github-actions[bot]
commented
2 months ago Test Results (powered by Planemo)
Test Summary
| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 0 |
| Error | 1 |
| Failure | 0 |
| Skipped | 0 |
Errored Tests
*❌ Generate-Nx-and-Size-plots-for-multiple-assemblies.ga_0
**Execution Problem:**
* ```
Failed to run workflow, at least one job is in [error] state.
```
#### Workflow invocation details
* Invocation Messages
*
Steps
- **Step 1: Collection of genomes to plot**: * step_state: scheduled - **Step 2: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**: * step_state: scheduled *Jobs
- **Job 1:** * Job state is ok **Command Line:** * ```console gfastats '/tmp/tmpj5tmc52d/files/5/f/2/dataset_5f285310-8f3b-45bf-9902-e090a75d08ac.dat' --out-size c --tabular > '/tmp/tmpj5tmc52d/job_working_directory/000/3/outputs/dataset_e605e0e6-0b7d-4d11-827d-fa0e39e63e45.dat' --threads ${GALAXY_SLOTS:-8} ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` | | chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | mode\_condition | ` {"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` | | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | - **Job 2:** * Job state is ok **Command Line:** * ```console gfastats '/tmp/tmpj5tmc52d/files/3/3/9/dataset_339cd22a-29c1-4b23-85cf-5c1e9eb9d4b8.dat' --out-size c --tabular > '/tmp/tmpj5tmc52d/job_working_directory/000/4/outputs/dataset_d21afd57-3026-4806-9720-f1e29b560e3c.dat' --threads ${GALAXY_SLOTS:-8} ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` | | chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | mode\_condition | ` {"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` | | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | - **Step 11: toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/5.1.0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filename | ` {"__current_case__": 1, "add_name": false} ` |
| one\_header | ` false ` |
</details>
- **Step 12: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c5,c6" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 13: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c4,c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 14: Nx Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| adv | ` {"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}} ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "7.0", "unit_output_dim": "in", "width_output_dim": "7.0"} ` |
| title | ` "" ` |
| xlab | ` "x" ` |
| xplot | ` "2" ` |
| ylab | ` "Nx (Mb)" ` |
| yplot | ` "3" ` |
</details>
- **Step 15: Size Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is new
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| adv | ` {"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}} ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "7.0", "unit_output_dim": "in", "width_output_dim": "7.0"} ` |
| title | ` "" ` |
| xlab | ` "Scaffold number" ` |
| xplot | ` "2" ` |
| ylab | ` "Cumulative Size (Mb)" ` |
| yplot | ` "3" ` |
</details>
- **Step 3: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpj5tmc52d/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpj5tmc52d/files/e/6/0/dataset_e605e0e6-0b7d-4d11-827d-fa0e39e63e45.dat' --output='/tmp/tmpj5tmc52d/job_working_directory/000/5/outputs/dataset_07f70bb6-0e05-4889-b535-364030e4c959.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpj5tmc52d/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpj5tmc52d/files/d/2/1/dataset_d21afd57-3026-4806-9720-f1e29b560e3c.dat' --output='/tmp/tmpj5tmc52d/job_working_directory/000/6/outputs/dataset_c384a092-2a78-409d-bd94-9dbb90f78777.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 4: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_awk\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmpj5tmc52d/job_working_directory/000/7/configs/tmpcxbveklx' '/tmp/tmpj5tmc52d/files/0/7/f/dataset_07f70bb6-0e05-4889-b535-364030e4c959.dat' > '/tmp/tmpj5tmc52d/job_working_directory/000/7/outputs/dataset_d4c0ed3d-098d-4c65-823d-07d0d1dc9469.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmpj5tmc52d/job_working_directory/000/8/configs/tmpdeak__y_' '/tmp/tmpj5tmc52d/files/c/3/8/dataset_c384a092-2a78-409d-bd94-9dbb90f78777.dat' > '/tmp/tmpj5tmc52d/job_working_directory/000/8/outputs/dataset_127f3343-5341-44de-9f21-e89798a2b133.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 5: toolshed.g2.bx.psu.edu/repos/iuc/datamash\_ops/datamash\_ops/1.8+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
datamash absmax 3 < /tmp/tmpj5tmc52d/files/d/4/c/dataset_d4c0ed3d-098d-4c65-823d-07d0d1dc9469.dat > '/tmp/tmpj5tmc52d/job_working_directory/000/9/outputs/dataset_b46ea0fe-164c-4b97-89ab-d9f7133f49c5.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/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": "absmax"}] ` |
| print\_full\_line | ` false ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
datamash absmax 3 < /tmp/tmpj5tmc52d/files/1/2/7/dataset_127f3343-5341-44de-9f21-e89798a2b133.dat > '/tmp/tmpj5tmc52d/job_working_directory/000/10/outputs/dataset_38c0df02-26a0-426c-9173-3a5064978533.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/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": "absmax"}] ` |
| print\_full\_line | ` false ` |
</details>
- **Step 6: toolshed.g2.bx.psu.edu/repos/devteam/add\_value/addValue/1.0.1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpj5tmc52d/files/d/4/c/dataset_d4c0ed3d-098d-4c65-823d-07d0d1dc9469.dat" "/tmp/tmpj5tmc52d/job_working_directory/000/11/outputs/dataset_de7b41bc-0ef6-464a-9350-aa36468eebb3.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpj5tmc52d/files/1/2/7/dataset_127f3343-5341-44de-9f21-e89798a2b133.dat" "/tmp/tmpj5tmc52d/job_working_directory/000/12/outputs/dataset_a8a40911-560d-4486-9f7e-2b942c257216.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 7: param\_value\_from\_file**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "2031175", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
- **Job 2:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1933626", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 9: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpj5tmc52d/job_working_directory/000/17/configs/tmpvb2stzww' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpj5tmc52d/files/d/e/7/dataset_de7b41bc-0ef6-464a-9350-aa36468eebb3.dat' '/tmp/tmpj5tmc52d/job_working_directory/000/17/outputs/dataset_287355f7-ab0b-4a7f-9486-7b6eeb015591.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
c3/2031175
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/2031175;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 86 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| error\_handling | ` {"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}} ` |
| ops | ` {"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/2031175"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"} ` |
- **Job 2:**
* Job state is error
**Command Line:**
* ```console
python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpj5tmc52d/job_working_directory/000/18/configs/tmp2buu97cm' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpj5tmc52d/files/a/8/a/dataset_a8a40911-560d-4486-9f7e-2b942c257216.dat' '/tmp/tmpj5tmc52d/job_working_directory/000/18/outputs/dataset_634700e8-66d8-4aa3-8409-9bd20e0035fe.dat'
```
**Exit Code:**
* ```console
127
```
**Standard Error:**
* ```console
/tmp/tmpj5tmc52d/job_working_directory/000/18/tool_script.sh: line 23: python: command not found
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| error\_handling | ` {"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}} ` |
| ops | ` {"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1933626"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"} ` |
</details>
- **Step 10: toolshed.g2.bx.psu.edu/repos/mvdbeek/add\_input\_name\_as\_column/addName/0.2.0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is queued
**Command Line:**
* ```console
python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/3284b72eef56/add_input_name_as_column/'add_input_name_as_column.py --input '/tmp/tmpj5tmc52d/files/2/8/7/dataset_287355f7-ab0b-4a7f-9486-7b6eeb015591.dat' --label 'Primary' --output '/tmp/tmpj5tmc52d/job_working_directory/000/19/outputs/dataset_8bc37262-2dbc-46c8-8379-29726f6a253d.dat'
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| header | ` {"__current_case__": 1, "contains_header": "no"} ` |
| prepend | ` false ` |
- **Job 2:**
* Job state is paused
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "c5f7416c609d11efbbd9bfe0d8417e29" ` |
| chromInfo | ` "/tmp/tmpj5tmc52d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| header | ` {"__current_case__": 1, "contains_header": "no"} ` |
| prepend | ` false ` |
</details>
</details>-
Other invocation details
- **error_message** * Failed to run workflow, at least one job is in [error] state. - **history_id** * 9695121e0bffa38c - **history_state** * error - **invocation_id** * 9695121e0bffa38c - **invocation_state** * scheduled - **workflow_id** * 9695121e0bffa38c
gxydevbot
Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Plot-Nx-Size. 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/devteam/column_maker/Add_a_column1/2.0should be updated totoolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1The workflow release number has been updated from 0.1.1 to 0.1.2.