt3zbjqgd/files/2/2/1/dataset_2218abb5-a1b0-41e2-84ab-d3c75bf1f2e9.dat
[main] Real time: 106.731 sec; CPU: 105.493 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 15, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 32, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": "", "DS": "", "DT": "", "FO": "", "KS": "", "PG": "", "PI": null, "PL": "ILLUMINA", "PU": "", "__current_case__": 1, "read_group_id_conditional": {"ID": "20L70_pool2", "__current_case__": 1, "do_auto_name": false}, "read_group_lb_conditional": {"LB": "", "__current_case__": 1, "do_auto_name": false}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"}`

Step 4: PE Reads Pool2:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmpt3zbjqgd/files/1/6/4/dataset_164a42bb-d854-43a1-b771-67f355b9f020.dat' infile && ln -s '/tmp/tmpt3zbjqgd/files/_metadata_files/e/3/2/metadata_e326b755-1825-4604-a8d2-730b1b1601f1.dat' infile.bai &&               samtools view -@ $addthreads -b  -q 20 -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "20", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 32: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmpt3zbjqgd/files/1/6/4/dataset_164a42bb-d854-43a1-b771-67f355b9f020.dat' infile && ln -s '/tmp/tmpt3zbjqgd/files/_metadata_files/e/3/2/metadata_e326b755-1825-4604-a8d2-730b1b1601f1.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmpt3zbjqgd/job_working_directory/000/31/outputs/dataset_778087ee-7f19-4d4e-9754-fb0a9030c7a5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmpt3zbjqgd/files/6/6/e/dataset_66e0235a-04e4-4d14-9bce-a000bc6cfded.dat' infile && ln -s '/tmp/tmpt3zbjqgd/files/_metadata_files/a/f/b/metadata_afb24db5-0b1f-4287-a7c3-edbc86a38020.dat' infile.bai &&               samtools view -@ $addthreads -b  -q 20 -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "20", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 34: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmpt3zbjqgd/files/6/6/e/dataset_66e0235a-04e4-4d14-9bce-a000bc6cfded.dat' infile && ln -s '/tmp/tmpt3zbjqgd/files/_metadata_files/a/f/b/metadata_afb24db5-0b1f-4287-a7c3-edbc86a38020.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmpt3zbjqgd/job_working_directory/000/33/outputs/dataset_7c8512a9-db4b-4a56-a809-ef2d6c85f5f4.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpt3zbjqgd/files/f/d/c/dataset_fdc90fe2-6ca3-4576-b45b-1cc47badb999.dat' 'multiqc_WDir/fastp_0/20L70fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/20L70fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/samtools_1 &&    mkdir 'multiqc_WDir/samtools_1/stats_0' &&      grep -q 'This file was produced by samtools stats' /tmp/tmpt3zbjqgd/files/7/7/8/dataset_778087ee-7f19-4d4e-9754-fb0a9030c7a5.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file '20L70'" && ln -s '/tmp/tmpt3zbjqgd/files/7/7/8/dataset_778087ee-7f19-4d4e-9754-fb0a9030c7a5.dat' 'multiqc_WDir/samtools_1/stats_0/20L70'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25.1 now available!
       file_search | Search path: /tmp/tmpt3zbjqgd/job_working_directory/000/34/working/multiqc_WDir

          samtools | Found 1 stats reports
             fastp | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1804
-rw-r--r-- 1 1001 127    8795 Oct 21 05:39 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 127    6804 Oct 21 05:39 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    6887 Oct 21 05:39 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    6689 Oct 21 05:39 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    6707 Oct 21 05:39 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127    4681 Oct 21 05:39 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    6283 Oct 21 05:39 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    4569 Oct 21 05:39 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    6096 Oct 21 05:39 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127    5488 Oct 21 05:39 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    5482 Oct 21 05:39 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    5477 Oct 21 05:39 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    5486 Oct 21 05:39 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127      67 Oct 21 05:39 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 127     183 Oct 21 05:39 multiqc_citations.txt
-rw-r--r-- 1 1001 127 1504430 Oct 21 05:39 multiqc_data.json
-rw-r--r-- 1 1001 127  193327 Oct 21 05:39 multiqc_fastp.txt
-rw-r--r-- 1 1001 127    1018 Oct 21 05:39 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    1360 Oct 21 05:39 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 127      51 Oct 21 05:39 multiqc_software_versions.txt
-rw-r--r-- 1 1001 127     263 Oct 21 05:39 multiqc_sources.txt
-rw-r--r-- 1 1001 127     313 Oct 21 05:39 samtools-stats-dp.txt
-rw-r--r-- 1 1001 127      53 Oct 21 05:39 samtools_alignment_plot.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 5, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 17, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}]`
saveLog	`"false"`
title	`""`

Step 36: __ZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "325ff7dc8f6e11ef92196f8305ca002a"

Step 37: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpt3zbjqgd/files/f/a/b/dataset_fabb3257-382e-433e-adf7-15e482ca996e.dat' 'multiqc_WDir/fastp_0/20L70fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/20L70fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/samtools_1 &&    mkdir 'multiqc_WDir/samtools_1/stats_0' &&      grep -q 'This file was produced by samtools stats' /tmp/tmpt3zbjqgd/files/7/c/8/dataset_7c8512a9-db4b-4a56-a809-ef2d6c85f5f4.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file '20L70'" && ln -s '/tmp/tmpt3zbjqgd/files/7/c/8/dataset_7c8512a9-db4b-4a56-a809-ef2d6c85f5f4.dat' 'multiqc_WDir/samtools_1/stats_0/20L70'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25.1 now available!
       file_search | Search path: /tmp/tmpt3zbjqgd/job_working_directory/000/36/working/multiqc_WDir

          samtools | Found 1 stats reports
             fastp | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1804
-rw-r--r-- 1 1001 127    8772 Oct 21 05:39 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 127    6871 Oct 21 05:39 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    6788 Oct 21 05:39 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    6854 Oct 21 05:39 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    6887 Oct 21 05:39 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127    4679 Oct 21 05:39 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    6226 Oct 21 05:39 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    4520 Oct 21 05:39 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    6173 Oct 21 05:39 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127    5475 Oct 21 05:39 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127    5485 Oct 21 05:39 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127    5488 Oct 21 05:39 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127    5482 Oct 21 05:39 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127      67 Oct 21 05:39 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 127     183 Oct 21 05:39 multiqc_citations.txt
-rw-r--r-- 1 1001 127 1505754 Oct 21 05:39 multiqc_data.json
-rw-r--r-- 1 1001 127  193477 Oct 21 05:39 multiqc_fastp.txt
-rw-r--r-- 1 1001 127    1065 Oct 21 05:39 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    1380 Oct 21 05:39 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 127      51 Oct 21 05:39 multiqc_software_versions.txt
-rw-r--r-- 1 1001 127     263 Oct 21 05:39 multiqc_sources.txt
-rw-r--r-- 1 1001 127     328 Oct 21 05:39 samtools-stats-dp.txt
-rw-r--r-- 1 1001 127      60 Oct 21 05:39 samtools_alignment_plot.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 10, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 19, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}]`
saveLog	`"false"`
title	`""`

Step 38: __APPLY_RULES__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
input	`{"values": [{"id": 20, "src": "hdca"}]}`
rules	{"mapping": [{"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [0, 1], "connectable": true, "editing": false, "is_workflow": false, "type": "list_identifiers"}], "rules": [{"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier1", "warn": null}]}

Step 39: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&  ln -s '/tmp/tmpt3zbjqgd/files/2/1/1/dataset_211bd6b1-267f-4d1c-8adc-9f841e2ca94d.dat' 0.sam && ln -s '/tmp/tmpt3zbjqgd/files/3/a/c/dataset_3ac510e9-7b59-495b-86b4-d84cca1d57f7.dat' 1.sam && samtools merge -@ $addthreads -s 1 -f  -p /tmp/tmpt3zbjqgd/job_working_directory/000/38/outputs/dataset_5b3a49c8-af5d-4b81-ba9c-5d5c2cc2b7a1.dat 0.sam 1.sam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
bed_file	`None`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
headerbam	`None`
idpg	`true`
idrg	`false`
region	`""`
seed	`"1"`

Step 40: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

export JAVA_OPTS="-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m" &&    ln -s '/tmp/tmpt3zbjqgd/files/5/b/3/dataset_5b3a49c8-af5d-4b81-ba9c-5d5c2cc2b7a1.dat' '20L70' &&  qualimap bamqc -bam '20L70' -outdir results -outformat html --collect-overlap-pairs -nw 400 --paint-chromosome-limits -hm 3  --skip-duplicated --skip-dup-mode 0 -nt ${GALAXY_SLOTS:-1} &&   sed 's|images_qualimapReport/||g;s|css/||g' results/qualimapReport.html > '/tmp/tmpt3zbjqgd/job_working_directory/000/39/outputs/dataset_7c5c4590-9dce-4d67-84f0-6ad4fe809245.dat' && mkdir '/tmp/tmpt3zbjqgd/job_working_directory/000/39/outputs/dataset_7c5c4590-9dce-4d67-84f0-6ad4fe809245_files' && mv results/css/*.css '/tmp/tmpt3zbjqgd/job_working_directory/000/39/outputs/dataset_7c5c4590-9dce-4d67-84f0-6ad4fe809245_files' && mv results/css/*.png '/tmp/tmpt3zbjqgd/job_working_directory/000/39/outputs/dataset_7c5c4590-9dce-4d67-84f0-6ad4fe809245_files' && if [ -d results/images_qualimapReport ]; then mv results/images_qualimapReport/* '/tmp/tmpt3zbjqgd/job_working_directory/000/39/outputs/dataset_7c5c4590-9dce-4d67-84f0-6ad4fe809245_files' && for file in $(ls -A results/raw_data_qualimapReport); do mv "results/raw_data_qualimapReport/$file" `echo "results/$file" | sed 's/(//;s/)//'`; done fi && mv results/genome_results.txt results/summary_report.txt

Exit Code:

```
0
```

Standard Output:

Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx1024m
QualiMap v.2.3
Built on 2023-05-19 16:57

Selected tool: bamqc
Available memory (Mb): 253
Max memory (Mb): 1037
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 400
Chunk of reads size: 1000
Number of threads: 1
Processed 50 out of 400 windows...
Processed 100 out of 400 windows...
Processed 150 out of 400 windows...
Processed 200 out of 400 windows...
Processed 250 out of 400 windows...
Processed 300 out of 400 windows...
Processed 350 out of 400 windows...
Processed 400 out of 400 windows...
Total processed windows:400
Number of reads: 1652137
Number of valid reads: 1652591
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 1652137
Num mapped first of pair: 826067
Num mapped second of pair: 826070
Num singletons: 0
Time taken to analyze reads: 47
Computing descriptors...
numberOfMappedBases: 407862885
referenceSize: 150773
numberOfSequencedBases: 407679920
numberOfAs: 144219774
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 48
end of bam qc
Computing report...
Writing HTML report...
HTML report created successfully

Finished

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicate_skipping	`["0"]`
per_base_coverage	`false`
plot_specific	`{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": true}`
stats_regions	`{"__current_case__": 0, "region_select": "all"}`

Step 5: Minimum quality score to call base:
- step_state: scheduled

Step 41: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpt3zbjqgd/files/1/b/6/dataset_1b6704a6-a9ea-4e67-8452-c3e60e9a762c.dat' bed.bed && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/sanitize_bed.py' bed.bed && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/write_amplicon_info_file.py' bed.bed amplicon_info_raw.tsv && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/prepare_amplicon_info.py' bed.bed amplicon_info_raw.tsv amplicon_info.tsv && ln -s '/tmp/tmpt3zbjqgd/files/5/b/3/dataset_5b3a49c8-af5d-4b81-ba9c-5d5c2cc2b7a1.dat' sorted.bam && ln -s '/tmp/tmpt3zbjqgd/files/_metadata_files/5/3/0/metadata_5302f5c1-9863-4ea1-ae85-379b8d7aebe2.dat' sorted.bam.bai &&  ivar trim -i sorted.bam -b bed.bed -f amplicon_info.tsv -x 0 -e -m -1 -q 20 -s 4 | samtools sort -@ ${GALAXY_SLOTS:-1} -T "${TMPDIR:-.}" -o trimmed.sorted.bam -

Exit Code:

```
0
```

Standard Error:

Found 46 primers in BED file
Amplicons detected: 
[235, 7801] max = 150538
[6789, 14482] max = 150538
[13515, 21229] max = 150538
[20192, 27814] max = 150538
[26787, 34395] max = 150538
[33277, 40897] max = 150538
[39894, 47453] max = 150538
[46393, 54069] max = 150538
[52864, 60559] max = 150538
[59439, 66989] max = 150538
[66008, 73601] max = 150538
[72534, 80202] max = 150538
[79081, 86781] max = 150538
[85743, 93351] max = 150538
[92208, 100000] max = 150538
[98974, 106612] max = 150538
[105634, 113144] max = 150538
[112082, 119675] max = 150538
[118617, 126328] max = 150538
[125361, 132988] max = 150538
[131713, 139365] max = 150538
[138437, 146219] max = 150538
[143117, 150538] max = 150538
Reading from sorted.bam
Minimum Read Length based on 1000 reads: 124
Processed 1000000 reads ... 

-------
Results: 
Primer Name	Read Count
CaPV-V1_1_LEFT	164
CaPV-V1_2_LEFT	538
CaPV-V1_1_RIGHT	1656
CaPV-V1_3_LEFT	148
CaPV-V1_2_RIGHT	1971
CaPV-V1_4_LEFT	294
CaPV-V1_3_RIGHT	1951
CaPV-V1_5_LEFT	166
CaPV-V1_4_RIGHT	1856
CaPV-V1_6_LEFT	3453
CaPV-V1_5_RIGHT	224
CaPV-V1_7_LEFT	507
CaPV-V1_6_RIGHT	222
CaPV-V1_8_LEFT	396
CaPV-V1_7_RIGHT	91
CaPV-V1_9_LEFT	80
CaPV-V1_8_RIGHT	461
CaPV-V1_10_LEFT	88
CaPV-V1_9_RIGHT	373
CaPV-V1_11_LEFT	478
CaPV-V1_10_RIGHT	132
CaPV-V1_12_LEFT	1210
CaPV-V1_11_RIGHT	442
CaPV-V1_13_LEFT	1247
CaPV-V1_12_RIGHT	671
CaPV-V1_14_LEFT	375
CaPV-V1_13_RIGHT	187
CaPV-V1_15_LEFT	313
CaPV-V1_14_RIGHT	105
CaPV-V1_16_LEFT	83
CaPV-V1_15_RIGHT	401
CaPV-V1_17_LEFT	85
CaPV-V1_16_RIGHT	131
CaPV-V1_18_LEFT	473
CaPV-V1_17_RIGHT	3575
CaPV-V1a_19_LEFT	518
CaPV-V1_18_RIGHT	97
CaPV-V1_20_LEFT	1659
CaPV-V1_19_RIGHT	2221
CaPV-V1_21_LEFT	297
CaPV-V1_20_RIGHT	278
CaPV-V1_22_LEFT	590
CaPV-V1_21_RIGHT	297
CaPV-V1_23_LEFT	237
CaPV-V1_22_RIGHT	731
CaPV-V1_23_RIGHT	277

Trimmed primers from 1.92% (31749) of reads.
12.02% (198671) of reads were quality trimmed below the minimum length of 124 bp and were not written to file.
86.36% (1427241) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.
0% (12) reads were ignored because they did not fall within an amplicon
57.87% (956350) of reads had their insert size smaller than their read length

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
amplicons	`{"__current_case__": 0, "filter_by": "yes_compute"}`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inc_primers	`true`
min_len	`"30"`
min_qual	`"20"`
primer	`{"__current_case__": 0, "input_bed": {"values": [{"id": 2, "src": "hda"}]}, "source": "history"}`
primer_pos_wiggle	`"0"`
trimmed_length	`{"__current_case__": 1, "filter": "auto"}`
window_width	`"4"`

Step 42: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "325ff7dc8f6e11ef92196f8305ca002a"
      
      input {"values": [{"id": 37, "src": "dce"}]}

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpt3zbjqgd/files/e/5/7/dataset_e57e6821-8d7c-41e5-9030-13b00f64f04c.dat' sorted.bam && samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus -p consensus -q 20 -t 0.7 -c 0.8 -m 50 -n N && sed -i "s|consensus|20L70|" consensus.fa

Exit Code:

```
0
```

Standard Error:

[mpileup] 1 samples in 1 input files
[mpileup] Max depth set to maximum value (2147483647)

Standard Output:

Minimum Quality: 20
Threshold: 0.7
Minimum depth: 50
Minimum Insert Threshold: 0.8
Regions with depth less than minimum depth covered by: N
Reference length: 150773
Positions with 0 depth: 532
Positions with depth below 50: 532

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
depth_action	`"-n N"`
min_depth	`"50"`
min_freq	`"0.7"`
min_indel_freq	`"0.8"`
min_qual	`"20"`

Step 44: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "325ff7dc8f6e11ef92196f8305ca002a"
      
      input {"values": [{"id": 28, "src": "hdca"}]}
      
      join_identifier "_"

Step 45: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmpt3zbjqgd/job_working_directory/000/42/configs/tmp2jtcyt2c' '/tmp/tmpt3zbjqgd/files/6/1/a/dataset_61afaac9-62d4-40ed-920b-0023e85051bf.dat' > '/tmp/tmpt3zbjqgd/job_working_directory/000/42/outputs/dataset_7b3d8827-fdba-4dce-b232-62254a40ad69.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^>/s/Consensus_(.)_threshold_./\\1/"`
dbkey	`"?"`

Step 46: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/qualimap_0 &&  sample="$(grep 'bam file = ' /tmp/tmpt3zbjqgd/files/6/7/7/dataset_6771fe28-fbd3-4b2b-ab6f-1040e1ac87bd.dat | sed 's/bam file = //g' | sed 's: ::g')" && dir_name="multiqc_WDir/qualimap_0/${sample}" && mkdir -p ${dir_name} && filepath_1="${dir_name}/genome_results.txt" && ln -sf '/tmp/tmpt3zbjqgd/files/6/7/7/dataset_6771fe28-fbd3-4b2b-ab6f-1040e1ac87bd.dat' ${filepath_1} && nested_dir_name="${dir_name}/raw_data_qualimapReport/" && mkdir -p ${nested_dir_name} && filepath_2="${nested_dir_name}/coverage_histogram.txt" && ln -sf '/tmp/tmpt3zbjqgd/files/9/9/7/dataset_997944d3-a89c-4003-8a88-82ce2ca643a9.dat' ${filepath_2} && nested_dir_name="${dir_name}/raw_data_qualimapReport/" && mkdir -p ${nested_dir_name} && filepath_3="${nested_dir_name}/mapped_reads_gc-content_distribution.txt" && ln -sf '/tmp/tmpt3zbjqgd/files/7/6/0/dataset_76072557-ce6a-4ddc-9e05-be123ef56da0.dat' ${filepath_3} &&   multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25.1 now available!
       file_search | Search path: /tmp/tmpt3zbjqgd/job_working_directory/000/46/working/multiqc_WDir

          qualimap | Found 1 BamQC reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete
cp: cannot stat './report_data/*plot*.txt': No such file or directory

Standard Output:

total 284
-rw-r--r-- 1 1001 127    186 Oct 21 05:41 multiqc_citations.txt
-rw-r--r-- 1 1001 127 247688 Oct 21 05:41 multiqc_data.json
-rw-r--r-- 1 1001 127    900 Oct 21 05:41 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    324 Oct 21 05:41 multiqc_qualimap_bamqc_genome_results.txt
-rw-r--r-- 1 1001 127    519 Oct 21 05:41 multiqc_sources.txt
-rw-r--r-- 1 1001 127   8119 Oct 21 05:41 qualimap_coverage_histogram.txt
-rw-r--r-- 1 1001 127   1962 Oct 21 05:41 qualimap_gc_content.txt
-rw-r--r-- 1 1001 127  12175 Oct 21 05:41 qualimap_genome_fraction.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 20, "input": {"values": [{"id": 29, "src": "hdca"}]}, "software": "qualimap"}}]`
saveLog	`"false"`
title	`""`

Step 47: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpt3zbjqgd/files/7/b/3/dataset_7b3d8827-fdba-4dce-b232-62254a40ad69.dat' >> '/tmp/tmpt3zbjqgd/job_working_directory/000/43/outputs/dataset_f164eea5-099a-414b-8199-4d80d1a72dec.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

Step 6: Allele frequency to call SNV:
- step_state: scheduled
Step 7: Allele frequency to call indel:
- step_state: scheduled

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/5cbde03c1103/fasta_compute_length/fasta_compute_length.py' '/tmp/tmpt3zbjqgd/files/1/6/a/dataset_16adfa79-0bae-4550-b9e1-156a0ac99204.dat' '/tmp/tmpt3zbjqgd/job_working_directory/000/7/outputs/dataset_043bf2f2-1c31-42e9-b30a-b4dc3c4a732d.dat' 0 id_and_desc

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref	`{"__current_case__": 0, "input": {"values": [{"id": 1, "src": "hda"}]}, "keep_first": "0", "keep_first_word": false, "ref_source": "history"}`

Step 9: Select pool1 primers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -eo pipefail; cat '/tmp/tmpt3zbjqgd/files/1/b/6/dataset_1b6704a6-a9ea-4e67-8452-c3e60e9a762c.dat' | grep -P -f '/tmp/tmpt3zbjqgd/job_working_directory/000/8/configs/tmpsxhtseqt'  >> '/tmp/tmpt3zbjqgd/job_working_directory/000/8/outputs/dataset_dea12fd7-6b6e-4d46-b201-26e91f3839c0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	` "[p

Step 10: Select pool2 primers:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -eo pipefail; cat '/tmp/tmpt3zbjqgd/files/1/b/6/dataset_1b6704a6-a9ea-4e67-8452-c3e60e9a762c.dat' | grep -P -f '/tmp/tmpt3zbjqgd/job_working_directory/000/9/configs/tmp33yk4gzu'  >> '/tmp/tmpt3zbjqgd/job_working_directory/000/9/outputs/dataset_3ec79b76-e566-458e-ab8a-166666d75d67.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"325ff7dc8f6e11ef92196f8305ca002a"`
chromInfo	`"/tmp/tmpt3zbjqgd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	` "[p

Other invocation details
- history_id
  - 67afc6ab1f7612be
- history_state
  - ok
- invocation_id
  - 67afc6ab1f7612be
- invocation_state
  - scheduled
- workflow_id
  - 67afc6ab1f7612be

bgruening previously approved these changes Jul 1, 2024

View reviewed changes

wm75 requested changes Jul 1, 2024

View reviewed changes

gxydevbot changed the title ~~Updating workflows/virology/pox-virus-amplicon from 0.2 to 0.3~~ Updating workflows/virology/pox-virus-amplicon from 0.2 to 0.3 Jul 15, 2024

gxydevbot dismissed bgruening’s stale review via 19ab3b9 July 15, 2024 04:56

gxydevbot force-pushed the workflows/virology/pox-virus-amplicon branch from 19ab3b9 to f59122a Compare September 23, 2024 14:59

gxydevbot force-pushed the workflows/virology/pox-virus-amplicon branch from f59122a to 9fe8701 Compare September 24, 2024 14:35

gxydevbot force-pushed the workflows/virology/pox-virus-amplicon branch from 9fe8701 to c7faa99 Compare October 7, 2024 05:36

Updating workflows/virology/pox-virus-amplicon from 0.2 to 0.3

2ee0471

gxydevbot force-pushed the workflows/virology/pox-virus-amplicon branch from c7faa99 to 2ee0471 Compare October 21, 2024 05:24

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Updating workflows/virology/pox-virus-amplicon from 0.2 to 0.3 #462

Updating workflows/virology/pox-virus-amplicon from 0.2 to 0.3 #462

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

Updating workflows/virology/pox-virus-amplicon from 0.2 to 0.3 #462

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Updating workflows/virology/pox-virus-amplicon from 0.2 to 0.3 #462

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Workflow invocation details

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Test Results (powered by Planemo)

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Workflow invocation details

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Test Results (powered by Planemo)

Test Summary

Workflow invocation details