Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 to 0.1.6 #305

gxydevbot · 2023-11-27T21:39:10Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/chemteam/md_converter/md_converter/1.9.6+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.7+galaxy0

The workflow release number has been updated from 0.1.5 to 0.1.6.

…to 0.1.6

…to 0.1.7

…to 0.1.8

…to 0.1.9

…to 0.1.10

… to 0.1.11

… to 0.1.12

… to 0.1.13

… to 0.1.14

… to 0.1.15

… to 0.1.16

… to 0.1.17

… to 0.1.18

… to 0.1.19

… to 0.1.20

…gbsa

… to 0.1.21

…to 0.1.7

…to 0.1.8

…to 0.1.9

…to 0.1.10

… to 0.1.11

… to 0.1.12

… to 0.1.13

… to 0.1.14

… to 0.1.15

… to 0.1.16

… to 0.1.17

… to 0.1.18

… to 0.1.19

… to 0.1.20

… to 0.1.21

github-actions · 2024-06-17T04:38:06Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ gromacs-mmgbsa.ga_0

Execution Problem:

Final state of invocation 1def5d18cc38e9eb is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 12 requires a dataset created by step 7, but dataset entered a failed state.

Steps

Step 1: Salt concentration:
- step_state: scheduled
Step 2: Number of simulations:
- step_state: scheduled

Step 11: 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__	`"034e01fa2c6311ef88e03bf34557171e"`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 2, "component_value": "0.1", "select_param_type": "float"}}]`
dbkey	`"?"`

Step 12: Unlabelled step:

step_state: new

Subworkflow Steps

Step 1: Ligand SDF:
- step_state: scheduled
Step 2: pH:
- step_state: scheduled

Step 11: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"034e01fb2c6311ef88e03bf34557171e"`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 12: Unlabelled step:
- step_state: new
Step 13: Unlabelled step:
- step_state: new
Step 14: Unlabelled step:
- step_state: new
Step 3: Apoprotein PDB:
- step_state: scheduled
Step 4: Water model:
- step_state: scheduled
Step 5: Force field:
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/ctb_rdkit_descriptors/2020.03.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/0993ac4f4a23/ctb_rdkit_descriptors/rdkit_descriptors.py' -i '/tmp/tmp_zdaiuyi/files/5/d/b/dataset_5dba5f2d-e982-4db3-a76c-0a647093ed89.dat' --iformat 'sdf' -o '/tmp/tmp_zdaiuyi/job_working_directory/000/4/outputs/dataset_a18d3aee-df1a-49c1-9c99-779f7f120201.dat' -s 'FormalCharge'

Exit Code:

```
0
```

Standard Error:

[04:36:43] ERROR: End of data field name not found
[04:36:43] ERROR: moving to the beginning of the next molecule

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sdf"`
__workflow_invocation_uuid__	`"034e01fb2c6311ef88e03bf34557171e"`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
select_multiple	`["FormalCharge"]`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

obabel -i 'sdf'  '/tmp/tmp_zdaiuyi/files/5/d/b/dataset_5dba5f2d-e982-4db3-a76c-0a647093ed89.dat' -o 'pdb' -O '/tmp/tmp_zdaiuyi/job_working_directory/000/5/outputs/dataset_89b0699e-18e9-4909-b1fb-16673c25d9a1.dat' -e

Exit Code:

```
0
```

Standard Error:

```
1 molecule converted
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sdf"`
__workflow_invocation_uuid__	`"034e01fb2c6311ef88e03bf34557171e"`
appendtotitle	`""`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dative_bonds	`false`
dbkey	`"?"`
oformat	`{"__current_case__": 51, "oformat_opts_selector": "pdb"}`
ph	`"-1.0"`
remove_h	`false`
split	`false`
unique	`{"__current_case__": 0, "unique_opts_selector": ""}`

Step 8: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp_zdaiuyi/files/a/0/c/dataset_a0cddb5c-bd42-4ebd-a057-f759233a35b4.dat' ./pdb_input.pdb && gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water tip3p -ff amber99sb -noignh -merge all &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"pqr"`
__workflow_invocation_uuid__	`"034e01fb2c6311ef88e03bf34557171e"`
capture_log	`true`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ff	`"amber99sb"`
ignore_h	`false`
water	`"tip3p"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

perl '/tmp/tmp_zdaiuyi/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp_zdaiuyi/files/a/1/8/dataset_a18d3aee-df1a-49c1-9c99-779f7f120201.dat' 'c2' T '/tmp/tmp_zdaiuyi/job_working_directory/000/7/outputs/dataset_de0c61e2-0d68-43d4-833d-8032e305042b.dat'

Exit Code:

```
125
```

Standard Error:

Unable to find image 'quay.io/biocontainers/perl:5.26' locally
5.26: Pulling from biocontainers/perl
docker: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/perl:5.26 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/.
See 'docker run --help'.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"034e01fb2c6311ef88e03bf34557171e"`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator  -i -- 'HETATM' '/tmp/tmp_zdaiuyi/files/8/9/b/dataset_89b0699e-18e9-4909-b1fb-16673c25d9a1.dat' > '/tmp/tmp_zdaiuyi/job_working_directory/000/8/outputs/dataset_f11754ed-c9cc-4d3b-9ff1-31ffb66fda73.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"034e01fb2c6311ef88e03bf34557171e"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"HETATM"`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=2; yes -- '0.1' 2>/dev/null | head -n $times >> '/tmp/tmp_zdaiuyi/job_working_directory/000/10/outputs/dataset_e9454074-7e22-40b3-b1f0-1d46e1eeabb9.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"034e01fa2c6311ef88e03bf34557171e"`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "0.1", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "2"}}]`

Step 14: Unlabelled step:
- step_state: new

Step 15: 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 error

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/tmp_zdaiuyi/files/e/9/4/dataset_e9454074-7e22-40b3-b1f0-1d46e1eeabb9.dat' --ftype 'txt' --chunksize 1 --file_names 'split_file' --file_ext 'txt'

Exit Code:

```
125
```

Standard Error:

Unable to find image 'quay.io/biocontainers/python:3.5' locally
3.5: Pulling from biocontainers/python
docker: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/python:3.5 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/.
See 'docker run --help'.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"034e01fa2c6311ef88e03bf34557171e"`
chromInfo	`"/tmp/tmp_zdaiuyi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 13, "src": "hda"}]}, "newfilenames": "split_file", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 16: Unlabelled step:
- step_state: scheduled
Step 17: Unlabelled step:
- step_state: new
Step 18: Unlabelled step:
- step_state: new
Step 19: Unlabelled step:
- step_state: new
Step 20: Unlabelled step:
- step_state: new
Step 3: Apoprotein PDB:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 25: Unlabelled step:
- step_state: new
Step 26: Unlabelled step:
- step_state: new
Step 27: Unlabelled step:
- step_state: new
Step 28: Unlabelled step:
- step_state: new
Step 4: Water model:
- step_state: scheduled
Step 5: pH:
- step_state: scheduled
Step 6: Force field:
- step_state: scheduled
Step 7: Ligand SDF:
- step_state: scheduled
Step 8: NVT equilibration steps:
- step_state: scheduled
Step 9: NPT equilibration steps:
- step_state: scheduled
Step 10: Production steps:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 1def5d18cc38e9eb is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - 1def5d18cc38e9eb
- history_state
  - error
- invocation_id
  - 1def5d18cc38e9eb
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 6, 'hda_id': 'e411f036ab1c3361', 'reason': 'dataset_failed', 'workflow_step_id': 11}]
- workflow_id
  - 624124eebc3108e9

… to 0.1.22

… to 0.1.23

… to 0.1.24

workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga

mvdbeek

Drop inputs additions. Need to check out why Galaxy thinks these are disconnected ...

workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga

…to 0.1.7

…to 0.1.8

…to 0.1.9

…to 0.1.10

github-actions · 2024-07-29T04:34:54Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ gromacs-mmgbsa.ga_0

Execution Problem:

Final state of invocation bf6069c0fa995563 is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 12 requires a dataset created by step 7, but dataset entered a failed state.

Steps

Step 1: Salt concentration:
- step_state: scheduled
Step 2: Number of simulations:
- step_state: scheduled

Step 11: 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__	`"a16a4e864d6311efad3e7b5ae8e10c29"`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 2, "component_value": "0.1", "select_param_type": "float"}}]`
dbkey	`"?"`

Step 12: Unlabelled step:

step_state: new

Subworkflow Steps

Step 1: Ligand SDF:
- step_state: scheduled
Step 2: pH:
- step_state: scheduled

Step 11: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"a16a4e874d6311efad3e7b5ae8e10c29"`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 12: Unlabelled step:
- step_state: new
Step 13: Unlabelled step:
- step_state: new
Step 14: Unlabelled step:
- step_state: new
Step 3: Apoprotein PDB:
- step_state: scheduled
Step 4: Water model:
- step_state: scheduled
Step 5: Force field:
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/ctb_rdkit_descriptors/2020.03.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/0993ac4f4a23/ctb_rdkit_descriptors/rdkit_descriptors.py' -i '/tmp/tmpswonut2s/files/3/6/3/dataset_3639637f-7e6f-4be4-881c-7075a6585d4a.dat' --iformat 'sdf' -o '/tmp/tmpswonut2s/job_working_directory/000/4/outputs/dataset_c5a797d5-2f45-40e5-a67f-1fd27f6e0bba.dat' -s 'FormalCharge'

Exit Code:

```
1
```

Standard Error:

Traceback (most recent call last):
  File "/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/0993ac4f4a23/ctb_rdkit_descriptors/rdkit_descriptors.py", line 7, in <module>
    from rdkit import Chem
ModuleNotFoundError: No module named 'rdkit'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sdf"`
__workflow_invocation_uuid__	`"a16a4e874d6311efad3e7b5ae8e10c29"`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
select_multiple	`["FormalCharge"]`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

obabel -i 'sdf'  '/tmp/tmpswonut2s/files/3/6/3/dataset_3639637f-7e6f-4be4-881c-7075a6585d4a.dat' -o 'pdb' -O '/tmp/tmpswonut2s/job_working_directory/000/5/outputs/dataset_f135f085-d75d-4143-963e-3872171d0327.dat' -e

Exit Code:

```
127
```

Standard Error:

/tmp/tmpswonut2s/job_working_directory/000/5/tool_script.sh: line 9: obabel: command not found

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sdf"`
__workflow_invocation_uuid__	`"a16a4e874d6311efad3e7b5ae8e10c29"`
appendtotitle	`""`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dative_bonds	`false`
dbkey	`"?"`
oformat	`{"__current_case__": 51, "oformat_opts_selector": "pdb"}`
ph	`"-1.0"`
remove_h	`false`
split	`false`
unique	`{"__current_case__": 0, "unique_opts_selector": ""}`

Step 8: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/tmp/tmpswonut2s/files/0/d/6/dataset_0d6b466b-49ff-4c62-ba3e-6488344722cd.dat' ./pdb_input.pdb && gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water tip3p -ff amber99sb -noignh -merge all &>> verbose.txt

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"pqr"`
__workflow_invocation_uuid__	`"a16a4e874d6311efad3e7b5ae8e10c29"`
capture_log	`true`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ff	`"amber99sb"`
ignore_h	`false`
water	`"tip3p"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"a16a4e874d6311efad3e7b5ae8e10c29"`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a16a4e874d6311efad3e7b5ae8e10c29"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"HETATM"`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=2; yes -- '0.1' 2>/dev/null | head -n $times >> '/tmp/tmpswonut2s/job_working_directory/000/10/outputs/dataset_33b445e9-8d5f-4859-84f3-e7ff1409b007.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a16a4e864d6311efad3e7b5ae8e10c29"`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "0.1", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "2"}}]`

Step 14: Unlabelled step:
- step_state: new

Step 15: 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/tmpswonut2s/files/3/3/b/dataset_33b445e9-8d5f-4859-84f3-e7ff1409b007.dat' --ftype 'txt' --chunksize 1 --file_names 'split_file' --file_ext 'txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"a16a4e864d6311efad3e7b5ae8e10c29"`
chromInfo	`"/tmp/tmpswonut2s/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 13, "src": "hda"}]}, "newfilenames": "split_file", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 16: Unlabelled step:
- step_state: new
Step 17: Unlabelled step:
- step_state: new
Step 18: Unlabelled step:
- step_state: new
Step 19: Unlabelled step:
- step_state: new
Step 20: Unlabelled step:
- step_state: new
Step 3: Apoprotein PDB:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 25: Unlabelled step:
- step_state: new
Step 26: Unlabelled step:
- step_state: new
Step 27: Unlabelled step:
- step_state: new
Step 28: Unlabelled step:
- step_state: new
Step 4: Water model:
- step_state: scheduled
Step 5: pH:
- step_state: scheduled
Step 6: Force field:
- step_state: scheduled
Step 7: Ligand SDF:
- step_state: scheduled
Step 8: NVT equilibration steps:
- step_state: scheduled
Step 9: NPT equilibration steps:
- step_state: scheduled
Step 10: Production steps:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation bf6069c0fa995563 is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - 3f697dfaf89b2701
- history_state
  - error
- invocation_id
  - 3f697dfaf89b2701
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 6, 'hda_id': '64a8949b0a9bad02', 'reason': 'dataset_failed', 'workflow_step_id': 11}]
- workflow_id
  - bf6069c0fa995563

… to 0.1.11

… to 0.1.12

lldelisle · 2024-09-24T12:36:48Z

If someone look at this PR, would it be possible to incorporate:
https://github.com/galaxyproject/iwc/pull/530/files#diff-6cb346aaf5b88d9a286d77f4a0873f79b7e62441127cc22c09c6411a4cfcb68f

bgruening · 2024-09-24T20:47:08Z

Something is strange here. toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0 was not updated.

I will close this one and will try to get a new one :)

lldelisle · 2024-09-24T20:49:35Z

This is one of the workflows that autoupdate command raises an error. I guess someone needs to do it manually, a parameter may have changed names.

github-actions · 2024-09-24T21:00:35Z

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ gromacs-mmgbsa.ga_0

Problems:

Output with path /tmp/tmpaeuz71w7/MMGBSA statistics__48bbd3e5-a2d8-4cc5-922e-67a894414d42 different than expected
Expected text 'Generalized Born ESURF calculated using LCPO' in output ('| Run on Tue Sep 24 20:58:44 2024
|
|Input file:
|--------------------------------------------------------------
|# Template for mmpbsa in Galaxy
|#  
|&general
|startframe=1, endframe=9999999, interval=10,
|verbose=2, keep_files=1, strip_mask=:NA,CL,SOL, use_sander=0, entropy=0, netcdf=1
|/
|&gb
|igb=5, saltcon=0.1, surfoff=0.0, molsurf=0, probe=1.4, msoffset=0.0
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file:  /tmp/tmp3wfahwpn/files/b/f/d/dataset_bfd22eba-e286-4f1c-8097-359f00e491c4.dat
|Complex topology file:           /tmp/tmp3wfahwpn/files/9/c/2/dataset_9c249e90-ee37-4ee3-8964-1c778e828b8c.dat
|Receptor topology file:          /tmp/tmp3wfahwpn/files/6/c/5/dataset_6c5a3dbf-01b0-4182-b1bf-5a3fa90e3e8e.dat
|Ligand topology file:            /tmp/tmp3wfahwpn/files/3/2/4/dataset_32471799-0fb5-4542-8129-c06e23807bea.dat
|Initial mdcrd(s):                /tmp/tmp3wfahwpn/files/5/9/e/dataset_59e788e6-667d-447b-8c85-cdb810726760.dat
|
|Receptor mask:                  ":1-304"
|Ligand mask:                    ":305"
|Ligand residue name is "UNL"
|
|Calculations performed using 1.0 complex frames.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------

GENERALIZED BORN:

Complex:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
BOND                       520.8303                0.0000              0.0000
ANGLE                     1400.3898                0.0000              0.0000
DIHED                     2926.7943                0.0000              0.0000
VDWAALS                  -2515.1887                0.0000              0.0000
EEL                     -21333.6154                0.0000              0.0000
1-4 VDW                   1046.7673                0.0000              0.0000
1-4 EEL                  11898.9341                0.0000              0.0000
EGB                      -2577.1999                0.0000              0.0000
ESURF                       98.9912                0.0000              0.0000

G gas                    -6055.0883                0.0000              0.0000
G solv                   -2478.2087                0.0000              0.0000

TOTAL                    -8533.2970                0.0000              0.0000


Receptor:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
BOND                       472.8661                0.0000              0.0000
ANGLE                     1165.0848                0.0000              0.0000
DIHED                     2882.6777                0.0000              0.0000
VDWAALS                  -2489.8101                0.0000              0.0000
EEL                     -21506.6997                0.0000              0.0000
1-4 VDW                   1008.6370                0.0000              0.0000
1-4 EEL                  12129.1681                0.0000              0.0000
EGB                      -2453.0736                0.0000              0.0000
ESURF                       98.5009                0.0000              0.0000

G gas                    -6338.0761                0.0000              0.0000
G solv                   -2354.5727                0.0000              0.0000

TOTAL                    -8692.6488                0.0000              0.0000


Ligand:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
BOND                        47.9642                0.0000              0.0000
ANGLE                      235.3050                0.0000              0.0000
DIHED                       44.1167                0.0000              0.0000
VDWAALS                     -1.8785                0.0000              0.0000
EEL                        105.8143                0.0000              0.0000
1-4 VDW                     38.1303                0.0000              0.0000
1-4 EEL                   -230.2340                0.0000              0.0000
EGB                        -87.0102                0.0000              0.0000
ESURF                        3.2806                0.0000              0.0000

G gas                      239.2180                0.0000              0.0000
G solv                     -83.7296                0.0000              0.0000

TOTAL                      155.4884                0.0000              0.0000


Differences (Complex - Receptor - Ligand):
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
BOND                        -0.0000                0.0000              0.0000
ANGLE                       -0.0000                0.0000              0.0000
DIHED                       -0.0001                0.0000              0.0000
VDWAALS                    -23.5001                0.0000              0.0000
EEL                         67.2700                0.0000              0.0000
1-4 VDW                      0.0000                0.0000              0.0000
1-4 EEL                     -0.0000                0.0000              0.0000
EGB                        -37.1161                0.0000              0.0000
ESURF                       -2.7903                0.0000              0.0000

DELTA G gas                 43.7698                0.0000              0.0000
DELTA G solv               -39.9064                0.0000              0.0000

DELTA TOTAL                  3.8634                0.0000              0.0000


-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Salt concentration:
- step_state: scheduled
Step 2: Number of simulations:
- step_state: scheduled

Step 11: 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__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 2, "component_value": "0.1", "select_param_type": "float"}}]`
dbkey	`"?"`

Step 12: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Ligand SDF:
- step_state: scheduled
Step 2: pH:
- step_state: scheduled

Step 11: 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	`"tabular"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 12: toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_antechamber/ambertools_antechamber/21.10+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

antechamber -i '/tmp/tmp3wfahwpn/files/2/1/a/dataset_21ac10bc-3ab3-41af-a283-06f494740919.dat' -o '/tmp/tmp3wfahwpn/job_working_directory/000/14/outputs/dataset_cf32db77-531b-491f-ac37-dd9565d75892.dat' -fi 'pdb' -fo 'mol2' -c 'bcc' -pf 'yes' -nc '-1' -at 'gaff' -j '4' -rn 'UNL' -m '1'

Exit Code:

```
0
```

Standard Error:

sh: /usr/local/lib/libtinfo.so.6: no version information available (required by sh)
/bin/bash: /usr/local/lib/libtinfo.so.6: no version information available (required by /bin/bash)
sh: /usr/local/lib/libtinfo.so.6: no version information available (required by sh)
/bin/bash: /usr/local/lib/libtinfo.so.6: no version information available (required by /bin/bash)
sh: /usr/local/lib/libtinfo.so.6: no version information available (required by sh)
sh: /usr/local/lib/libtinfo.so.6: no version information available (required by sh)
/bin/bash: /usr/local/lib/libtinfo.so.6: no version information available (required by /bin/bash)
sh: /usr/local/lib/libtinfo.so.6: no version information available (required by sh)
/bin/bash: /usr/local/lib/libtinfo.so.6: no version information available (required by /bin/bash)
sh: /usr/local/lib/libtinfo.so.6: no version information available (required by sh)

Standard Output:

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for pdb File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
Warning: This molecule has no hydrogens nor halogens.
         It is quite possible that there are unfilled valences.
-- Check Geometry --
      for those bonded   
      for those not bonded   
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Warning: The assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or 
(2) adjust atom valence penalty parameters in APS.DAT, and/or 
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    (be cautious, using a large value of PSCUTOFF (>100) will 
    significantly increase the computation time).
Info: Total number of electrons: 136; net charge: -1

Running: /usr/local/bin/sqm -O -i sqm.in -o sqm.out

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"pdb"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
allparams	`{"at": "gaff", "c": "bcc", "j": "4", "m": "1", "nc": "-1", "resname": "UNL"}`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extraparams	`{"pf": true, "usenc": true}`
selected_output_format	`"mol2"`

Step 13: toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/21.10+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/files/c/f/3/dataset_cf32db77-531b-491f-ac37-dd9565d75892.dat' ./input1.mol2 && acpype -i './input1.mol2' -n '-1' -b base -m '1' -a 'gaff' -c 'user' -o gmx

Exit Code:

```
0
```

Standard Output:

========================================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2021-02-05T22:15:50CET (c) 2024 AWSdS |
========================================================================================
==> Reading user's charges from mol2 file...
==> ... charge set to -1
==> Executing Antechamber...
==> * Antechamber OK *
==> * Parmchk OK *
==> Executing Tleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Checking 'UNL'....

/usr/local/bin/teLeap: Warning!
The unperturbed charge of the unit (-1.001000) is not zero.
Checking parameters for unit 'UNL'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
==> * Tleap OK *
==> Removing temporary files...
==> Writing GROMACS files

==> Writing GMX dihedrals for GMX 4.5 and higher.

==> Writing pickle file base.pkl
Total time of execution: less than a second

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mol2"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
atomtype	`"gaff"`
charge	`"-1"`
charge_method	`"user"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
multiplicity	`"1"`
save_gro	`true`

Step 14: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.4.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/bc31d02be922/gmx_merge_topology_files/merge_top.py' --lig-top /tmp/tmp3wfahwpn/files/b/5/a/dataset_b5ac6722-8e08-43b3-97aa-8c028c0f8641.dat --prot-top /tmp/tmp3wfahwpn/files/2/3/3/dataset_2337c29d-667d-44e9-9757-7ba8fb61840f.dat --lig-gro /tmp/tmp3wfahwpn/files/4/2/6/dataset_426b5a14-4e6a-4bcd-af66-81712eaf5bec.dat --prot-gro /tmp/tmp3wfahwpn/files/c/e/b/dataset_ceb0c5c0-72a1-4b9d-97c4-2c297a534e92.dat --complex-top complex.top --complex-gro complex.gro

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"top"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Apoprotein PDB:
- step_state: scheduled
Step 4: Water model:
- step_state: scheduled
Step 5: Force field:
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/ctb_rdkit_descriptors/2020.03.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/0993ac4f4a23/ctb_rdkit_descriptors/rdkit_descriptors.py' -i '/tmp/tmp3wfahwpn/files/d/a/3/dataset_da344f82-2dee-4328-a54b-629361afdd44.dat' --iformat 'sdf' -o '/tmp/tmp3wfahwpn/job_working_directory/000/4/outputs/dataset_2741c392-7f5f-4571-8e6d-c7ee123c7585.dat' -s 'FormalCharge'

Exit Code:

```
0
```

Standard Error:

[20:53:56] ERROR: End of data field name not found
[20:53:56] ERROR: moving to the beginning of the next molecule

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sdf"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
select_multiple	`["FormalCharge"]`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

obabel -i 'sdf'  '/tmp/tmp3wfahwpn/files/d/a/3/dataset_da344f82-2dee-4328-a54b-629361afdd44.dat' -o 'pdb' -O '/tmp/tmp3wfahwpn/job_working_directory/000/5/outputs/dataset_16e8b901-4ed4-400f-94f3-c938512b7dd5.dat' -e

Exit Code:

```
0
```

Standard Error:

```
1 molecule converted
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sdf"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
appendtotitle	`""`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dative_bonds	`false`
dbkey	`"?"`
oformat	`{"__current_case__": 51, "oformat_opts_selector": "pdb"}`
ph	`"-1.0"`
remove_h	`false`
split	`false`
unique	`{"__current_case__": 0, "unique_opts_selector": ""}`

Step 8: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/files/7/8/a/dataset_78a6bf65-87ce-49b8-87c1-539b347a8d89.dat' ./pdb_input.pdb && gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water tip3p -ff amber99sb -noignh -merge all &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"pqr"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ff	`"amber99sb"`
ignore_h	`false`
water	`"tip3p"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp3wfahwpn/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp3wfahwpn/files/2/7/4/dataset_2741c392-7f5f-4571-8e6d-c7ee123c7585.dat' 'c2' T '/tmp/tmp3wfahwpn/job_working_directory/000/7/outputs/dataset_a9a80591-6d90-42fa-b78c-cae2f81de3a6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator  -i -- 'HETATM' '/tmp/tmp3wfahwpn/files/1/6/e/dataset_16e8b901-4ed4-400f-94f3-c938512b7dd5.dat' > '/tmp/tmp3wfahwpn/job_working_directory/000/8/outputs/dataset_21ac10bc-3ab3-41af-a283-06f494740919.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"05d7781f7ab711ef8add9b963d0e3b74"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"HETATM"`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=2; yes -- '0.1' 2>/dev/null | head -n $times >> '/tmp/tmp3wfahwpn/job_working_directory/000/10/outputs/dataset_bbd9f213-37f6-473b-a111-a881bd40c512.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "0.1", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "2"}}]`

Step 14: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/files/9/2/4/dataset_924fa461-5964-4c6f-8b5c-1e85e0a5d9c1.dat' ./input.gro && gmx editconf -f ./input.gro -o ./output.gro -d 1.0 -bt triclinic &>> verbose.txt &&  cp ./output.gro '/tmp/tmp3wfahwpn/job_working_directory/000/17/outputs/dataset_d491e0ab-4fb4-4b05-9af3-18eb222007e0.dat'

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
box	`{"__current_case__": 0, "config": "true", "dim": "1.0", "type": "triclinic"}`
capture_log	`false`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output_format	`"gro"`

Step 15: 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/tmp3wfahwpn/files/b/b/d/dataset_bbd9f213-37f6-473b-a111-a881bd40c512.dat' --ftype 'txt' --chunksize 1 --file_names 'split_file' --file_ext 'txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 13, "src": "hda"}]}, "newfilenames": "split_file", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 16: 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__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"float"`
remove_newlines	`true`

Job 2:

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__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"float"`
remove_newlines	`true`

Step 17: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/18/configs/tmptt22l4jf' ./ions.mdp && ln -s '/tmp/tmp3wfahwpn/files/d/4/9/dataset_d491e0ab-4fb4-4b05-9af3-18eb222007e0.dat' ./gro_input.gro && ln -s '/tmp/tmp3wfahwpn/files/6/0/9/dataset_609da073-7fee-4e35-894d-b07574f66217.dat' ./top_input.top &&  gmx solvate -cp ./gro_input.gro -cs spc216.gro -o solv.gro -p ./top_input.top &>> verbose.txt && gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn '0' &>> verbose.txt && echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral -conc 0.1 -seed 1 &>> verbose.txt && mv solv_ions.gro solv.gro

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`false`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
conc	`"0.1"`
dbkey	`"?"`
mxw	`"0"`
neutralise	`"-neutral"`
seed	`"1"`
water_model	`"spc216"`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/19/configs/tmp2ftn4sdi' ./ions.mdp && ln -s '/tmp/tmp3wfahwpn/files/d/4/9/dataset_d491e0ab-4fb4-4b05-9af3-18eb222007e0.dat' ./gro_input.gro && ln -s '/tmp/tmp3wfahwpn/files/6/0/9/dataset_609da073-7fee-4e35-894d-b07574f66217.dat' ./top_input.top &&  gmx solvate -cp ./gro_input.gro -cs spc216.gro -o solv.gro -p ./top_input.top &>> verbose.txt && gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn '0' &>> verbose.txt && echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral -conc 0.1 -seed 1 &>> verbose.txt && mv solv_ions.gro solv.gro

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`false`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
conc	`"0.1"`
dbkey	`"?"`
mxw	`"0"`
neutralise	`"-neutral"`
seed	`"1"`
water_model	`"spc216"`

Step 18: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/20/configs/tmp4_gcjnof' ./minim.mdp &&  ln -s '/tmp/tmp3wfahwpn/files/9/2/a/dataset_92a18db1-df14-420c-b700-49d88e16a803.dat' ./solv_ions.gro && ln -s '/tmp/tmp3wfahwpn/files/4/6/d/dataset_46ddf942-0231-4b25-831b-7dd2bb30686d.dat' ./top_input.top &&  gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr -maxwarn '0' &>> verbose.txt && gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm em &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mdp	`{"__current_case__": 1, "coulombtype": "PME", "cutoffscheme": "Verlet", "emstep": "0.01", "emtol": "1000.0", "integrator": "steep", "md_steps": "50000", "mdpfile": "default", "rcoulomb": "1.0", "rlist": "1.0", "rvdw": "1.0", "seed": "1"}`
mxw	`"0"`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/21/configs/tmpidai9ufi' ./minim.mdp &&  ln -s '/tmp/tmp3wfahwpn/files/1/5/4/dataset_154516c0-e2a4-47f4-9cb7-14d9e2af2749.dat' ./solv_ions.gro && ln -s '/tmp/tmp3wfahwpn/files/2/8/1/dataset_281dc264-7a9e-4c49-b57d-3f98e0c7adfd.dat' ./top_input.top &&  gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr -maxwarn '0' &>> verbose.txt && gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm em &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mdp	`{"__current_case__": 1, "coulombtype": "PME", "cutoffscheme": "Verlet", "emstep": "0.01", "emtol": "1000.0", "integrator": "steep", "md_steps": "50000", "mdpfile": "default", "rcoulomb": "1.0", "rlist": "1.0", "rvdw": "1.0", "seed": "1"}`
mxw	`"0"`

Step 19: toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/parmconv/21.10+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/6d0677a148fe/parmconv/parmconv.py' --istr '/tmp/tmp3wfahwpn/files/9/2/a/dataset_92a18db1-df14-420c-b700-49d88e16a803.dat' --itop '/tmp/tmp3wfahwpn/files/4/6/d/dataset_46ddf942-0231-4b25-831b-7dd2bb30686d.dat' --removedihe --removebox --iradii 'mbondi' --istripmask '!:UNL' --o_prmtop '/tmp/tmp3wfahwpn/job_working_directory/000/22/outputs/dataset_32471799-0fb5-4542-8129-c06e23807bea.dat' 2>&1  && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/6d0677a148fe/parmconv/parmconv.py' --istr '/tmp/tmp3wfahwpn/files/9/2/a/dataset_92a18db1-df14-420c-b700-49d88e16a803.dat' --itop '/tmp/tmp3wfahwpn/files/4/6/d/dataset_46ddf942-0231-4b25-831b-7dd2bb30686d.dat' --removedihe --removebox --iradii 'mbondi' --istripmask ':NA,CL,SOL,UNL' --o_prmtop '/tmp/tmp3wfahwpn/job_working_directory/000/22/outputs/dataset_6c5a3dbf-01b0-4182-b1bf-5a3fa90e3e8e.dat' 2>&1 && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/6d0677a148fe/parmconv/parmconv.py' --istr '/tmp/tmp3wfahwpn/files/9/2/a/dataset_92a18db1-df14-420c-b700-49d88e16a803.dat' --itop '/tmp/tmp3wfahwpn/files/4/6/d/dataset_46ddf942-0231-4b25-831b-7dd2bb30686d.dat' --removedihe --removebox --iradii 'mbondi' --istripmask ':NA,CL,SOL' --o_prmtop '/tmp/tmp3wfahwpn/job_working_directory/000/22/outputs/dataset_9c249e90-ee37-4ee3-8964-1c778e828b8c.dat' 2>&1 && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/6d0677a148fe/parmconv/parmconv.py' --istr '/tmp/tmp3wfahwpn/files/9/2/a/dataset_92a18db1-df14-420c-b700-49d88e16a803.dat' --itop '/tmp/tmp3wfahwpn/files/4/6/d/dataset_46ddf942-0231-4b25-831b-7dd2bb30686d.dat' --removedihe --removebox --iradii 'mbondi' --istripmask '' --o_prmtop '/tmp/tmp3wfahwpn/job_working_directory/000/22/outputs/dataset_bfd22eba-e286-4f1c-8097-359f00e491c4.dat' 2>&1

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package. 
Original number of dihedrals 13366
Update number of dihedrals 10600
Original number of dihedrals 13366
Update number of dihedrals 10600
Original number of dihedrals 13366
Update number of dihedrals 10600
Original number of dihedrals 13366
Update number of dihedrals 10600

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"top"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_inputs	`{"__current_case__": 1, "fmt": "GROMACS", "modbehaviour": {"radii": "mbondi", "removebox": true, "removedihe": true}, "str_in": {"values": [{"id": 5, "src": "dce"}]}, "top_in": {"values": [{"id": 7, "src": "dce"}]}}`
stripmask_complex	`":NA,CL,SOL"`
stripmask_ligand	`"!:UNL"`
stripmask_receptor	`":NA,CL,SOL,UNL"`
stripmask_solvatedcomplex	`""`

Job 2:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/6d0677a148fe/parmconv/parmconv.py' --istr '/tmp/tmp3wfahwpn/files/1/5/4/dataset_154516c0-e2a4-47f4-9cb7-14d9e2af2749.dat' --itop '/tmp/tmp3wfahwpn/files/2/8/1/dataset_281dc264-7a9e-4c49-b57d-3f98e0c7adfd.dat' --removedihe --removebox --iradii 'mbondi' --istripmask '!:UNL' --o_prmtop '/tmp/tmp3wfahwpn/job_working_directory/000/23/outputs/dataset_6b40d9f7-1377-4515-9579-7706de7a6d82.dat' 2>&1  && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/6d0677a148fe/parmconv/parmconv.py' --istr '/tmp/tmp3wfahwpn/files/1/5/4/dataset_154516c0-e2a4-47f4-9cb7-14d9e2af2749.dat' --itop '/tmp/tmp3wfahwpn/files/2/8/1/dataset_281dc264-7a9e-4c49-b57d-3f98e0c7adfd.dat' --removedihe --removebox --iradii 'mbondi' --istripmask ':NA,CL,SOL,UNL' --o_prmtop '/tmp/tmp3wfahwpn/job_working_directory/000/23/outputs/dataset_8ad56b29-f211-40cf-9d73-d4066195ee76.dat' 2>&1 && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/6d0677a148fe/parmconv/parmconv.py' --istr '/tmp/tmp3wfahwpn/files/1/5/4/dataset_154516c0-e2a4-47f4-9cb7-14d9e2af2749.dat' --itop '/tmp/tmp3wfahwpn/files/2/8/1/dataset_281dc264-7a9e-4c49-b57d-3f98e0c7adfd.dat' --removedihe --removebox --iradii 'mbondi' --istripmask ':NA,CL,SOL' --o_prmtop '/tmp/tmp3wfahwpn/job_working_directory/000/23/outputs/dataset_e69d8556-ec5d-4fa0-bb7b-6e34be06e09f.dat' 2>&1 && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/6d0677a148fe/parmconv/parmconv.py' --istr '/tmp/tmp3wfahwpn/files/1/5/4/dataset_154516c0-e2a4-47f4-9cb7-14d9e2af2749.dat' --itop '/tmp/tmp3wfahwpn/files/2/8/1/dataset_281dc264-7a9e-4c49-b57d-3f98e0c7adfd.dat' --removedihe --removebox --iradii 'mbondi' --istripmask '' --o_prmtop '/tmp/tmp3wfahwpn/job_working_directory/000/23/outputs/dataset_b7dfa046-bceb-4b95-b621-9384f1b14fcd.dat' 2>&1

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package. 
Original number of dihedrals 13366
Update number of dihedrals 10600
Original number of dihedrals 13366
Update number of dihedrals 10600
Original number of dihedrals 13366
Update number of dihedrals 10600
Original number of dihedrals 13366
Update number of dihedrals 10600

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"top"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_inputs	`{"__current_case__": 1, "fmt": "GROMACS", "modbehaviour": {"radii": "mbondi", "removebox": true, "removedihe": true}, "str_in": {"values": [{"id": 6, "src": "dce"}]}, "top_in": {"values": [{"id": 8, "src": "dce"}]}}`
stripmask_complex	`":NA,CL,SOL"`
stripmask_ligand	`"!:UNL"`
stripmask_receptor	`":NA,CL,SOL,UNL"`
stripmask_solvatedcomplex	`""`

Step 20: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/24/configs/tmpgtx_w7_s' ./md.mdp &&  ln -s '/tmp/tmp3wfahwpn/files/3/b/e/dataset_3be1c5fc-24ca-41b8-a992-a670f3bc410d.dat' ./inp.gro && ln -s '/tmp/tmp3wfahwpn/files/4/6/d/dataset_46ddf942-0231-4b25-831b-7dd2bb30686d.dat' ./top_input.top &&  ln -s '/tmp/tmp3wfahwpn/files/f/f/9/dataset_ff9ebcf5-805d-4240-848c-b0fc57da256a.dat' ./posres.itp &&    gmx grompp -f ./md.mdp -c ./inp.gro -r ./inp.gro -p ./top_input.top -o outp.tpr -maxwarn '0' &>> verbose.txt &&  gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt   && cat md.mdp &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__job_resource	`{"__current_case__": 1, "__job_resource__select": "yes", "gpu": "1"}`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inps	`{"cpt_in": null, "itp_in": {"values": [{"id": 8, "src": "hda"}]}, "ndx_in": null}`
mxw	`"0"`
outps	`{"cpt_out": "true", "edr_out": "false", "str": "gro", "tpr_out": "false", "traj": "xtc", "xvg_out": "false"}`
sets	`{"ensembleselect": {"__current_case__": 0, "ensemble": "nvt", "startvel": "false"}, "mdp": {"__current_case__": 1, "constraints": "h-bonds", "coulombtype": "PME", "cutoffscheme": "Verlet", "integrator": "md", "md_steps": "50", "mdpfile": "default", "rcoulomb": "1.0", "rlist": "1.0", "rvdw": "1.0", "step_length": "0.001", "systemTcouple": "false", "temperature": "300", "write_freq": "1000"}}`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/25/configs/tmp5ac70na7' ./md.mdp &&  ln -s '/tmp/tmp3wfahwpn/files/2/e/2/dataset_2e281498-7a48-4ce0-8dc3-56ca281ecedc.dat' ./inp.gro && ln -s '/tmp/tmp3wfahwpn/files/2/8/1/dataset_281dc264-7a9e-4c49-b57d-3f98e0c7adfd.dat' ./top_input.top &&  ln -s '/tmp/tmp3wfahwpn/files/f/f/9/dataset_ff9ebcf5-805d-4240-848c-b0fc57da256a.dat' ./posres.itp &&    gmx grompp -f ./md.mdp -c ./inp.gro -r ./inp.gro -p ./top_input.top -o outp.tpr -maxwarn '0' &>> verbose.txt &&  gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt   && cat md.mdp &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__job_resource	`{"__current_case__": 1, "__job_resource__select": "yes", "gpu": "1"}`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inps	`{"cpt_in": null, "itp_in": {"values": [{"id": 8, "src": "hda"}]}, "ndx_in": null}`
mxw	`"0"`
outps	`{"cpt_out": "true", "edr_out": "false", "str": "gro", "tpr_out": "false", "traj": "xtc", "xvg_out": "false"}`
sets	`{"ensembleselect": {"__current_case__": 0, "ensemble": "nvt", "startvel": "false"}, "mdp": {"__current_case__": 1, "constraints": "h-bonds", "coulombtype": "PME", "cutoffscheme": "Verlet", "integrator": "md", "md_steps": "50", "mdpfile": "default", "rcoulomb": "1.0", "rlist": "1.0", "rvdw": "1.0", "step_length": "0.001", "systemTcouple": "false", "temperature": "300", "write_freq": "1000"}}`

Step 3: Apoprotein PDB:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/26/configs/tmpaf1vfck4' ./md.mdp &&  ln -s '/tmp/tmp3wfahwpn/files/2/f/b/dataset_2fbd5e2c-f92c-42cb-b016-ec1d9550bedd.dat' ./inp.gro && ln -s '/tmp/tmp3wfahwpn/files/4/6/d/dataset_46ddf942-0231-4b25-831b-7dd2bb30686d.dat' ./top_input.top &&  ln -s '/tmp/tmp3wfahwpn/files/f/f/9/dataset_ff9ebcf5-805d-4240-848c-b0fc57da256a.dat' ./posres.itp &&  ln -s '/tmp/tmp3wfahwpn/files/e/b/6/dataset_eb6bbfd2-8768-4aac-98dd-9321f30d1732.dat' ./inp.cpt &&   gmx grompp -f ./md.mdp -c ./inp.gro -t ./inp.cpt -r ./inp.gro -p ./top_input.top -o outp.tpr -maxwarn '0' &>> verbose.txt &&  gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt   && cat md.mdp &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__job_resource	`{"__current_case__": 1, "__job_resource__select": "yes", "gpu": "1"}`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inps	`{"cpt_in": {"values": [{"id": 27, "src": "dce"}]}, "itp_in": {"values": [{"id": 8, "src": "hda"}]}, "ndx_in": null}`
mxw	`"0"`
outps	`{"cpt_out": "true", "edr_out": "false", "str": "gro", "tpr_out": "false", "traj": "xtc", "xvg_out": "false"}`
sets	`{"ensembleselect": {"__current_case__": 0, "ensemble": "nvt", "startvel": "false"}, "mdp": {"__current_case__": 1, "constraints": "h-bonds", "coulombtype": "PME", "cutoffscheme": "Verlet", "integrator": "md", "md_steps": "50", "mdpfile": "default", "rcoulomb": "1.0", "rlist": "1.0", "rvdw": "1.0", "step_length": "0.001", "systemTcouple": "false", "temperature": "300", "write_freq": "1000"}}`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/27/configs/tmpq8tkyibf' ./md.mdp &&  ln -s '/tmp/tmp3wfahwpn/files/d/4/1/dataset_d41c4a53-e79b-44f6-9d57-af6139f73771.dat' ./inp.gro && ln -s '/tmp/tmp3wfahwpn/files/2/8/1/dataset_281dc264-7a9e-4c49-b57d-3f98e0c7adfd.dat' ./top_input.top &&  ln -s '/tmp/tmp3wfahwpn/files/f/f/9/dataset_ff9ebcf5-805d-4240-848c-b0fc57da256a.dat' ./posres.itp &&  ln -s '/tmp/tmp3wfahwpn/files/3/6/2/dataset_3622fc5f-9e34-4ec7-b4ee-652de174a5ab.dat' ./inp.cpt &&   gmx grompp -f ./md.mdp -c ./inp.gro -t ./inp.cpt -r ./inp.gro -p ./top_input.top -o outp.tpr -maxwarn '0' &>> verbose.txt &&  gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt   && cat md.mdp &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__job_resource	`{"__current_case__": 1, "__job_resource__select": "yes", "gpu": "1"}`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inps	`{"cpt_in": {"values": [{"id": 28, "src": "dce"}]}, "itp_in": {"values": [{"id": 8, "src": "hda"}]}, "ndx_in": null}`
mxw	`"0"`
outps	`{"cpt_out": "true", "edr_out": "false", "str": "gro", "tpr_out": "false", "traj": "xtc", "xvg_out": "false"}`
sets	`{"ensembleselect": {"__current_case__": 0, "ensemble": "nvt", "startvel": "false"}, "mdp": {"__current_case__": 1, "constraints": "h-bonds", "coulombtype": "PME", "cutoffscheme": "Verlet", "integrator": "md", "md_steps": "50", "mdpfile": "default", "rcoulomb": "1.0", "rlist": "1.0", "rvdw": "1.0", "step_length": "0.001", "systemTcouple": "false", "temperature": "300", "write_freq": "1000"}}`

Step 22: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/28/configs/tmp1ns1cchd' ./md.mdp &&  ln -s '/tmp/tmp3wfahwpn/files/f/0/d/dataset_f0dfaf02-33a4-46a5-bfa4-7cc74bbe21d9.dat' ./inp.gro && ln -s '/tmp/tmp3wfahwpn/files/4/6/d/dataset_46ddf942-0231-4b25-831b-7dd2bb30686d.dat' ./top_input.top &&   ln -s '/tmp/tmp3wfahwpn/files/3/7/c/dataset_37c5f92c-7b4d-421d-a8b7-dc33af67a8e9.dat' ./inp.cpt &&   gmx grompp -f ./md.mdp -c ./inp.gro -t ./inp.cpt -p ./top_input.top -o outp.tpr -maxwarn '0' &>> verbose.txt &&  gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt   && cat md.mdp &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__job_resource	`{"__current_case__": 1, "__job_resource__select": "yes", "gpu": "1"}`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inps	`{"cpt_in": {"values": [{"id": 35, "src": "dce"}]}, "itp_in": null, "ndx_in": null}`
mxw	`"0"`
outps	`{"cpt_out": "false", "edr_out": "false", "str": "gro", "tpr_out": "true", "traj": "xtc", "xvg_out": "false"}`
sets	`{"ensembleselect": {"__current_case__": 0, "ensemble": "nvt", "startvel": "false"}, "mdp": {"__current_case__": 1, "constraints": "none", "coulombtype": "PME", "cutoffscheme": "Verlet", "integrator": "md", "md_steps": "100", "mdpfile": "default", "rcoulomb": "1.0", "rlist": "1.0", "rvdw": "1.0", "step_length": "0.001", "systemTcouple": "false", "temperature": "300", "write_freq": "1000"}}`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/job_working_directory/000/29/configs/tmpadd1gxad' ./md.mdp &&  ln -s '/tmp/tmp3wfahwpn/files/c/a/2/dataset_ca258cb9-646e-4081-a593-4f5821d8e6b3.dat' ./inp.gro && ln -s '/tmp/tmp3wfahwpn/files/2/8/1/dataset_281dc264-7a9e-4c49-b57d-3f98e0c7adfd.dat' ./top_input.top &&   ln -s '/tmp/tmp3wfahwpn/files/3/c/a/dataset_3ca25b08-04ae-442d-a1d3-59ae1a0cf445.dat' ./inp.cpt &&   gmx grompp -f ./md.mdp -c ./inp.gro -t ./inp.cpt -p ./top_input.top -o outp.tpr -maxwarn '0' &>> verbose.txt &&  gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt   && cat md.mdp &>> verbose.txt

Exit Code:

```
0
```

Standard Output:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or 
- Make your system-wide implementation visible by installing ocl-icd-system conda package.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gro"`
__job_resource	`{"__current_case__": 1, "__job_resource__select": "yes", "gpu": "1"}`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
capture_log	`true`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inps	`{"cpt_in": {"values": [{"id": 36, "src": "dce"}]}, "itp_in": null, "ndx_in": null}`
mxw	`"0"`
outps	`{"cpt_out": "false", "edr_out": "false", "str": "gro", "tpr_out": "true", "traj": "xtc", "xvg_out": "false"}`
sets	`{"ensembleselect": {"__current_case__": 0, "ensemble": "nvt", "startvel": "false"}, "mdp": {"__current_case__": 1, "constraints": "none", "coulombtype": "PME", "cutoffscheme": "Verlet", "integrator": "md", "md_steps": "100", "mdpfile": "default", "rcoulomb": "1.0", "rlist": "1.0", "rvdw": "1.0", "step_length": "0.001", "systemTcouple": "false", "temperature": "300", "write_freq": "1000"}}`

Step 23: toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/files/3/e/0/dataset_3e0777db-ea1e-4b80-b4b2-892a2e92ed5f.dat' ./input.xtc && mdconvert ./input.xtc -o ./output.netcdf && cp ./output.netcdf /tmp/tmp3wfahwpn/job_working_directory/000/30/outputs/dataset_59e788e6-667d-447b-8c85-cdb810726760.dat

Exit Code:

```
0
```

Standard Error:

Warning: 'step' data from input file(s) will be discarded. output format only supports fields: 'xyz', 'time', 'cell_lengths', 'cell_angles'

Standard Output:

```
converted 1 frames, 37834 atoms 
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"xtc"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output_format	`"netcdf"`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp3wfahwpn/files/9/7/e/dataset_97ef7b91-b6a4-440d-a6ed-0731d12c7e2a.dat' ./input.xtc && mdconvert ./input.xtc -o ./output.netcdf && cp ./output.netcdf /tmp/tmp3wfahwpn/job_working_directory/000/31/outputs/dataset_9a39e4ae-e59e-4d94-8581-747b21ea355d.dat

Exit Code:

```
0
```

Standard Error:

Warning: 'step' data from input file(s) will be discarded. output format only supports fields: 'xyz', 'time', 'cell_lengths', 'cell_angles'

Standard Output:

```
converted 1 frames, 37834 atoms 
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"xtc"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output_format	`"netcdf"`

Step 24: toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.10+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp3wfahwpn/job_working_directory/000/32/configs/tmpq9wr0jbd' '/tmp/tmp3wfahwpn/job_working_directory/000/32/configs/tmpfc2aj_v8' && PATH_TO_MMPBSA=$(dirname `which MMPBSA.py`) && export AMBERHOME=$(dirname $PATH_TO_MMPBSA) && MMPBSA.py -O -i '/tmp/tmp3wfahwpn/job_working_directory/000/32/outputs/dataset_22151c3b-3d36-4a05-a7e1-7da67dd05189.dat' -sp '/tmp/tmp3wfahwpn/files/b/f/d/dataset_bfd22eba-e286-4f1c-8097-359f00e491c4.dat' -cp '/tmp/tmp3wfahwpn/files/9/c/2/dataset_9c249e90-ee37-4ee3-8964-1c778e828b8c.dat' -rp '/tmp/tmp3wfahwpn/files/6/c/5/dataset_6c5a3dbf-01b0-4182-b1bf-5a3fa90e3e8e.dat' -lp '/tmp/tmp3wfahwpn/files/3/2/4/dataset_32471799-0fb5-4542-8129-c06e23807bea.dat' -y '/tmp/tmp3wfahwpn/files/5/9/e/dataset_59e788e6-667d-447b-8c85-cdb810726760.dat' -o '/tmp/tmp3wfahwpn/job_working_directory/000/32/outputs/dataset_48bbd3e5-a2d8-4cc5-922e-67a894414d42.dat' -do 'XXXX'

Exit Code:

```
0
```

Standard Error:

/usr/local/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)

Standard Output:

{'input': {'simulation': {'simtype': 'single'}}, 'allparams': {'startframe': 1, 'endframe': 9999999, 'interval': 10, 'entropy': False, 'use_sander': False, 'keep_files': True, 'strip_mask': ':NA,CL,SOL'}, 'calcdetails': {'gb_pb_calc': {'igb': '5', 'saltcon': 0.1, 'surfoff': 0.0, 'molsurf': False, 'probe': 1.4, 'msoffset': 0.0, 'calctype': 'gb'}, 'decomposition': {'decomposition': 'no'}}}
Loading and checking parameter files for compatibility...
cpptraj found! Using /usr/local/bin/cpptraj
mmpbsa_py_energy found! Using /usr/local/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
1 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /usr/local/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...

Timing:
Total setup time:                           0.510 sec.
Creating trajectories with cpptraj:         1.693 sec.
Total calculation time:                     5.882 sec.

Total GB calculation time:                  5.882 sec.

Statistics calculation & output writing:    0.002 sec.
Total time taken:                           8.089 sec.


MMPBSA.py Finished! Thank you for using. Please cite us if you publish this work with this paper:
   Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E.
   J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
allparams	`{"endframe": "9999999", "entropy": false, "interval": "10", "keep_files": true, "startframe": "1", "strip_mask": ":NA,CL,SOL", "use_sander": false}`
calcdetails	`{"decomposition": {"__current_case__": 1, "decomposition": "no"}, "gb_pb_calc": {"__current_case__": 0, "calctype": "gb", "igb": "5", "molsurf": false, "msoffset": "0.0", "probe": "1.4", "saltcon": "0.1", "surfoff": "0.0"}}`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"simulation": {"__current_case__": 0, "complex": {"values": [{"id": 19, "src": "dce"}]}, "ligand": {"values": [{"id": 15, "src": "dce"}]}, "receptor": {"values": [{"id": 17, "src": "dce"}]}, "simtype": "single", "solvatedcomplex": {"values": [{"id": 21, "src": "dce"}]}, "trajcomplex": {"values": [{"id": 47, "src": "dce"}]}}}`

Job 2:

Job state is ok

Command Line:

python '/tmp/tmp3wfahwpn/job_working_directory/000/33/configs/tmpt4xu3jl9' '/tmp/tmp3wfahwpn/job_working_directory/000/33/configs/tmpwdl9qz2e' && PATH_TO_MMPBSA=$(dirname `which MMPBSA.py`) && export AMBERHOME=$(dirname $PATH_TO_MMPBSA) && MMPBSA.py -O -i '/tmp/tmp3wfahwpn/job_working_directory/000/33/outputs/dataset_0c77d4f0-7bf8-4114-8c41-1f095e1b3194.dat' -sp '/tmp/tmp3wfahwpn/files/b/7/d/dataset_b7dfa046-bceb-4b95-b621-9384f1b14fcd.dat' -cp '/tmp/tmp3wfahwpn/files/e/6/9/dataset_e69d8556-ec5d-4fa0-bb7b-6e34be06e09f.dat' -rp '/tmp/tmp3wfahwpn/files/8/a/d/dataset_8ad56b29-f211-40cf-9d73-d4066195ee76.dat' -lp '/tmp/tmp3wfahwpn/files/6/b/4/dataset_6b40d9f7-1377-4515-9579-7706de7a6d82.dat' -y '/tmp/tmp3wfahwpn/files/9/a/3/dataset_9a39e4ae-e59e-4d94-8581-747b21ea355d.dat' -o '/tmp/tmp3wfahwpn/job_working_directory/000/33/outputs/dataset_d8663e8c-43d6-4039-9a24-63657a7c9a18.dat' -do 'XXXX'

Exit Code:

```
0
```

Standard Error:

/usr/local/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)

Standard Output:

{'input': {'simulation': {'simtype': 'single'}}, 'allparams': {'startframe': 1, 'endframe': 9999999, 'interval': 10, 'entropy': False, 'use_sander': False, 'keep_files': True, 'strip_mask': ':NA,CL,SOL'}, 'calcdetails': {'gb_pb_calc': {'igb': '5', 'saltcon': 0.1, 'surfoff': 0.0, 'molsurf': False, 'probe': 1.4, 'msoffset': 0.0, 'calctype': 'gb'}, 'decomposition': {'decomposition': 'no'}}}
Loading and checking parameter files for compatibility...
cpptraj found! Using /usr/local/bin/cpptraj
mmpbsa_py_energy found! Using /usr/local/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
1 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /usr/local/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...

Timing:
Total setup time:                           0.493 sec.
Creating trajectories with cpptraj:         1.725 sec.
Total calculation time:                     5.963 sec.

Total GB calculation time:                  5.963 sec.

Statistics calculation & output writing:    0.001 sec.
Total time taken:                           8.185 sec.


MMPBSA.py Finished! Thank you for using. Please cite us if you publish this work with this paper:
   Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E.
   J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
allparams	`{"endframe": "9999999", "entropy": false, "interval": "10", "keep_files": true, "startframe": "1", "strip_mask": ":NA,CL,SOL", "use_sander": false}`
calcdetails	`{"decomposition": {"__current_case__": 1, "decomposition": "no"}, "gb_pb_calc": {"__current_case__": 0, "calctype": "gb", "igb": "5", "molsurf": false, "msoffset": "0.0", "probe": "1.4", "saltcon": "0.1", "surfoff": "0.0"}}`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"simulation": {"__current_case__": 0, "complex": {"values": [{"id": 20, "src": "dce"}]}, "ligand": {"values": [{"id": 16, "src": "dce"}]}, "receptor": {"values": [{"id": 18, "src": "dce"}]}, "simtype": "single", "solvatedcomplex": {"values": [{"id": 22, "src": "dce"}]}, "trajcomplex": {"values": [{"id": 48, "src": "dce"}]}}}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator  -i -- 'DELTA TOTAL' '/tmp/tmp3wfahwpn/files/4/8/b/dataset_48bbd3e5-a2d8-4cc5-922e-67a894414d42.dat' > '/tmp/tmp3wfahwpn/job_working_directory/000/34/outputs/dataset_fb9601f4-459a-48ac-becf-4b0fce14ee32.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"DELTA TOTAL"`

Job 2:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator  -i -- 'DELTA TOTAL' '/tmp/tmp3wfahwpn/files/d/8/6/dataset_d8663e8c-43d6-4039-9a24-63657a7c9a18.dat' > '/tmp/tmp3wfahwpn/job_working_directory/000/35/outputs/dataset_2577a262-f6c4-4e94-8262-0f402dc828b8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"DELTA TOTAL"`

Step 26: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmp3wfahwpn/files/f/b/9/dataset_fb9601f4-459a-48ac-becf-4b0fce14ee32.dat" ;   cat "/tmp/tmp3wfahwpn/files/2/5/7/dataset_2577a262-f6c4-4e94-8262-0f402dc828b8.dat" ;   ) > /tmp/tmp3wfahwpn/job_working_directory/000/36/outputs/dataset_fab1ddc9-d76f-47b9-9cee-6b6bfcf1cd72.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 27: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp3wfahwpn/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp3wfahwpn/files/f/a/b/dataset_fab1ddc9-d76f-47b9-9cee-6b6bfcf1cd72.dat' 'c3' Sp '/tmp/tmp3wfahwpn/job_working_directory/000/37/outputs/dataset_188458ba-7e3d-4b6d-81ff-6f58e6e08fdc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"Sp"`

Step 28: Summary_Statistics1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp3wfahwpn/galaxy-dev/tools/stats/gsummary.py' '/tmp/tmp3wfahwpn/files/1/8/8/dataset_188458ba-7e3d-4b6d-81ff-6f58e6e08fdc.dat' '/tmp/tmp3wfahwpn/job_working_directory/000/38/outputs/dataset_fa94c11c-2616-4175-9006-29c9cf3bb5c5.dat' 'c1'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"05d7781e7ab711ef8add9b963d0e3b74"`
chromInfo	`"/tmp/tmp3wfahwpn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"c1"`
dbkey	`"?"`

Step 4: Water model:
- step_state: scheduled
Step 5: pH:
- step_state: scheduled
Step 6: Force field:
- step_state: scheduled
Step 7: Ligand SDF:
- step_state: scheduled
Step 8: NVT equilibration steps:
- step_state: scheduled
Step 9: NPT equilibration steps:
- step_state: scheduled
Step 10: Production steps:
- step_state: scheduled

Other invocation details
- history_id
  - 09433e1469602eee
- history_state
  - ok
- invocation_id
  - 09433e1469602eee
- invocation_state
  - scheduled
- workflow_id
  - cfcfe42bedef3f98

planemo-autoupdate added 2 commits November 27, 2023 21:39

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 …

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Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.6 …

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gxydevbot changed the title ~~Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 to 0.1.6~~ Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 to 0.1.6 Nov 27, 2023

planemo-autoupdate and others added 16 commits November 27, 2023 23:59

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.7 …

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Merge branch 'main' into workflows/computational-chemistry/gromacs-mm…

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Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.20…

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reset workflow version

e3d7457

bgruening previously approved these changes Mar 6, 2024

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Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.6 …

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…to 0.1.7

gxydevbot dismissed bgruening’s stale review via ff01d3d March 13, 2024 15:32

planemo-autoupdate added 8 commits March 14, 2024 11:48

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.7 …

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planemo-autoupdate added 6 commits April 22, 2024 04:27

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.15…

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planemo-autoupdate added 3 commits June 24, 2024 04:27

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mvdbeek reviewed Jul 1, 2024

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Make gromacs-mmgbsa update ready to merge

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mvdbeek enabled auto-merge July 1, 2024 14:51

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…to 0.1.7

auto-merge was automatically disabled July 8, 2024 04:25
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planemo-autoupdate added 3 commits July 15, 2024 04:33

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.7 …

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planemo-autoupdate added 2 commits August 5, 2024 04:20

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.10…

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Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.11…

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adapt test syntax

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bgruening closed this Sep 24, 2024

bgruening deleted the workflows/computational-chemistry/gromacs-mmgbsa branch September 24, 2024 20:47

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Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 to 0.1.6 #305

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 to 0.1.6 #305

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 to 0.1.6 #305

Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 to 0.1.6 #305

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Test Results (powered by Planemo)

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