Closed Delphine-L closed 3 months ago
Delphine-L
commented
3 months ago 
github-actions[bot]
commented
3 months ago | Test State | Count |
|---|---|
| Total | 1 |
| Passed | 1 |
| Error | 0 |
| Failure | 0 |
| Skipped | 0 |
- **Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_grep\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
grep -G -A 0 -B 0 --no-group-separator -i -- 'Haploid' '/tmp/tmpn_oimiq5/files/7/4/d/dataset_74db09ef-d9ea-4e7e-9c4a-d509bb2cc7f6.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/8/outputs/dataset_5ee1eb3b-c24a-4fb0-a256-021cda53b4f9.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| case\_sensitive | ` "-i" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| color | ` "NOCOLOR" ` |
| dbkey | ` "?" ` |
| invert | ` "" ` |
| lines\_after | ` "0" ` |
| lines\_before | ` "0" ` |
| regex\_type | ` "-G" ` |
| url\_paste | ` "Haploid" ` |
</details>
- **Step 15: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int --file '/tmp/tmpn_oimiq5/job_working_directory/000/9/configs/tmpmsddcnr5' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpn_oimiq5/files/1/5/8/dataset_1583daaa-2867-40a5-96d9-24b3c4e98565.dat' '/tmp/tmpn_oimiq5/job_working_directory/000/9/outputs/dataset_58f114fd-5bd0-4a73-9d41-7b4d93081a6b.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 1 new columns with instructions ['c3*2;;']
Computed new column values for 100.00% of 1 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/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*2"}], "header_lines_select": "no"} ` |
</details>
- **Step 16: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmpn_oimiq5/files/3/0/e/dataset_30e98224-abcf-49e1-b44f-ea92a3637570.dat' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && multiqc multiqc_WDir --filename 'report'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/// MultiQC 🔍 | v1.11
| multiqc | MultiQC Version v1.23 now available!
| multiqc | Search path : /tmp/tmpn_oimiq5/job_working_directory/000/10/working/multiqc_WDir
| cutadapt | Found 1 reports
| multiqc | Compressing plot data
| multiqc | Report : report.html
| multiqc | Data : report_data
| multiqc | MultiQC complete
```
**Standard Output:**
* ```console
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 2/2
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| comment | ` "" ` |
| dbkey | ` "?" ` |
| export | ` false ` |
| flat | ` false ` |
| results | ` [{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}] ` |
| saveLog | ` false ` |
| title | ` "" ` |
</details>
- **Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_replace\_in\_line/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpn_oimiq5/files/5/e/e/dataset_5ee1eb3b-c24a-4fb0-a256-021cda53b4f9.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/11/outputs/dataset_31a72970-a120-4682-a8e2-19225f12c04c.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| replacements | ` [{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}] ` |
</details>
- **Step 18: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpn_oimiq5/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpn_oimiq5/files/5/8/f/dataset_58f114fd-5bd0-4a73-9d41-7b4d93081a6b.dat' 'c7' T '/tmp/tmpn_oimiq5/job_working_directory/000/12/outputs/dataset_c1f52da8-ed2e-40fe-8db4-df51001db15c.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 19: Convert characters1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python /tmp/tmpn_oimiq5/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpn_oimiq5/files/3/1/a/dataset_31a72970-a120-4682-a8e2-19225f12c04c.dat s /tmp/tmpn_oimiq5/job_working_directory/000/13/outputs/dataset_4995b47b-78b1-41a0-810e-19837488e7b7.dat
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "txt" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| condense | ` true ` |
| convert\_from | ` "s" ` |
| dbkey | ` "?" ` |
| strip | ` true ` |
</details>
- **Step 20: Estimated homozygous read coverage**:
* 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\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 3: HiC reverse reads**:
* step_state: scheduled
- **Step 21: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpn_oimiq5/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpn_oimiq5/files/4/9/9/dataset_4995b47b-78b1-41a0-810e-19837488e7b7.dat' 'c3' T '/tmp/tmpn_oimiq5/job_working_directory/000/15/outputs/dataset_e0224fe2-8f22-4ec3-b733-068d87d1be51.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c3" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 22: Homozygous read coverage for Hifiasm**:
* 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\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": null}, {"__index__": 1, "value": "21"}]}} ` |
</details>
- **Step 23: Estimated genome size**:
* 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\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmpn_oimiq5/files/0/0/4/dataset_004eb475-a251-458c-a9de-e3a8553b75df.dat' input_0.fastq.gz && mkdir HiCF HiCR && ln -s '/tmp/tmpn_oimiq5/files/f/6/4/dataset_f64d4397-65fa-4945-ab1f-3afd7afda76c.dat' ./HiCF/input_0.fastqsanger.gz && ln -s '/tmp/tmpn_oimiq5/files/6/b/d/dataset_6bd25a07-1701-4c2c-bda0-441c81379d83.dat' ./HiCR/input_0.fastqsanger.gz && hifiasm -t ${GALAXY_SLOTS:-1} -o output -f 32 -a 4 -z 0 -m 10000000 -p 100000 -n 3 -x 0.8 -y 0.2 --hom-cov 21 --h1 './HiCF/input_0.fastqsanger.gz' --h2 './HiCR/input_0.fastqsanger.gz' --l-msjoin 500000 --primary input_0.fastq.gz 2> output.log && mkdir noseq_files && mv *.noseq.gfa noseq_files
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "fastq.gz" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| advanced\_options | ` {"__current_case__": 0, "advanced_selector": "blank"} ` |
| assembly\_options | ` {"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"} ` |
| bins\_out | ` false ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_bits | ` "32" ` |
| hic\_partition | ` {"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null} ` |
| log\_out | ` true ` |
| mode | ` {"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}} ` |
| ont\_integration | ` {"__current_case__": 0, "ont_integration_selector": "blank"} ` |
| purge\_options | ` {"__current_case__": 0, "purge_selector": "blank"} ` |
| scaffolding\_options | ` {"__current_case__": 0, "scaffold_selector": "blank"} ` |
</details>
- **Step 25: Raw Unitig Image**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmpn_oimiq5/files/7/0/c/dataset_70c69111-776b-4cf3-ba7b-528b8c2b81bf.dat' input.gfa && export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.png' --height '2000' --nodewidth '25.0'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| fontsize | ` None ` |
| height | ` "2000" ` |
| lengths | ` false ` |
| names | ` false ` |
| nodewidth | ` "25.0" ` |
| output\_format | ` "png" ` |
| width | ` None ` |
</details>
- **Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpn_oimiq5/files/2/4/7/dataset_247205be-1fcb-43d4-bc4c-93b6a0f75a2c.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpn_oimiq5/job_working_directory/000/20/outputs/dataset_a9458b89-649f-47b5-8c2d-bc6f8e2760b1.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpn_oimiq5/files/6/8/2/dataset_68269120-0ada-4825-bac7-0a48363199f4.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpn_oimiq5/job_working_directory/000/21/outputs/dataset_14915225-2251-4541-9dc0-9e3c564c7e3a.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpn_oimiq5/files/2/4/7/dataset_247205be-1fcb-43d4-bc4c-93b6a0f75a2c.dat' --out-size c --discover-paths --tabular > '/tmp/tmpn_oimiq5/job_working_directory/000/22/outputs/dataset_063c9578-0b9d-4808-a53b-7ab559b1a48a.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpn_oimiq5/files/2/4/7/dataset_247205be-1fcb-43d4-bc4c-93b6a0f75a2c.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 35
Total scaffold length: 1008829
Average scaffold length: 28823.69
Scaffold N50: 24719
Scaffold auN: 47664.45
Scaffold L50: 10
Largest scaffold: 132637
Smallest scaffold: 11730
# contigs: 35
Total contig length: 1008829
Average contig length: 28823.69
Contig N50: 24719
Contig auN: 47664.45
Contig L50: 10
Largest contig: 132637
Smallest contig: 11730
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 303859:199058:199884:306028
GC content %: 39.55
# soft-masked bases: 0
# segments: 35
Total segment length: 1008829
Average segment length: 28823.69
# gaps: 0
# paths: 35
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpn_oimiq5/files/6/8/2/dataset_68269120-0ada-4825-bac7-0a48363199f4.dat' --out-size c --discover-paths --tabular > '/tmp/tmpn_oimiq5/job_working_directory/000/24/outputs/dataset_192ebf30-8ba5-4346-b267-6b86d34ed3ac.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 4: Genomescope Summary**:
* step_state: scheduled
- **Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpn_oimiq5/files/6/8/2/dataset_68269120-0ada-4825-bac7-0a48363199f4.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 72
Total scaffold length: 1778748
Average scaffold length: 24704.83
Scaffold N50: 22121
Scaffold auN: 35945.06
Scaffold L50: 25
Largest scaffold: 132637
Smallest scaffold: 11410
# contigs: 72
Total contig length: 1778748
Average contig length: 24704.83
Contig N50: 22121
Contig auN: 35945.06
Contig L50: 25
Largest contig: 132637
Smallest contig: 11410
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 543138:342989:347557:545064
GC content %: 38.82
# soft-masked bases: 0
# segments: 72
Total segment length: 1778748
Average segment length: 24704.83
# gaps: 0
# paths: 72
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpn_oimiq5/files/2/4/7/dataset_247205be-1fcb-43d4-bc4c-93b6a0f75a2c.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 35
Total scaffold length: 1008829
Average scaffold length: 28823.69
Scaffold N50: 24719
Scaffold auN: 47664.45
Scaffold L50: 10
Largest scaffold: 132637
Smallest scaffold: 11730
# contigs: 35
Total contig length: 1008829
Average contig length: 28823.69
Contig N50: 24719
Contig auN: 47664.45
Contig L50: 10
Largest contig: 132637
Smallest contig: 11730
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 303859:199058:199884:306028
GC content %: 39.55
# soft-masked bases: 0
# segments: 35
Total segment length: 1008829
Average segment length: 28823.69
# gaps: 0
# paths: 35
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpn_oimiq5/files/6/8/2/dataset_68269120-0ada-4825-bac7-0a48363199f4.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 72
Total scaffold length: 1778748
Average scaffold length: 24704.83
Scaffold N50: 22121
Scaffold auN: 35945.06
Scaffold L50: 25
Largest scaffold: 132637
Smallest scaffold: 11410
# contigs: 72
Total contig length: 1778748
Average contig length: 24704.83
Contig N50: 22121
Contig auN: 35945.06
Contig L50: 25
Largest contig: 132637
Smallest contig: 11410
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 543138:342989:347557:545064
GC content %: 38.82
# soft-masked bases: 0
# segments: 72
Total segment length: 1778748
Average segment length: 24704.83
# gaps: 0
# paths: 72
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 34: 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/tmpn_oimiq5/job_working_directory/000/28/configs/tmpbcnjpha5' '/tmp/tmpn_oimiq5/files/a/9/4/dataset_a9458b89-649f-47b5-8c2d-bc6f8e2760b1.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/28/outputs/dataset_e3147b59-89dc-48e1-b7e2-e41ff6765537.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "BEGIN{print \"Metric\\thap2\"}; {print}; " ` |
| dbkey | ` "?" ` |
</details>
- **Step 35: 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/tmpn_oimiq5/job_working_directory/000/29/configs/tmp7ri7ufp8' '/tmp/tmpn_oimiq5/files/1/4/9/dataset_14915225-2251-4541-9dc0-9e3c564c7e3a.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/29/outputs/dataset_103b18c8-5652-4a50-9bd6-838e5f479436.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "BEGIN{print \"Metric\\thap1\"}; {print}; " ` |
| dbkey | ` "?" ` |
</details>
- **Step 36: Data Prep Hap2**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: gfa_stats**:
* step_state: scheduled
- **Step 2: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpn_oimiq5/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpn_oimiq5/files/0/6/3/dataset_063c9578-0b9d-4808-a53b-7ab559b1a48a.dat' --output='/tmp/tmpn_oimiq5/job_working_directory/000/30/outputs/dataset_5937a88a-0bb7-4b37-8b43-f53098b94e2a.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463307406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 3: 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/tmpn_oimiq5/job_working_directory/000/31/configs/tmpskgerneu' '/tmp/tmpn_oimiq5/files/5/9/3/dataset_5937a88a-0bb7-4b37-8b43-f53098b94e2a.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/31/outputs/dataset_b5020ad7-001c-474e-8d28-146118cd2a64.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463307406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 4: 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/tmpn_oimiq5/files/b/5/0/dataset_b5020ad7-001c-474e-8d28-146118cd2a64.dat > '/tmp/tmpn_oimiq5/job_working_directory/000/32/outputs/dataset_101d1074-fa98-4e2f-a129-744238736e93.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463307406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/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 5: 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/tmpn_oimiq5/files/b/5/0/dataset_b5020ad7-001c-474e-8d28-146118cd2a64.dat" "/tmp/tmpn_oimiq5/job_working_directory/000/33/outputs/dataset_520eaaa4-2015-4692-9ab7-00366529ef95.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463307406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 6: 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\_\_ | ` "85463307406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 7: 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\_\_ | ` "85463307406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/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": "1008829", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpn_oimiq5/job_working_directory/000/50/configs/tmp866_94_1' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpn_oimiq5/files/5/2/0/dataset_520eaaa4-2015-4692-9ab7-00366529ef95.dat' '/tmp/tmpn_oimiq5/job_working_directory/000/50/outputs/dataset_52dc7213-e9db-473b-a4de-2a8544f20dce.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 3 new columns with instructions ['c3/1008829;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 35 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463307406a11efbbeac7935956aae8" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/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": "c3/1008829"}, {"__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>
</details>
- **Step 37: Data Prep Hap1**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: gfa_stats**:
* step_state: scheduled
- **Step 2: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpn_oimiq5/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpn_oimiq5/files/1/9/2/dataset_192ebf30-8ba5-4346-b267-6b86d34ed3ac.dat' --output='/tmp/tmpn_oimiq5/job_working_directory/000/35/outputs/dataset_7aabee37-71f0-4fb1-adae-ce954464772b.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463308406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 3: 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/tmpn_oimiq5/job_working_directory/000/36/configs/tmpgfs1yqyz' '/tmp/tmpn_oimiq5/files/7/a/a/dataset_7aabee37-71f0-4fb1-adae-ce954464772b.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/36/outputs/dataset_b6976f25-4733-4699-b4aa-6d7565f0181d.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463308406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 4: 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/tmpn_oimiq5/files/b/6/9/dataset_b6976f25-4733-4699-b4aa-6d7565f0181d.dat > '/tmp/tmpn_oimiq5/job_working_directory/000/37/outputs/dataset_a11af5fd-e545-4786-aaf5-bd173a9ecbc0.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463308406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/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 5: 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/tmpn_oimiq5/files/b/6/9/dataset_b6976f25-4733-4699-b4aa-6d7565f0181d.dat" "/tmp/tmpn_oimiq5/job_working_directory/000/38/outputs/dataset_f18f79ca-633e-4b82-ba58-33f1b3cfd8ea.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463308406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 6: 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\_\_ | ` "85463308406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 7: 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\_\_ | ` "85463308406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/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": "1778748", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpn_oimiq5/job_working_directory/000/49/configs/tmp1hzbsyh1' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpn_oimiq5/files/f/1/8/dataset_f18f79ca-633e-4b82-ba58-33f1b3cfd8ea.dat' '/tmp/tmpn_oimiq5/job_working_directory/000/49/outputs/dataset_e7c4c7ef-e3c3-432f-940b-032b0dd79267.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 3 new columns with instructions ['c3/1778748;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 72 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463308406a11efbbeac7935956aae8" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/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": "c3/1778748"}, {"__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>
</details>
- **Step 38: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpn_oimiq5/job_working_directory/000/40/configs/tmpa8eh4uh2' '/tmp/tmpn_oimiq5/files/e/e/3/dataset_ee3ad7de-efaa-4d83-a6fe-3b72d3127939.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/40/outputs/dataset_40b80358-c72a-4b6a-8268-fcf888ebfaad.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/_path//g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 39: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpn_oimiq5/job_working_directory/000/41/configs/tmpqc_y1y08' '/tmp/tmpn_oimiq5/files/d/6/9/dataset_d69147a6-bcae-4df3-a89d-af5582b83db3.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/41/outputs/dataset_d7ba5db2-ccd6-40f7-8b88-2d34bf98d145.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/_path//g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 40: join1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpn_oimiq5/galaxy-dev/tools/filters/join.py' '/tmp/tmpn_oimiq5/files/1/0/3/dataset_103b18c8-5652-4a50-9bd6-838e5f479436.dat' '/tmp/tmpn_oimiq5/files/e/3/1/dataset_e3147b59-89dc-48e1-b7e2-e41ff6765537.dat' 1 1 '/tmp/tmpn_oimiq5/job_working_directory/000/42/outputs/dataset_91aed122-1095-44e8-9ce6-a25491375a70.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpn_oimiq5/job_working_directory/000/42/configs/tmpv8de1q02
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| field1 | ` "1" ` |
| field2 | ` "1" ` |
| fill\_empty\_columns | ` {"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"} ` |
| header | ` "" ` |
| partial | ` "-p" ` |
| unmatched | ` "-u" ` |
</details>
- **Step 5: Meryl Database**:
* step_state: scheduled
- **Step 41: Plot Data**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: Primary data**:
* step_state: scheduled
- **Step 2: Alternate data**:
* step_state: scheduled
- **Step 11: Size Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpn_oimiq5/job_working_directory/000/57/configs/tmp9cap_ind' && Rscript '/tmp/tmpn_oimiq5/job_working_directory/000/57/configs/tmp9cap_ind'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library(ggplot2)
#Choose between automatically scaled x and y axis or user defined
gg_scalex = NULL
gg_scaley = NULL
gg_theme = theme_bw()
gg_legend = theme(legend.position="right")
input <- read.csv('/tmp/tmpn_oimiq5/files/5/c/4/dataset_5c4f18a2-50ce-4169-91f2-b51de2845716.dat', sep='\t', header=TRUE)
names(input)[2] <- "xcol"
names(input)[3] <- "ycol"
gg_facet = NULL
gg_factor = aes(colour=factor(factor))
gg_line = geom_line(size=1, alpha=1, gg_factor)
color_scale = scale_color_brewer(palette='Set1', direction='1')
names(input)[1] <- "factor"
gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
gg_gridline = NULL
gg_point = NULL
#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('6.0')
gg_height <- as.double('4.0')
gg_unit <- 'in'
gg_dpi <- as.double('300.0')
gg_add_device <- 'none'
output1 <- '/tmp/tmpn_oimiq5/job_working_directory/000/57/outputs/dataset_b77265a0-4c8c-4e38-8c6f-ed2fe510e12e.dat'
output2 <- 'XXXX'
ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
if(gg_add_device != "none"){
ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
}
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463309406a11efbbeac7935956aae8" ` |
| 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/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` |
| title | ` "" ` |
| xlab | ` "Scaffold number" ` |
| xplot | ` "2" ` |
| ylab | ` "Cumulative Size (Mb)" ` |
| yplot | ` "3" ` |
</details>
- **Step 3: Name of primary assembly**:
* step_state: scheduled
- **Step 4: Name of alternate assembly**:
* step_state: scheduled
- **Step 5: 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/tmpn_oimiq5/files/e/7/c/dataset_e7c4c7ef-e3c3-432f-940b-032b0dd79267.dat" "/tmp/tmpn_oimiq5/job_working_directory/000/51/outputs/dataset_61871971-8bec-4763-9b79-8cadccd5f46d.dat" "Hap1" "no"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463309406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "Hap1" ` |
| iterate | ` "no" ` |
</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/tmpn_oimiq5/files/5/2/d/dataset_52dc7213-e9db-473b-a4de-2a8544f20dce.dat" "/tmp/tmpn_oimiq5/job_working_directory/000/52/outputs/dataset_36bdcb6c-41a9-4f31-bf2a-27369c847a4e.dat" "Hap2" "no"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463309406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "Hap2" ` |
| iterate | ` "no" ` |
</details>
- **Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cat/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpn_oimiq5/files/6/1/8/dataset_61871971-8bec-4763-9b79-8cadccd5f46d.dat' >> '/tmp/tmpn_oimiq5/job_working_directory/000/53/outputs/dataset_bbb8ba76-8807-49e6-ac16-46761d5de1a9.dat' && cat '/tmp/tmpn_oimiq5/files/3/6/b/dataset_36bdcb6c-41a9-4f31-bf2a-27369c847a4e.dat' >> '/tmp/tmpn_oimiq5/job_working_directory/000/53/outputs/dataset_bbb8ba76-8807-49e6-ac16-46761d5de1a9.dat' && exit 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463309406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| queries | ` [{"__index__": 0, "inputs2": {"values": [{"id": 76, "src": "hda"}]}}] ` |
</details>
- **Step 8: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpn_oimiq5/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpn_oimiq5/files/b/b/b/dataset_bbb8ba76-8807-49e6-ac16-46761d5de1a9.dat' 'c8,c5,c6' T '/tmp/tmpn_oimiq5/job_working_directory/000/54/outputs/dataset_8f3ac44d-a819-4d6b-b3cb-7e87a30ae86e.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463309406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c5,c6" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 9: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpn_oimiq5/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpn_oimiq5/files/b/b/b/dataset_bbb8ba76-8807-49e6-ac16-46761d5de1a9.dat' 'c8,c4,c7' T '/tmp/tmpn_oimiq5/job_working_directory/000/55/outputs/dataset_5c4f18a2-50ce-4169-91f2-b51de2845716.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463309406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c4,c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 10: Nx Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpn_oimiq5/job_working_directory/000/56/configs/tmp8xxk07o2' && Rscript '/tmp/tmpn_oimiq5/job_working_directory/000/56/configs/tmp8xxk07o2'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library(ggplot2)
#Choose between automatically scaled x and y axis or user defined
gg_scalex = NULL
gg_scaley = NULL
gg_theme = theme_bw()
gg_legend = theme(legend.position="right")
input <- read.csv('/tmp/tmpn_oimiq5/files/8/f/3/dataset_8f3ac44d-a819-4d6b-b3cb-7e87a30ae86e.dat', sep='\t', header=TRUE)
names(input)[2] <- "xcol"
names(input)[3] <- "ycol"
gg_facet = NULL
gg_factor = aes(colour=factor(factor))
gg_line = geom_line(size=1, alpha=1, gg_factor)
color_scale = scale_color_brewer(palette='Set1', direction='1')
names(input)[1] <- "factor"
gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
gg_gridline = NULL
gg_point = NULL
#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('6.0')
gg_height <- as.double('4.0')
gg_unit <- 'in'
gg_dpi <- as.double('300.0')
gg_add_device <- 'none'
output1 <- '/tmp/tmpn_oimiq5/job_working_directory/000/56/outputs/dataset_55a4c433-8da8-4453-a284-63d3663c1e31.dat'
output2 <- 'XXXX'
ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
if(gg_add_device != "none"){
ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
}
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463309406a11efbbeac7935956aae8" ` |
| 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/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` |
| title | ` "" ` |
| xlab | ` "x" ` |
| xplot | ` "2" ` |
| ylab | ` "Nx (Mb)" ` |
| yplot | ` "3" ` |
</details>
</details>
- **Step 42: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
busco --in '/tmp/tmpn_oimiq5/files/4/0/b/dataset_40b80358-c72a-4b6a-8268-fcf888ebfaad.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --update-data --lineage_dataset 'vertebrata_odb10' && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
2024-07-12 16:39:24 ERROR:
Warning message:
package ‘ggplot2’ was built under R version 4.2.3
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
```
**Standard Output:**
* ```console
2024-07-12 16:27:56 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 07/12/2024 16:27:56 *****
2024-07-12 16:27:56 INFO: Configuring BUSCO with local environment
2024-07-12 16:27:56 INFO: Mode is genome
2024-07-12 16:27:56 INFO: Downloading information on latest versions of BUSCO data...
2024-07-12 16:28:03 INFO: Input file is /tmp/tmpn_oimiq5/files/4/0/b/dataset_40b80358-c72a-4b6a-8268-fcf888ebfaad.dat
2024-07-12 16:28:03 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/vertebrata_odb10.2024-01-08.tar.gz'
2024-07-12 16:28:18 INFO: Decompressing file '/tmp/tmpn_oimiq5/job_working_directory/000/43/working/busco_downloads/lineages/vertebrata_odb10.tar.gz'
2024-07-12 16:28:47 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:28:47 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:28:47 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2024-01-08)
2024-07-12 16:28:47 INFO: Running 1 job(s) on bbtools, starting at 07/12/2024 16:28:47
2024-07-12 16:28:48 INFO: [bbtools] 1 of 1 task(s) completed
2024-07-12 16:28:53 INFO: Running 1 job(s) on metaeuk, starting at 07/12/2024 16:28:53
2024-07-12 16:31:49 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-12 16:31:50 INFO: ***** Run HMMER on gene sequences *****
2024-07-12 16:31:50 INFO: Running 3354 job(s) on hmmsearch, starting at 07/12/2024 16:31:50
2024-07-12 16:31:55 INFO: [hmmsearch] 336 of 3354 task(s) completed
2024-07-12 16:32:00 INFO: [hmmsearch] 671 of 3354 task(s) completed
2024-07-12 16:32:04 INFO: [hmmsearch] 1007 of 3354 task(s) completed
2024-07-12 16:32:08 INFO: [hmmsearch] 1342 of 3354 task(s) completed
2024-07-12 16:32:12 INFO: [hmmsearch] 1677 of 3354 task(s) completed
2024-07-12 16:32:16 INFO: [hmmsearch] 2013 of 3354 task(s) completed
2024-07-12 16:32:19 INFO: [hmmsearch] 2348 of 3354 task(s) completed
2024-07-12 16:32:23 INFO: [hmmsearch] 2684 of 3354 task(s) completed
2024-07-12 16:32:27 INFO: [hmmsearch] 3019 of 3354 task(s) completed
2024-07-12 16:32:32 INFO: [hmmsearch] 3354 of 3354 task(s) completed
2024-07-12 16:32:35 INFO: Validating exons and removing overlapping matches
2024-07-12 16:32:36 INFO: 0 candidate overlapping regions found
2024-07-12 16:32:36 INFO: 26 exons in total
2024-07-12 16:32:36 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-07-12 16:34:18 INFO: Running 1 job(s) on metaeuk, starting at 07/12/2024 16:34:18
2024-07-12 16:38:34 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-12 16:38:35 INFO: ***** Run HMMER on gene sequences *****
2024-07-12 16:38:35 INFO: Running 3337 job(s) on hmmsearch, starting at 07/12/2024 16:38:35
2024-07-12 16:38:40 INFO: [hmmsearch] 334 of 3337 task(s) completed
2024-07-12 16:38:44 INFO: [hmmsearch] 668 of 3337 task(s) completed
2024-07-12 16:38:48 INFO: [hmmsearch] 1002 of 3337 task(s) completed
2024-07-12 16:38:52 INFO: [hmmsearch] 1335 of 3337 task(s) completed
2024-07-12 16:38:56 INFO: [hmmsearch] 1669 of 3337 task(s) completed
2024-07-12 16:39:01 INFO: [hmmsearch] 2003 of 3337 task(s) completed
2024-07-12 16:39:05 INFO: [hmmsearch] 2336 of 3337 task(s) completed
2024-07-12 16:39:10 INFO: [hmmsearch] 2670 of 3337 task(s) completed
2024-07-12 16:39:14 INFO: [hmmsearch] 3004 of 3337 task(s) completed
2024-07-12 16:39:18 INFO: [hmmsearch] 3337 of 3337 task(s) completed
2024-07-12 16:39:21 INFO: Validating exons and removing overlapping matches
2024-07-12 16:39:22 INFO: 0 candidate overlapping regions found
2024-07-12 16:39:22 INFO: 24 exons in total
2024-07-12 16:39:22 INFO: Results: C:0.5%[S:0.5%,D:0.0%],F:0.2%,M:99.3%,n:3354
2024-07-12 16:39:22 INFO:
---------------------------------------------------
|Results from dataset vertebrata_odb10 |
---------------------------------------------------
|C:0.5%[S:0.5%,D:0.0%],F:0.2%,M:99.3%,n:3354 |
|17 Complete BUSCOs (C) |
|16 Complete and single-copy BUSCOs (S) |
|1 Complete and duplicated BUSCOs (D) |
|6 Fragmented BUSCOs (F) |
|3331 Missing BUSCOs (M) |
|3354 Total BUSCO groups searched |
---------------------------------------------------
2024-07-12 16:39:22 INFO: BUSCO analysis done with WARNING(s). Total running time: 679 seconds
***** Summary of warnings: *****
2024-07-12 16:28:47 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:28:47 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:39:22 INFO: Results written in /tmp/tmpn_oimiq5/job_working_directory/000/43/working/busco_galaxy
2024-07-12 16:39:22 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
2024-07-12 16:39:22 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 136
drwxr-xr-x 5 1001 127 4096 Jul 12 16:28 busco_sequences
-rw-r--r-- 1 1001 127 72957 Jul 12 16:39 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Jul 12 16:32 hmmer_output
drwxr-xr-x 4 1001 127 4096 Jul 12 16:39 metaeuk_output
-rw-r--r-- 1 1001 127 42736 Jul 12 16:39 missing_busco_list.tsv
-rw-r--r-- 1 1001 127 2298 Jul 12 16:39 short_summary.json
-rw-r--r-- 1 1001 127 882 Jul 12 16:39 short_summary.txt
2024-07-12 16:39:22 INFO: ****************** Start plot generation at 07/12/2024 16:39:22 ******************
2024-07-12 16:39:22 INFO: Load data ...
2024-07-12 16:39:22 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-07-12 16:39:22 INFO: Generate the R code ...
2024-07-12 16:39:22 INFO: Run the R code ...
2024-07-12 16:39:24 INFO:
[1] "Plotting the figure ..."
[1] "Done"
2024-07-12 16:39:24 INFO: Plot generation done. Total running time: 2.4193501472473145 seconds
2024-07-12 16:39:24 INFO: Results written in BUSCO_summaries/
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| adv | ` {"contig_break": "10", "evalue": "0.001", "limit": "3"} ` |
| busco\_mode | ` {"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}} ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| lineage | ` {"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"} ` |
| lineage\_conditional | ` {"__current_case__": 1, "selector": "download"} ` |
| outputs | ` ["short_summary", "missing", "image", "gff"] ` |
</details>
- **Step 43: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpn_oimiq5/files/6/1/d/dataset_61d049bb-44f6-44cd-9c5b-77d1292f99d0.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpn_oimiq5/files/d/7/b/dataset_d7ba5db2-ccd6-40f7-8b88-2d34bf98d145.dat' assembly_01.fasta && ln -s '/tmp/tmpn_oimiq5/files/4/0/b/dataset_40b80358-c72a-4b6a-8268-fcf888ebfaad.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpn_oimiq5/job_working_directory/000/44/outputs/dataset_d4e17c65-0e1c-4a1b-826f-d0b6b18c2e75.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files && sed -i '1s/^/assembly\tk-mer set\tsolid k-mers in assembly\tsolid k-mers in reads\tcompleteness %\n/' 'output_files/output_merqury.completeness.stats' && sed -i '1s/^/assembly\tunique k-mers\tcommon k-mers\tQV\terror rate\n/' 'output_files/output_merqury.qv'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| label | ` "output_merqury" ` |
| mode | ` {"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 51, "src": "hda"}]}, "assembly_02": {"values": [{"id": 50, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"} ` |
| output\_add\_headers | ` true ` |
| output\_selector | ` ["qv", "plots", "stats", "log", "hist"] ` |
</details>
- **Step 44: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
busco --in '/tmp/tmpn_oimiq5/files/d/7/b/dataset_d7ba5db2-ccd6-40f7-8b88-2d34bf98d145.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --update-data --lineage_dataset 'vertebrata_odb10' && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
2024-07-12 16:42:00 ERROR:
Warning message:
package ‘ggplot2’ was built under R version 4.2.3
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
```
**Standard Output:**
* ```console
2024-07-12 16:27:56 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 07/12/2024 16:27:56 *****
2024-07-12 16:27:56 INFO: Configuring BUSCO with local environment
2024-07-12 16:27:56 INFO: Mode is genome
2024-07-12 16:27:56 INFO: Downloading information on latest versions of BUSCO data...
2024-07-12 16:28:02 INFO: Input file is /tmp/tmpn_oimiq5/files/d/7/b/dataset_d7ba5db2-ccd6-40f7-8b88-2d34bf98d145.dat
2024-07-12 16:28:02 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/vertebrata_odb10.2024-01-08.tar.gz'
2024-07-12 16:28:17 INFO: Decompressing file '/tmp/tmpn_oimiq5/job_working_directory/000/45/working/busco_downloads/lineages/vertebrata_odb10.tar.gz'
2024-07-12 16:28:46 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:28:46 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:28:47 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2024-01-08)
2024-07-12 16:28:47 INFO: Running 1 job(s) on bbtools, starting at 07/12/2024 16:28:47
2024-07-12 16:28:48 INFO: [bbtools] 1 of 1 task(s) completed
2024-07-12 16:28:53 INFO: Running 1 job(s) on metaeuk, starting at 07/12/2024 16:28:53
2024-07-12 16:32:21 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-12 16:32:22 INFO: ***** Run HMMER on gene sequences *****
2024-07-12 16:32:22 INFO: Running 3354 job(s) on hmmsearch, starting at 07/12/2024 16:32:22
2024-07-12 16:32:28 INFO: [hmmsearch] 336 of 3354 task(s) completed
2024-07-12 16:32:34 INFO: [hmmsearch] 671 of 3354 task(s) completed
2024-07-12 16:32:39 INFO: [hmmsearch] 1007 of 3354 task(s) completed
2024-07-12 16:32:44 INFO: [hmmsearch] 1342 of 3354 task(s) completed
2024-07-12 16:32:48 INFO: [hmmsearch] 1677 of 3354 task(s) completed
2024-07-12 16:32:52 INFO: [hmmsearch] 2013 of 3354 task(s) completed
2024-07-12 16:32:56 INFO: [hmmsearch] 2348 of 3354 task(s) completed
2024-07-12 16:33:00 INFO: [hmmsearch] 2684 of 3354 task(s) completed
2024-07-12 16:33:05 INFO: [hmmsearch] 3019 of 3354 task(s) completed
2024-07-12 16:33:12 INFO: [hmmsearch] 3354 of 3354 task(s) completed
2024-07-12 16:33:14 INFO: Validating exons and removing overlapping matches
2024-07-12 16:33:15 INFO: 0 candidate overlapping regions found
2024-07-12 16:33:15 INFO: 50 exons in total
2024-07-12 16:33:15 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-07-12 16:34:55 INFO: Running 1 job(s) on metaeuk, starting at 07/12/2024 16:34:55
2024-07-12 16:41:08 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-12 16:41:09 INFO: ***** Run HMMER on gene sequences *****
2024-07-12 16:41:09 INFO: Running 3320 job(s) on hmmsearch, starting at 07/12/2024 16:41:09
2024-07-12 16:41:14 INFO: [hmmsearch] 332 of 3320 task(s) completed
2024-07-12 16:41:18 INFO: [hmmsearch] 664 of 3320 task(s) completed
2024-07-12 16:41:23 INFO: [hmmsearch] 996 of 3320 task(s) completed
2024-07-12 16:41:27 INFO: [hmmsearch] 1328 of 3320 task(s) completed
2024-07-12 16:41:31 INFO: [hmmsearch] 1660 of 3320 task(s) completed
2024-07-12 16:41:36 INFO: [hmmsearch] 1992 of 3320 task(s) completed
2024-07-12 16:41:41 INFO: [hmmsearch] 2324 of 3320 task(s) completed
2024-07-12 16:41:45 INFO: [hmmsearch] 2656 of 3320 task(s) completed
2024-07-12 16:41:50 INFO: [hmmsearch] 2988 of 3320 task(s) completed
2024-07-12 16:41:54 INFO: [hmmsearch] 3320 of 3320 task(s) completed
2024-07-12 16:41:57 INFO: Validating exons and removing overlapping matches
2024-07-12 16:41:58 INFO: 0 candidate overlapping regions found
2024-07-12 16:41:58 INFO: 52 exons in total
2024-07-12 16:41:58 INFO: Results: C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354
2024-07-12 16:41:58 INFO:
---------------------------------------------------
|Results from dataset vertebrata_odb10 |
---------------------------------------------------
|C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354 |
|34 Complete BUSCOs (C) |
|33 Complete and single-copy BUSCOs (S) |
|1 Complete and duplicated BUSCOs (D) |
|13 Fragmented BUSCOs (F) |
|3307 Missing BUSCOs (M) |
|3354 Total BUSCO groups searched |
---------------------------------------------------
2024-07-12 16:41:58 INFO: BUSCO analysis done with WARNING(s). Total running time: 837 seconds
***** Summary of warnings: *****
2024-07-12 16:28:46 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:28:46 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:41:58 INFO: Results written in /tmp/tmpn_oimiq5/job_working_directory/000/45/working/busco_galaxy
2024-07-12 16:41:58 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
2024-07-12 16:41:58 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 140
drwxr-xr-x 5 1001 127 4096 Jul 12 16:28 busco_sequences
-rw-r--r-- 1 1001 127 76099 Jul 12 16:41 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Jul 12 16:33 hmmer_output
drwxr-xr-x 4 1001 127 4096 Jul 12 16:41 metaeuk_output
-rw-r--r-- 1 1001 127 42431 Jul 12 16:41 missing_busco_list.tsv
-rw-r--r-- 1 1001 127 2298 Jul 12 16:41 short_summary.json
-rw-r--r-- 1 1001 127 883 Jul 12 16:41 short_summary.txt
2024-07-12 16:41:58 INFO: ****************** Start plot generation at 07/12/2024 16:41:58 ******************
2024-07-12 16:41:58 INFO: Load data ...
2024-07-12 16:41:58 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-07-12 16:41:58 INFO: Generate the R code ...
2024-07-12 16:41:58 INFO: Run the R code ...
2024-07-12 16:42:00 INFO:
[1] "Plotting the figure ..."
[1] "Done"
2024-07-12 16:42:00 INFO: Plot generation done. Total running time: 2.148916482925415 seconds
2024-07-12 16:42:00 INFO: Results written in BUSCO_summaries/
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| adv | ` {"contig_break": "10", "evalue": "0.001", "limit": "3"} ` |
| busco\_mode | ` {"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}} ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| lineage | ` {"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"} ` |
| lineage\_conditional | ` {"__current_case__": 1, "selector": "download"} ` |
| outputs | ` ["short_summary", "missing", "image", "gff"] ` |
</details>
- **Step 45: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cut\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cut --complement -f '3' '/tmp/tmpn_oimiq5/files/9/1/a/dataset_91aed122-1095-44e8-9ce6-a25491375a70.dat' > '/tmp/tmpn_oimiq5/job_working_directory/000/46/outputs/dataset_1353da59-e652-4e10-844d-a4fecdce9af6.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| chromInfo | ` "/tmp/tmpn_oimiq5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| complement | ` "--complement" ` |
| cut\_type\_options | ` {"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""} ` |
| dbkey | ` "?" ` |
</details>
- **Step 46: output_merqury.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 47: output_merqury.spectra-asm.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 48: merqury_qv**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| input | ` {"values": [{"id": 7, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"} ` |
</details>
- **Step 49: output_merqury.assembly_01.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 50: merqury_stats**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| input | ` {"values": [{"id": 9, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.completeness", "which_dataset": "by_identifier"} ` |
</details>
- **Step 6: Lineage**:
* step_state: scheduled
- **Step 51: output_merqury.assembly_02.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "85463306406a11efbbeac7935956aae8" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 7: Name for Haplotype 1**:
* step_state: scheduled
- **Step 8: Name for Haplotype 2**:
* step_state: scheduled
- **Step 9: Bits for bloom filter**:
* step_state: scheduled
- **Step 10: SAK input file**:
* step_state: scheduled
</details>| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 1 |
| Error | 0 |
| Failure | 0 |
| Skipped | 0 |
- **Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_grep\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
grep -G -A 0 -B 0 --no-group-separator -i -- 'Haploid' '/tmp/tmpjis3ih9p/files/7/e/6/dataset_7e68e8ad-7291-40e1-90d7-c624d1e00832.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/8/outputs/dataset_610a9c41-8ea9-4f43-8f4a-7a3a2152e1ca.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| case\_sensitive | ` "-i" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| color | ` "NOCOLOR" ` |
| dbkey | ` "?" ` |
| invert | ` "" ` |
| lines\_after | ` "0" ` |
| lines\_before | ` "0" ` |
| regex\_type | ` "-G" ` |
| url\_paste | ` "Haploid" ` |
</details>
- **Step 15: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int --file '/tmp/tmpjis3ih9p/job_working_directory/000/9/configs/tmptcwsveld' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpjis3ih9p/files/0/3/9/dataset_03922885-2241-42fa-8ddc-389d626c703b.dat' '/tmp/tmpjis3ih9p/job_working_directory/000/9/outputs/dataset_5e8715d5-1a68-4a57-81be-7b34b4cf941a.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 1 new columns with instructions ['c3*2;;']
Computed new column values for 100.00% of 1 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/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*2"}], "header_lines_select": "no"} ` |
</details>
- **Step 16: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmpjis3ih9p/files/e/8/3/dataset_e83f5dcc-c73e-4fcb-ad6a-2c8528e432a1.dat' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && multiqc multiqc_WDir --filename 'report'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/// MultiQC 🔍 | v1.11
| multiqc | MultiQC Version v1.23 now available!
| multiqc | Search path : /tmp/tmpjis3ih9p/job_working_directory/000/10/working/multiqc_WDir
| cutadapt | Found 1 reports
| multiqc | Compressing plot data
| multiqc | Report : report.html
| multiqc | Data : report_data
| multiqc | MultiQC complete
```
**Standard Output:**
* ```console
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 2/2
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| comment | ` "" ` |
| dbkey | ` "?" ` |
| export | ` false ` |
| flat | ` false ` |
| results | ` [{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}] ` |
| saveLog | ` false ` |
| title | ` "" ` |
</details>
- **Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_replace\_in\_line/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpjis3ih9p/files/6/1/0/dataset_610a9c41-8ea9-4f43-8f4a-7a3a2152e1ca.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/11/outputs/dataset_92437ae6-b174-486d-bae3-15d760641b3e.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| replacements | ` [{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}] ` |
</details>
- **Step 18: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpjis3ih9p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpjis3ih9p/files/5/e/8/dataset_5e8715d5-1a68-4a57-81be-7b34b4cf941a.dat' 'c7' T '/tmp/tmpjis3ih9p/job_working_directory/000/12/outputs/dataset_fec803b0-0aa0-4c04-806e-a0530b5669d9.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 19: Convert characters1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python /tmp/tmpjis3ih9p/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpjis3ih9p/files/9/2/4/dataset_92437ae6-b174-486d-bae3-15d760641b3e.dat s /tmp/tmpjis3ih9p/job_working_directory/000/13/outputs/dataset_ce49f67a-f949-468f-bfa8-5f24a24eaa07.dat
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "txt" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| condense | ` true ` |
| convert\_from | ` "s" ` |
| dbkey | ` "?" ` |
| strip | ` true ` |
</details>
- **Step 20: Estimated homozygous read coverage**:
* 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\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 3: HiC reverse reads**:
* step_state: scheduled
- **Step 21: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpjis3ih9p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpjis3ih9p/files/c/e/4/dataset_ce49f67a-f949-468f-bfa8-5f24a24eaa07.dat' 'c3' T '/tmp/tmpjis3ih9p/job_working_directory/000/15/outputs/dataset_d88f951e-a1b8-4d36-8d92-8000ad07f729.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c3" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 22: Homozygous read coverage for Hifiasm**:
* 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\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": null}, {"__index__": 1, "value": "21"}]}} ` |
</details>
- **Step 23: Estimated genome size**:
* 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\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmpjis3ih9p/files/4/9/b/dataset_49b0373a-583f-4b3f-8e93-a01772e94eec.dat' input_0.fastq.gz && mkdir HiCF HiCR && ln -s '/tmp/tmpjis3ih9p/files/8/c/8/dataset_8c8c3996-a8ce-46b6-8d25-2960946c8fed.dat' ./HiCF/input_0.fastqsanger.gz && ln -s '/tmp/tmpjis3ih9p/files/9/6/7/dataset_9670fddd-f2c8-46fb-a0ed-755c9b01915e.dat' ./HiCR/input_0.fastqsanger.gz && hifiasm -t ${GALAXY_SLOTS:-1} -o output -f 32 -a 4 -z 0 -m 10000000 -p 100000 -n 3 -x 0.8 -y 0.2 --hom-cov 21 --h1 './HiCF/input_0.fastqsanger.gz' --h2 './HiCR/input_0.fastqsanger.gz' --l-msjoin 500000 --primary input_0.fastq.gz 2> output.log && mkdir noseq_files && mv *.noseq.gfa noseq_files
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "fastq.gz" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| advanced\_options | ` {"__current_case__": 0, "advanced_selector": "blank"} ` |
| assembly\_options | ` {"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"} ` |
| bins\_out | ` false ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_bits | ` "32" ` |
| hic\_partition | ` {"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null} ` |
| log\_out | ` true ` |
| mode | ` {"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}} ` |
| ont\_integration | ` {"__current_case__": 0, "ont_integration_selector": "blank"} ` |
| purge\_options | ` {"__current_case__": 0, "purge_selector": "blank"} ` |
| scaffolding\_options | ` {"__current_case__": 0, "scaffold_selector": "blank"} ` |
</details>
- **Step 25: Raw Unitig Image**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmpjis3ih9p/files/4/8/3/dataset_483a8947-e009-4e28-bb23-a4290e43e82a.dat' input.gfa && export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.png' --height '2000' --nodewidth '25.0'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| fontsize | ` None ` |
| height | ` "2000" ` |
| lengths | ` false ` |
| names | ` false ` |
| nodewidth | ` "25.0" ` |
| output\_format | ` "png" ` |
| width | ` None ` |
</details>
- **Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpjis3ih9p/files/0/a/0/dataset_0a08157b-39e5-4575-aaa6-3185125ea7fc.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpjis3ih9p/job_working_directory/000/20/outputs/dataset_055ec80c-45f3-4854-a281-2008f481b7bf.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpjis3ih9p/files/5/b/a/dataset_5ba1fb30-2046-4905-a842-54d3317a46f4.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpjis3ih9p/job_working_directory/000/21/outputs/dataset_9fa6fb7b-0da0-4984-a8b3-2e5489d20f4a.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpjis3ih9p/files/0/a/0/dataset_0a08157b-39e5-4575-aaa6-3185125ea7fc.dat' --out-size c --discover-paths --tabular > '/tmp/tmpjis3ih9p/job_working_directory/000/22/outputs/dataset_271c3de5-c709-4a37-a5bd-41bd23ec2d2d.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpjis3ih9p/files/0/a/0/dataset_0a08157b-39e5-4575-aaa6-3185125ea7fc.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 35
Total scaffold length: 1008829
Average scaffold length: 28823.69
Scaffold N50: 24719
Scaffold auN: 47664.45
Scaffold L50: 10
Largest scaffold: 132637
Smallest scaffold: 11730
# contigs: 35
Total contig length: 1008829
Average contig length: 28823.69
Contig N50: 24719
Contig auN: 47664.45
Contig L50: 10
Largest contig: 132637
Smallest contig: 11730
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 303859:199058:199884:306028
GC content %: 39.55
# soft-masked bases: 0
# segments: 35
Total segment length: 1008829
Average segment length: 28823.69
# gaps: 0
# paths: 35
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpjis3ih9p/files/5/b/a/dataset_5ba1fb30-2046-4905-a842-54d3317a46f4.dat' --out-size c --discover-paths --tabular > '/tmp/tmpjis3ih9p/job_working_directory/000/24/outputs/dataset_c2bef6bf-2e88-4897-b255-344d1ed787ee.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 4: Genomescope Summary**:
* step_state: scheduled
- **Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpjis3ih9p/files/5/b/a/dataset_5ba1fb30-2046-4905-a842-54d3317a46f4.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 72
Total scaffold length: 1778748
Average scaffold length: 24704.83
Scaffold N50: 22121
Scaffold auN: 35945.06
Scaffold L50: 25
Largest scaffold: 132637
Smallest scaffold: 11410
# contigs: 72
Total contig length: 1778748
Average contig length: 24704.83
Contig N50: 22121
Contig auN: 35945.06
Contig L50: 25
Largest contig: 132637
Smallest contig: 11410
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 543138:342989:347557:545064
GC content %: 38.82
# soft-masked bases: 0
# segments: 72
Total segment length: 1778748
Average segment length: 24704.83
# gaps: 0
# paths: 72
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpjis3ih9p/files/0/a/0/dataset_0a08157b-39e5-4575-aaa6-3185125ea7fc.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 35
Total scaffold length: 1008829
Average scaffold length: 28823.69
Scaffold N50: 24719
Scaffold auN: 47664.45
Scaffold L50: 10
Largest scaffold: 132637
Smallest scaffold: 11730
# contigs: 35
Total contig length: 1008829
Average contig length: 28823.69
Contig N50: 24719
Contig auN: 47664.45
Contig L50: 10
Largest contig: 132637
Smallest contig: 11730
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 303859:199058:199884:306028
GC content %: 39.55
# soft-masked bases: 0
# segments: 35
Total segment length: 1008829
Average segment length: 28823.69
# gaps: 0
# paths: 35
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpjis3ih9p/files/5/b/a/dataset_5ba1fb30-2046-4905-a842-54d3317a46f4.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 72
Total scaffold length: 1778748
Average scaffold length: 24704.83
Scaffold N50: 22121
Scaffold auN: 35945.06
Scaffold L50: 25
Largest scaffold: 132637
Smallest scaffold: 11410
# contigs: 72
Total contig length: 1778748
Average contig length: 24704.83
Contig N50: 22121
Contig auN: 35945.06
Contig L50: 25
Largest contig: 132637
Smallest contig: 11410
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 543138:342989:347557:545064
GC content %: 38.82
# soft-masked bases: 0
# segments: 72
Total segment length: 1778748
Average segment length: 24704.83
# gaps: 0
# paths: 72
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 34: 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/tmpjis3ih9p/job_working_directory/000/28/configs/tmp7lu9n93y' '/tmp/tmpjis3ih9p/files/0/5/5/dataset_055ec80c-45f3-4854-a281-2008f481b7bf.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/28/outputs/dataset_a185a2a6-2bbd-4a0a-8ddb-7d5bdd0e85d6.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "BEGIN{print \"Metric\\thap2\"}; {print}; " ` |
| dbkey | ` "?" ` |
</details>
- **Step 35: 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/tmpjis3ih9p/job_working_directory/000/29/configs/tmpov0oea_t' '/tmp/tmpjis3ih9p/files/9/f/a/dataset_9fa6fb7b-0da0-4984-a8b3-2e5489d20f4a.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/29/outputs/dataset_3f02f899-a4e3-44f0-8410-224f4d08ad7f.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "BEGIN{print \"Metric\\thap1\"}; {print}; " ` |
| dbkey | ` "?" ` |
</details>
- **Step 36: Data Prep Hap2**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: gfa_stats**:
* step_state: scheduled
- **Step 2: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpjis3ih9p/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpjis3ih9p/files/2/7/1/dataset_271c3de5-c709-4a37-a5bd-41bd23ec2d2d.dat' --output='/tmp/tmpjis3ih9p/job_working_directory/000/30/outputs/dataset_a4eb020a-3de3-48cf-ad15-33910071c1ac.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a717406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 3: 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/tmpjis3ih9p/job_working_directory/000/31/configs/tmpj_4bj5xx' '/tmp/tmpjis3ih9p/files/a/4/e/dataset_a4eb020a-3de3-48cf-ad15-33910071c1ac.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/31/outputs/dataset_281863a5-ae82-4024-9984-81dab5b221c8.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a717406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 4: 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/tmpjis3ih9p/files/2/8/1/dataset_281863a5-ae82-4024-9984-81dab5b221c8.dat > '/tmp/tmpjis3ih9p/job_working_directory/000/32/outputs/dataset_07eedcc7-8194-4b9d-b3ff-622a19dae7bc.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a717406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/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 5: 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/tmpjis3ih9p/files/2/8/1/dataset_281863a5-ae82-4024-9984-81dab5b221c8.dat" "/tmp/tmpjis3ih9p/job_working_directory/000/33/outputs/dataset_c9d39be7-b5cf-40f8-b01d-4e9d6c910a76.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a717406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 6: 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\_\_ | ` "22d3a717406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 7: 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\_\_ | ` "22d3a717406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/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": "1008829", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpjis3ih9p/job_working_directory/000/55/configs/tmprlv36k0m' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpjis3ih9p/files/c/9/d/dataset_c9d39be7-b5cf-40f8-b01d-4e9d6c910a76.dat' '/tmp/tmpjis3ih9p/job_working_directory/000/55/outputs/dataset_e260ec73-a198-4449-a00e-a8dbae3f5078.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 3 new columns with instructions ['c3/1008829;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 35 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a717406b11efbb5951aecbe85f2c" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/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": "c3/1008829"}, {"__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>
</details>
- **Step 37: Data Prep Hap1**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: gfa_stats**:
* step_state: scheduled
- **Step 2: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpjis3ih9p/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpjis3ih9p/files/c/2/b/dataset_c2bef6bf-2e88-4897-b255-344d1ed787ee.dat' --output='/tmp/tmpjis3ih9p/job_working_directory/000/35/outputs/dataset_5c49d623-0c3f-4151-8622-2dbf44448cb2.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a718406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 3: 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/tmpjis3ih9p/job_working_directory/000/36/configs/tmpdl3yu8bz' '/tmp/tmpjis3ih9p/files/5/c/4/dataset_5c49d623-0c3f-4151-8622-2dbf44448cb2.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/36/outputs/dataset_3991dadd-134b-4578-a54d-a1552a8a743a.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a718406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 4: 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/tmpjis3ih9p/files/3/9/9/dataset_3991dadd-134b-4578-a54d-a1552a8a743a.dat > '/tmp/tmpjis3ih9p/job_working_directory/000/37/outputs/dataset_d493a85e-0341-4b10-8b64-46441d137e46.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a718406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/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 5: 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/tmpjis3ih9p/files/3/9/9/dataset_3991dadd-134b-4578-a54d-a1552a8a743a.dat" "/tmp/tmpjis3ih9p/job_working_directory/000/38/outputs/dataset_3f542d8b-990c-4eec-be39-8f4da183e898.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a718406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 6: 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\_\_ | ` "22d3a718406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 7: 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\_\_ | ` "22d3a718406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/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": "1778748", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpjis3ih9p/job_working_directory/000/56/configs/tmp9rl_2cxg' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpjis3ih9p/files/3/f/5/dataset_3f542d8b-990c-4eec-be39-8f4da183e898.dat' '/tmp/tmpjis3ih9p/job_working_directory/000/56/outputs/dataset_930d1d27-88c1-408c-8268-773fe17e92c8.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 3 new columns with instructions ['c3/1778748;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 72 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a718406b11efbb5951aecbe85f2c" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/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": "c3/1778748"}, {"__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>
</details>
- **Step 38: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpjis3ih9p/job_working_directory/000/40/configs/tmpbqcs_v3_' '/tmp/tmpjis3ih9p/files/1/9/5/dataset_195fcd79-4a2f-444d-bdea-570305741965.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/40/outputs/dataset_52e96321-e60f-4f30-a51d-b67abd92abb7.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/_path//g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 39: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpjis3ih9p/job_working_directory/000/41/configs/tmpmniav_r8' '/tmp/tmpjis3ih9p/files/d/c/5/dataset_dc515e27-2863-4e61-b9fc-f982bbec1421.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/41/outputs/dataset_49a13fe7-297b-4165-8f2e-c38d5e147554.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/_path//g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 40: join1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpjis3ih9p/galaxy-dev/tools/filters/join.py' '/tmp/tmpjis3ih9p/files/3/f/0/dataset_3f02f899-a4e3-44f0-8410-224f4d08ad7f.dat' '/tmp/tmpjis3ih9p/files/a/1/8/dataset_a185a2a6-2bbd-4a0a-8ddb-7d5bdd0e85d6.dat' 1 1 '/tmp/tmpjis3ih9p/job_working_directory/000/42/outputs/dataset_fc18ae5e-12c6-4a23-b019-e2fca8ff2858.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpjis3ih9p/job_working_directory/000/42/configs/tmpv_zb8v3d
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| field1 | ` "1" ` |
| field2 | ` "1" ` |
| fill\_empty\_columns | ` {"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"} ` |
| header | ` "" ` |
| partial | ` "-p" ` |
| unmatched | ` "-u" ` |
</details>
- **Step 5: Meryl Database**:
* step_state: scheduled
- **Step 41: Plot Data**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: Primary data**:
* step_state: scheduled
- **Step 2: Alternate data**:
* step_state: scheduled
- **Step 11: Size Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpjis3ih9p/job_working_directory/000/63/configs/tmp8spvfelu' && Rscript '/tmp/tmpjis3ih9p/job_working_directory/000/63/configs/tmp8spvfelu'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library(ggplot2)
#Choose between automatically scaled x and y axis or user defined
gg_scalex = NULL
gg_scaley = NULL
gg_theme = theme_bw()
gg_legend = theme(legend.position="right")
input <- read.csv('/tmp/tmpjis3ih9p/files/c/e/e/dataset_cee54d5f-f795-4563-ae35-abfe04a58db5.dat', sep='\t', header=TRUE)
names(input)[2] <- "xcol"
names(input)[3] <- "ycol"
gg_facet = NULL
gg_factor = aes(colour=factor(factor))
gg_line = geom_line(size=1, alpha=1, gg_factor)
color_scale = scale_color_brewer(palette='Set1', direction='1')
names(input)[1] <- "factor"
gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
gg_gridline = NULL
gg_point = NULL
#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('6.0')
gg_height <- as.double('4.0')
gg_unit <- 'in'
gg_dpi <- as.double('300.0')
gg_add_device <- 'none'
output1 <- '/tmp/tmpjis3ih9p/job_working_directory/000/63/outputs/dataset_075c73da-90a5-468d-bbcc-5c11e462b952.dat'
output2 <- 'XXXX'
ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
if(gg_add_device != "none"){
ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
}
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a719406b11efbb5951aecbe85f2c" ` |
| 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/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` |
| title | ` "" ` |
| xlab | ` "Scaffold number" ` |
| xplot | ` "2" ` |
| ylab | ` "Cumulative Size (Mb)" ` |
| yplot | ` "3" ` |
</details>
- **Step 3: Name of primary assembly**:
* step_state: scheduled
- **Step 4: Name of alternate assembly**:
* step_state: scheduled
- **Step 5: 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/tmpjis3ih9p/files/9/3/0/dataset_930d1d27-88c1-408c-8268-773fe17e92c8.dat" "/tmp/tmpjis3ih9p/job_working_directory/000/57/outputs/dataset_a52d6da4-31e5-46c5-bf7f-dc72e7636f64.dat" "Hap1" "no"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a719406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "Hap1" ` |
| iterate | ` "no" ` |
</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/tmpjis3ih9p/files/e/2/6/dataset_e260ec73-a198-4449-a00e-a8dbae3f5078.dat" "/tmp/tmpjis3ih9p/job_working_directory/000/58/outputs/dataset_075e539c-64ed-460c-8fe9-a89218115b79.dat" "Hap2" "no"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a719406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "Hap2" ` |
| iterate | ` "no" ` |
</details>
- **Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cat/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpjis3ih9p/files/a/5/2/dataset_a52d6da4-31e5-46c5-bf7f-dc72e7636f64.dat' >> '/tmp/tmpjis3ih9p/job_working_directory/000/59/outputs/dataset_376c3622-891b-4701-96fb-8669d7192481.dat' && cat '/tmp/tmpjis3ih9p/files/0/7/5/dataset_075e539c-64ed-460c-8fe9-a89218115b79.dat' >> '/tmp/tmpjis3ih9p/job_working_directory/000/59/outputs/dataset_376c3622-891b-4701-96fb-8669d7192481.dat' && exit 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a719406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| queries | ` [{"__index__": 0, "inputs2": {"values": [{"id": 106, "src": "hda"}]}}] ` |
</details>
- **Step 8: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpjis3ih9p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpjis3ih9p/files/3/7/6/dataset_376c3622-891b-4701-96fb-8669d7192481.dat' 'c8,c5,c6' T '/tmp/tmpjis3ih9p/job_working_directory/000/60/outputs/dataset_c4222dcb-51ea-4ed3-8cd2-26b390831c8f.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a719406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c5,c6" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 9: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpjis3ih9p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpjis3ih9p/files/3/7/6/dataset_376c3622-891b-4701-96fb-8669d7192481.dat' 'c8,c4,c7' T '/tmp/tmpjis3ih9p/job_working_directory/000/61/outputs/dataset_cee54d5f-f795-4563-ae35-abfe04a58db5.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a719406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c4,c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 10: Nx Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpjis3ih9p/job_working_directory/000/62/configs/tmpiq0nwmd6' && Rscript '/tmp/tmpjis3ih9p/job_working_directory/000/62/configs/tmpiq0nwmd6'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library(ggplot2)
#Choose between automatically scaled x and y axis or user defined
gg_scalex = NULL
gg_scaley = NULL
gg_theme = theme_bw()
gg_legend = theme(legend.position="right")
input <- read.csv('/tmp/tmpjis3ih9p/files/c/4/2/dataset_c4222dcb-51ea-4ed3-8cd2-26b390831c8f.dat', sep='\t', header=TRUE)
names(input)[2] <- "xcol"
names(input)[3] <- "ycol"
gg_facet = NULL
gg_factor = aes(colour=factor(factor))
gg_line = geom_line(size=1, alpha=1, gg_factor)
color_scale = scale_color_brewer(palette='Set1', direction='1')
names(input)[1] <- "factor"
gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
gg_gridline = NULL
gg_point = NULL
#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('6.0')
gg_height <- as.double('4.0')
gg_unit <- 'in'
gg_dpi <- as.double('300.0')
gg_add_device <- 'none'
output1 <- '/tmp/tmpjis3ih9p/job_working_directory/000/62/outputs/dataset_a30e32a0-6882-488b-809c-9f6be6700b42.dat'
output2 <- 'XXXX'
ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
if(gg_add_device != "none"){
ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
}
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a719406b11efbb5951aecbe85f2c" ` |
| 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/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` |
| title | ` "" ` |
| xlab | ` "x" ` |
| xplot | ` "2" ` |
| ylab | ` "Nx (Mb)" ` |
| yplot | ` "3" ` |
</details>
</details>
- **Step 42: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
busco --in '/tmp/tmpjis3ih9p/files/5/2/e/dataset_52e96321-e60f-4f30-a51d-b67abd92abb7.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --update-data --lineage_dataset 'vertebrata_odb10' && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
2024-07-12 16:44:16 ERROR:
Warning message:
package ‘ggplot2’ was built under R version 4.2.3
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
```
**Standard Output:**
* ```console
2024-07-12 16:32:47 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 07/12/2024 16:32:47 *****
2024-07-12 16:32:47 INFO: Configuring BUSCO with local environment
2024-07-12 16:32:47 INFO: Mode is genome
2024-07-12 16:32:47 INFO: Downloading information on latest versions of BUSCO data...
2024-07-12 16:32:52 INFO: Input file is /tmp/tmpjis3ih9p/files/5/2/e/dataset_52e96321-e60f-4f30-a51d-b67abd92abb7.dat
2024-07-12 16:32:52 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/vertebrata_odb10.2024-01-08.tar.gz'
2024-07-12 16:33:10 INFO: Decompressing file '/tmp/tmpjis3ih9p/job_working_directory/000/43/working/busco_downloads/lineages/vertebrata_odb10.tar.gz'
2024-07-12 16:33:37 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:33:37 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:33:37 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2024-01-08)
2024-07-12 16:33:37 INFO: Running 1 job(s) on bbtools, starting at 07/12/2024 16:33:37
2024-07-12 16:33:39 INFO: [bbtools] 1 of 1 task(s) completed
2024-07-12 16:33:43 INFO: Running 1 job(s) on metaeuk, starting at 07/12/2024 16:33:43
2024-07-12 16:36:39 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-12 16:36:40 INFO: ***** Run HMMER on gene sequences *****
2024-07-12 16:36:40 INFO: Running 3354 job(s) on hmmsearch, starting at 07/12/2024 16:36:40
2024-07-12 16:36:46 INFO: [hmmsearch] 336 of 3354 task(s) completed
2024-07-12 16:36:50 INFO: [hmmsearch] 671 of 3354 task(s) completed
2024-07-12 16:36:55 INFO: [hmmsearch] 1007 of 3354 task(s) completed
2024-07-12 16:36:59 INFO: [hmmsearch] 1342 of 3354 task(s) completed
2024-07-12 16:37:03 INFO: [hmmsearch] 1677 of 3354 task(s) completed
2024-07-12 16:37:07 INFO: [hmmsearch] 2013 of 3354 task(s) completed
2024-07-12 16:37:10 INFO: [hmmsearch] 2348 of 3354 task(s) completed
2024-07-12 16:37:14 INFO: [hmmsearch] 2684 of 3354 task(s) completed
2024-07-12 16:37:18 INFO: [hmmsearch] 3019 of 3354 task(s) completed
2024-07-12 16:37:23 INFO: [hmmsearch] 3354 of 3354 task(s) completed
2024-07-12 16:37:26 INFO: Validating exons and removing overlapping matches
2024-07-12 16:37:27 INFO: 0 candidate overlapping regions found
2024-07-12 16:37:27 INFO: 26 exons in total
2024-07-12 16:37:27 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-07-12 16:39:08 INFO: Running 1 job(s) on metaeuk, starting at 07/12/2024 16:39:08
2024-07-12 16:43:25 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-12 16:43:26 INFO: ***** Run HMMER on gene sequences *****
2024-07-12 16:43:26 INFO: Running 3337 job(s) on hmmsearch, starting at 07/12/2024 16:43:26
2024-07-12 16:43:31 INFO: [hmmsearch] 334 of 3337 task(s) completed
2024-07-12 16:43:35 INFO: [hmmsearch] 668 of 3337 task(s) completed
2024-07-12 16:43:39 INFO: [hmmsearch] 1002 of 3337 task(s) completed
2024-07-12 16:43:44 INFO: [hmmsearch] 1335 of 3337 task(s) completed
2024-07-12 16:43:48 INFO: [hmmsearch] 1669 of 3337 task(s) completed
2024-07-12 16:43:52 INFO: [hmmsearch] 2003 of 3337 task(s) completed
2024-07-12 16:43:57 INFO: [hmmsearch] 2336 of 3337 task(s) completed
2024-07-12 16:44:01 INFO: [hmmsearch] 2670 of 3337 task(s) completed
2024-07-12 16:44:05 INFO: [hmmsearch] 3004 of 3337 task(s) completed
2024-07-12 16:44:09 INFO: [hmmsearch] 3337 of 3337 task(s) completed
2024-07-12 16:44:12 INFO: Validating exons and removing overlapping matches
2024-07-12 16:44:13 INFO: 0 candidate overlapping regions found
2024-07-12 16:44:13 INFO: 24 exons in total
2024-07-12 16:44:13 INFO: Results: C:0.5%[S:0.5%,D:0.0%],F:0.2%,M:99.3%,n:3354
2024-07-12 16:44:13 INFO:
---------------------------------------------------
|Results from dataset vertebrata_odb10 |
---------------------------------------------------
|C:0.5%[S:0.5%,D:0.0%],F:0.2%,M:99.3%,n:3354 |
|17 Complete BUSCOs (C) |
|16 Complete and single-copy BUSCOs (S) |
|1 Complete and duplicated BUSCOs (D) |
|6 Fragmented BUSCOs (F) |
|3331 Missing BUSCOs (M) |
|3354 Total BUSCO groups searched |
---------------------------------------------------
2024-07-12 16:44:13 INFO: BUSCO analysis done with WARNING(s). Total running time: 681 seconds
***** Summary of warnings: *****
2024-07-12 16:33:37 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:33:37 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:44:13 INFO: Results written in /tmp/tmpjis3ih9p/job_working_directory/000/43/working/busco_galaxy
2024-07-12 16:44:13 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
2024-07-12 16:44:13 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 136
drwxr-xr-x 5 1001 127 4096 Jul 12 16:33 busco_sequences
-rw-r--r-- 1 1001 127 72957 Jul 12 16:44 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Jul 12 16:37 hmmer_output
drwxr-xr-x 4 1001 127 4096 Jul 12 16:44 metaeuk_output
-rw-r--r-- 1 1001 127 42736 Jul 12 16:44 missing_busco_list.tsv
-rw-r--r-- 1 1001 127 2298 Jul 12 16:44 short_summary.json
-rw-r--r-- 1 1001 127 882 Jul 12 16:44 short_summary.txt
2024-07-12 16:44:13 INFO: ****************** Start plot generation at 07/12/2024 16:44:13 ******************
2024-07-12 16:44:13 INFO: Load data ...
2024-07-12 16:44:13 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-07-12 16:44:13 INFO: Generate the R code ...
2024-07-12 16:44:13 INFO: Run the R code ...
2024-07-12 16:44:16 INFO:
[1] "Plotting the figure ..."
[1] "Done"
2024-07-12 16:44:16 INFO: Plot generation done. Total running time: 2.4948322772979736 seconds
2024-07-12 16:44:16 INFO: Results written in BUSCO_summaries/
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| adv | ` {"contig_break": "10", "evalue": "0.001", "limit": "3"} ` |
| busco\_mode | ` {"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}} ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| lineage | ` {"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"} ` |
| lineage\_conditional | ` {"__current_case__": 1, "selector": "download"} ` |
| outputs | ` ["short_summary", "missing", "image", "gff"] ` |
</details>
- **Step 43: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpjis3ih9p/files/a/e/8/dataset_ae85e6e5-8a9c-4200-9712-38d3e9cdd263.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpjis3ih9p/files/4/9/a/dataset_49a13fe7-297b-4165-8f2e-c38d5e147554.dat' assembly_01.fasta && ln -s '/tmp/tmpjis3ih9p/files/5/2/e/dataset_52e96321-e60f-4f30-a51d-b67abd92abb7.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpjis3ih9p/job_working_directory/000/44/outputs/dataset_376bba10-33a3-4000-9e31-f5099a032c98.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files && sed -i '1s/^/assembly\tk-mer set\tsolid k-mers in assembly\tsolid k-mers in reads\tcompleteness %\n/' 'output_files/output_merqury.completeness.stats' && sed -i '1s/^/assembly\tunique k-mers\tcommon k-mers\tQV\terror rate\n/' 'output_files/output_merqury.qv'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| label | ` "output_merqury" ` |
| mode | ` {"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 51, "src": "hda"}]}, "assembly_02": {"values": [{"id": 50, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"} ` |
| output\_add\_headers | ` true ` |
| output\_selector | ` ["qv", "plots", "stats", "log", "hist"] ` |
</details>
- **Step 44: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
busco --in '/tmp/tmpjis3ih9p/files/4/9/a/dataset_49a13fe7-297b-4165-8f2e-c38d5e147554.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --update-data --lineage_dataset 'vertebrata_odb10' && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
2024-07-12 16:47:15 ERROR:
Warning message:
package ‘ggplot2’ was built under R version 4.2.3
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
```
**Standard Output:**
* ```console
2024-07-12 16:32:48 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 07/12/2024 16:32:48 *****
2024-07-12 16:32:48 INFO: Configuring BUSCO with local environment
2024-07-12 16:32:48 INFO: Mode is genome
2024-07-12 16:32:48 INFO: Downloading information on latest versions of BUSCO data...
2024-07-12 16:32:53 INFO: Input file is /tmp/tmpjis3ih9p/files/4/9/a/dataset_49a13fe7-297b-4165-8f2e-c38d5e147554.dat
2024-07-12 16:32:53 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/vertebrata_odb10.2024-01-08.tar.gz'
2024-07-12 16:33:10 INFO: Decompressing file '/tmp/tmpjis3ih9p/job_working_directory/000/45/working/busco_downloads/lineages/vertebrata_odb10.tar.gz'
2024-07-12 16:33:37 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:33:38 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:33:38 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2024-01-08)
2024-07-12 16:33:38 INFO: Running 1 job(s) on bbtools, starting at 07/12/2024 16:33:38
2024-07-12 16:33:39 INFO: [bbtools] 1 of 1 task(s) completed
2024-07-12 16:33:44 INFO: Running 1 job(s) on metaeuk, starting at 07/12/2024 16:33:44
2024-07-12 16:37:21 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-12 16:37:22 INFO: ***** Run HMMER on gene sequences *****
2024-07-12 16:37:22 INFO: Running 3354 job(s) on hmmsearch, starting at 07/12/2024 16:37:22
2024-07-12 16:37:29 INFO: [hmmsearch] 336 of 3354 task(s) completed
2024-07-12 16:37:35 INFO: [hmmsearch] 671 of 3354 task(s) completed
2024-07-12 16:37:40 INFO: [hmmsearch] 1007 of 3354 task(s) completed
2024-07-12 16:37:45 INFO: [hmmsearch] 1342 of 3354 task(s) completed
2024-07-12 16:37:50 INFO: [hmmsearch] 1677 of 3354 task(s) completed
2024-07-12 16:37:54 INFO: [hmmsearch] 2013 of 3354 task(s) completed
2024-07-12 16:37:58 INFO: [hmmsearch] 2348 of 3354 task(s) completed
2024-07-12 16:38:02 INFO: [hmmsearch] 2684 of 3354 task(s) completed
2024-07-12 16:38:07 INFO: [hmmsearch] 3019 of 3354 task(s) completed
2024-07-12 16:38:13 INFO: [hmmsearch] 3354 of 3354 task(s) completed
2024-07-12 16:38:16 INFO: Validating exons and removing overlapping matches
2024-07-12 16:38:17 INFO: 0 candidate overlapping regions found
2024-07-12 16:38:17 INFO: 50 exons in total
2024-07-12 16:38:17 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-07-12 16:40:00 INFO: Running 1 job(s) on metaeuk, starting at 07/12/2024 16:40:00
2024-07-12 16:46:22 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-12 16:46:23 INFO: ***** Run HMMER on gene sequences *****
2024-07-12 16:46:23 INFO: Running 3320 job(s) on hmmsearch, starting at 07/12/2024 16:46:23
2024-07-12 16:46:28 INFO: [hmmsearch] 332 of 3320 task(s) completed
2024-07-12 16:46:33 INFO: [hmmsearch] 664 of 3320 task(s) completed
2024-07-12 16:46:37 INFO: [hmmsearch] 996 of 3320 task(s) completed
2024-07-12 16:46:42 INFO: [hmmsearch] 1328 of 3320 task(s) completed
2024-07-12 16:46:46 INFO: [hmmsearch] 1660 of 3320 task(s) completed
2024-07-12 16:46:51 INFO: [hmmsearch] 1992 of 3320 task(s) completed
2024-07-12 16:46:55 INFO: [hmmsearch] 2324 of 3320 task(s) completed
2024-07-12 16:47:00 INFO: [hmmsearch] 2656 of 3320 task(s) completed
2024-07-12 16:47:04 INFO: [hmmsearch] 2988 of 3320 task(s) completed
2024-07-12 16:47:09 INFO: [hmmsearch] 3320 of 3320 task(s) completed
2024-07-12 16:47:12 INFO: Validating exons and removing overlapping matches
2024-07-12 16:47:13 INFO: 0 candidate overlapping regions found
2024-07-12 16:47:13 INFO: 52 exons in total
2024-07-12 16:47:13 INFO: Results: C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354
2024-07-12 16:47:13 INFO:
---------------------------------------------------
|Results from dataset vertebrata_odb10 |
---------------------------------------------------
|C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354 |
|34 Complete BUSCOs (C) |
|33 Complete and single-copy BUSCOs (S) |
|1 Complete and duplicated BUSCOs (D) |
|13 Fragmented BUSCOs (F) |
|3307 Missing BUSCOs (M) |
|3354 Total BUSCO groups searched |
---------------------------------------------------
2024-07-12 16:47:13 INFO: BUSCO analysis done with WARNING(s). Total running time: 860 seconds
***** Summary of warnings: *****
2024-07-12 16:33:37 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:33:38 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-12 16:47:13 INFO: Results written in /tmp/tmpjis3ih9p/job_working_directory/000/45/working/busco_galaxy
2024-07-12 16:47:13 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
2024-07-12 16:47:13 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 140
drwxr-xr-x 5 1001 127 4096 Jul 12 16:33 busco_sequences
-rw-r--r-- 1 1001 127 76099 Jul 12 16:47 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Jul 12 16:38 hmmer_output
drwxr-xr-x 4 1001 127 4096 Jul 12 16:47 metaeuk_output
-rw-r--r-- 1 1001 127 42431 Jul 12 16:47 missing_busco_list.tsv
-rw-r--r-- 1 1001 127 2298 Jul 12 16:47 short_summary.json
-rw-r--r-- 1 1001 127 883 Jul 12 16:47 short_summary.txt
2024-07-12 16:47:13 INFO: ****************** Start plot generation at 07/12/2024 16:47:13 ******************
2024-07-12 16:47:13 INFO: Load data ...
2024-07-12 16:47:13 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-07-12 16:47:13 INFO: Generate the R code ...
2024-07-12 16:47:13 INFO: Run the R code ...
2024-07-12 16:47:15 INFO:
[1] "Plotting the figure ..."
[1] "Done"
2024-07-12 16:47:15 INFO: Plot generation done. Total running time: 2.211245536804199 seconds
2024-07-12 16:47:15 INFO: Results written in BUSCO_summaries/
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| adv | ` {"contig_break": "10", "evalue": "0.001", "limit": "3"} ` |
| busco\_mode | ` {"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}} ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| lineage | ` {"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"} ` |
| lineage\_conditional | ` {"__current_case__": 1, "selector": "download"} ` |
| outputs | ` ["short_summary", "missing", "image", "gff"] ` |
</details>
- **Step 45: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cut\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cut --complement -f '3' '/tmp/tmpjis3ih9p/files/f/c/1/dataset_fc18ae5e-12c6-4a23-b019-e2fca8ff2858.dat' > '/tmp/tmpjis3ih9p/job_working_directory/000/46/outputs/dataset_8adbecb5-ff9b-44c2-a9d5-1d60ec86d8d1.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| chromInfo | ` "/tmp/tmpjis3ih9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| complement | ` "--complement" ` |
| cut\_type\_options | ` {"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""} ` |
| dbkey | ` "?" ` |
</details>
- **Step 46: output_merqury.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 47: output_merqury.spectra-asm.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 48: merqury_qv**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| input | ` {"values": [{"id": 7, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"} ` |
</details>
- **Step 49: output_merqury.assembly_01.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 50: merqury_stats**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| input | ` {"values": [{"id": 9, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.completeness", "which_dataset": "by_identifier"} ` |
</details>
- **Step 6: Lineage**:
* step_state: scheduled
- **Step 51: output_merqury.assembly_02.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "22d3a716406b11efbb5951aecbe85f2c" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 7: Name for Haplotype 1**:
* step_state: scheduled
- **Step 8: Name for Haplotype 2**:
* step_state: scheduled
- **Step 9: Bits for bloom filter**:
* step_state: scheduled
- **Step 10: SAK input file**:
* step_state: scheduled
</details>| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 1 |
| Error | 0 |
| Failure | 0 |
| Skipped | 0 |
- **Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_grep\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
grep -G -A 0 -B 0 --no-group-separator -i -- 'Haploid' '/tmp/tmpwrj4k1w9/files/2/e/b/dataset_2ebda275-bedb-4dba-8265-026859d62cee.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/8/outputs/dataset_127639a8-c836-4325-8f2f-6260c9200ae9.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| case\_sensitive | ` "-i" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| color | ` "NOCOLOR" ` |
| dbkey | ` "?" ` |
| invert | ` "" ` |
| lines\_after | ` "0" ` |
| lines\_before | ` "0" ` |
| regex\_type | ` "-G" ` |
| url\_paste | ` "Haploid" ` |
</details>
- **Step 15: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int --file '/tmp/tmpwrj4k1w9/job_working_directory/000/9/configs/tmp53f8ww6g' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpwrj4k1w9/files/7/7/e/dataset_77ed909d-2775-4307-95a7-f882fe0582a2.dat' '/tmp/tmpwrj4k1w9/job_working_directory/000/9/outputs/dataset_5f89ac7e-e6ef-402f-8c91-677b3c6d20dd.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 1 new columns with instructions ['c3*2;;']
Computed new column values for 100.00% of 1 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/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*2"}], "header_lines_select": "no"} ` |
</details>
- **Step 16: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmpwrj4k1w9/files/c/b/c/dataset_cbcce6ee-9b2e-473c-8709-f1d4e202d3ff.dat' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && multiqc multiqc_WDir --filename 'report'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/// MultiQC 🔍 | v1.11
| multiqc | MultiQC Version v1.23 now available!
| multiqc | Search path : /tmp/tmpwrj4k1w9/job_working_directory/000/10/working/multiqc_WDir
| cutadapt | Found 1 reports
| multiqc | Compressing plot data
| multiqc | Report : report.html
| multiqc | Data : report_data
| multiqc | MultiQC complete
```
**Standard Output:**
* ```console
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 2/2
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| comment | ` "" ` |
| dbkey | ` "?" ` |
| export | ` false ` |
| flat | ` false ` |
| results | ` [{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}] ` |
| saveLog | ` false ` |
| title | ` "" ` |
</details>
- **Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_replace\_in\_line/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpwrj4k1w9/files/1/2/7/dataset_127639a8-c836-4325-8f2f-6260c9200ae9.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/11/outputs/dataset_07a465d2-438b-4ca8-9971-a092ccab13dc.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| replacements | ` [{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}] ` |
</details>
- **Step 18: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpwrj4k1w9/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwrj4k1w9/files/5/f/8/dataset_5f89ac7e-e6ef-402f-8c91-677b3c6d20dd.dat' 'c7' T '/tmp/tmpwrj4k1w9/job_working_directory/000/12/outputs/dataset_c546d44a-2cd0-4910-93e8-b68ca4e44183.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 19: Convert characters1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python /tmp/tmpwrj4k1w9/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpwrj4k1w9/files/0/7/a/dataset_07a465d2-438b-4ca8-9971-a092ccab13dc.dat s /tmp/tmpwrj4k1w9/job_working_directory/000/13/outputs/dataset_22ada637-679f-4937-9502-9d8a1d12f801.dat
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "txt" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| condense | ` true ` |
| convert\_from | ` "s" ` |
| dbkey | ` "?" ` |
| strip | ` true ` |
</details>
- **Step 20: Estimated homozygous read coverage**:
* 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\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 3: HiC reverse reads**:
* step_state: scheduled
- **Step 21: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpwrj4k1w9/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwrj4k1w9/files/2/2/a/dataset_22ada637-679f-4937-9502-9d8a1d12f801.dat' 'c3' T '/tmp/tmpwrj4k1w9/job_working_directory/000/15/outputs/dataset_b55fbca3-b097-4f8f-8ba1-86efce3a727c.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c3" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 22: Homozygous read coverage for Hifiasm**:
* 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\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": null}, {"__index__": 1, "value": "21"}]}} ` |
</details>
- **Step 23: Estimated genome size**:
* 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\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmpwrj4k1w9/files/c/0/0/dataset_c00ca9ae-87af-4990-83b3-2867db1d984e.dat' input_0.fastq.gz && mkdir HiCF HiCR && ln -s '/tmp/tmpwrj4k1w9/files/5/4/a/dataset_54a04cd9-5e7f-4f8a-93b3-5152b15ab23d.dat' ./HiCF/input_0.fastqsanger.gz && ln -s '/tmp/tmpwrj4k1w9/files/c/5/1/dataset_c517bb6a-fa1f-4330-930a-4440aff0bbe1.dat' ./HiCR/input_0.fastqsanger.gz && hifiasm -t ${GALAXY_SLOTS:-1} -o output -f 32 -a 4 -z 0 -m 10000000 -p 100000 -n 3 -x 0.8 -y 0.2 --hom-cov 21 --h1 './HiCF/input_0.fastqsanger.gz' --h2 './HiCR/input_0.fastqsanger.gz' --l-msjoin 500000 --primary input_0.fastq.gz 2> output.log && mkdir noseq_files && mv *.noseq.gfa noseq_files
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "fastq.gz" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| advanced\_options | ` {"__current_case__": 0, "advanced_selector": "blank"} ` |
| assembly\_options | ` {"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"} ` |
| bins\_out | ` false ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_bits | ` "32" ` |
| hic\_partition | ` {"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null} ` |
| log\_out | ` true ` |
| mode | ` {"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}} ` |
| ont\_integration | ` {"__current_case__": 0, "ont_integration_selector": "blank"} ` |
| purge\_options | ` {"__current_case__": 0, "purge_selector": "blank"} ` |
| scaffolding\_options | ` {"__current_case__": 0, "scaffold_selector": "blank"} ` |
</details>
- **Step 25: Raw Unitig Image**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmpwrj4k1w9/files/b/a/e/dataset_baec60f2-8ccf-45b8-8eda-9abde8052b30.dat' input.gfa && export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.png' --height '2000' --nodewidth '25.0'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| fontsize | ` None ` |
| height | ` "2000" ` |
| lengths | ` false ` |
| names | ` false ` |
| nodewidth | ` "25.0" ` |
| output\_format | ` "png" ` |
| width | ` None ` |
</details>
- **Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpwrj4k1w9/files/b/3/a/dataset_b3a22a86-faf8-4239-8de8-119a5666b454.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpwrj4k1w9/job_working_directory/000/20/outputs/dataset_7e391502-7753-479c-a94d-0a4c330cea1f.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpwrj4k1w9/files/6/f/1/dataset_6f159fb6-0ae5-4eb3-b205-ce45488d5c00.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpwrj4k1w9/job_working_directory/000/21/outputs/dataset_d327ec9c-b825-475c-bf6a-260168f5cf78.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpwrj4k1w9/files/b/3/a/dataset_b3a22a86-faf8-4239-8de8-119a5666b454.dat' --out-size c --discover-paths --tabular > '/tmp/tmpwrj4k1w9/job_working_directory/000/22/outputs/dataset_793ea023-552c-4ea2-9e50-4dff9ad910de.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpwrj4k1w9/files/b/3/a/dataset_b3a22a86-faf8-4239-8de8-119a5666b454.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 35
Total scaffold length: 1008829
Average scaffold length: 28823.69
Scaffold N50: 24719
Scaffold auN: 47664.45
Scaffold L50: 10
Largest scaffold: 132637
Smallest scaffold: 11730
# contigs: 35
Total contig length: 1008829
Average contig length: 28823.69
Contig N50: 24719
Contig auN: 47664.45
Contig L50: 10
Largest contig: 132637
Smallest contig: 11730
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 303859:199058:199884:306028
GC content %: 39.55
# soft-masked bases: 0
# segments: 35
Total segment length: 1008829
Average segment length: 28823.69
# gaps: 0
# paths: 35
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpwrj4k1w9/files/6/f/1/dataset_6f159fb6-0ae5-4eb3-b205-ce45488d5c00.dat' --out-size c --discover-paths --tabular > '/tmp/tmpwrj4k1w9/job_working_directory/000/24/outputs/dataset_e47da8bf-08cd-4738-8b31-db97d5736859.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 4: Genomescope Summary**:
* step_state: scheduled
- **Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpwrj4k1w9/files/6/f/1/dataset_6f159fb6-0ae5-4eb3-b205-ce45488d5c00.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 72
Total scaffold length: 1778748
Average scaffold length: 24704.83
Scaffold N50: 22121
Scaffold auN: 35945.06
Scaffold L50: 25
Largest scaffold: 132637
Smallest scaffold: 11410
# contigs: 72
Total contig length: 1778748
Average contig length: 24704.83
Contig N50: 22121
Contig auN: 35945.06
Contig L50: 25
Largest contig: 132637
Smallest contig: 11410
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 543138:342989:347557:545064
GC content %: 38.82
# soft-masked bases: 0
# segments: 72
Total segment length: 1778748
Average segment length: 24704.83
# gaps: 0
# paths: 72
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpwrj4k1w9/files/b/3/a/dataset_b3a22a86-faf8-4239-8de8-119a5666b454.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 35
Total scaffold length: 1008829
Average scaffold length: 28823.69
Scaffold N50: 24719
Scaffold auN: 47664.45
Scaffold L50: 10
Largest scaffold: 132637
Smallest scaffold: 11730
# contigs: 35
Total contig length: 1008829
Average contig length: 28823.69
Contig N50: 24719
Contig auN: 47664.45
Contig L50: 10
Largest contig: 132637
Smallest contig: 11730
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 303859:199058:199884:306028
GC content %: 39.55
# soft-masked bases: 0
# segments: 35
Total segment length: 1008829
Average segment length: 28823.69
# gaps: 0
# paths: 35
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpwrj4k1w9/files/6/f/1/dataset_6f159fb6-0ae5-4eb3-b205-ce45488d5c00.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 72
Total scaffold length: 1778748
Average scaffold length: 24704.83
Scaffold N50: 22121
Scaffold auN: 35945.06
Scaffold L50: 25
Largest scaffold: 132637
Smallest scaffold: 11410
# contigs: 72
Total contig length: 1778748
Average contig length: 24704.83
Contig N50: 22121
Contig auN: 35945.06
Contig L50: 25
Largest contig: 132637
Smallest contig: 11410
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 543138:342989:347557:545064
GC content %: 38.82
# soft-masked bases: 0
# segments: 72
Total segment length: 1778748
Average segment length: 24704.83
# gaps: 0
# paths: 72
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 34: 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/tmpwrj4k1w9/job_working_directory/000/28/configs/tmpbvx2oztl' '/tmp/tmpwrj4k1w9/files/7/e/3/dataset_7e391502-7753-479c-a94d-0a4c330cea1f.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/28/outputs/dataset_0ec35f04-286b-43db-9147-7614b783b2d4.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "BEGIN{print \"Metric\\thap2\"}; {print}; " ` |
| dbkey | ` "?" ` |
</details>
- **Step 35: 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/tmpwrj4k1w9/job_working_directory/000/29/configs/tmpbeopd5_z' '/tmp/tmpwrj4k1w9/files/d/3/2/dataset_d327ec9c-b825-475c-bf6a-260168f5cf78.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/29/outputs/dataset_a4a3d42e-d2ad-4a6a-9452-3030b50f081d.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "BEGIN{print \"Metric\\thap1\"}; {print}; " ` |
| dbkey | ` "?" ` |
</details>
- **Step 36: Data Prep Hap2**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: gfa_stats**:
* step_state: scheduled
- **Step 2: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpwrj4k1w9/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpwrj4k1w9/files/7/9/3/dataset_793ea023-552c-4ea2-9e50-4dff9ad910de.dat' --output='/tmp/tmpwrj4k1w9/job_working_directory/000/30/outputs/dataset_58d73ebb-761d-4c41-b5f8-a8480075e651.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3f43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 3: 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/tmpwrj4k1w9/job_working_directory/000/31/configs/tmpa9qzy6eo' '/tmp/tmpwrj4k1w9/files/5/8/d/dataset_58d73ebb-761d-4c41-b5f8-a8480075e651.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/31/outputs/dataset_9286db39-eaa9-4737-bb4b-c1ed04a33ab5.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3f43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 4: 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/tmpwrj4k1w9/files/9/2/8/dataset_9286db39-eaa9-4737-bb4b-c1ed04a33ab5.dat > '/tmp/tmpwrj4k1w9/job_working_directory/000/32/outputs/dataset_5b705203-de6e-4590-8ee2-cf36789a3c23.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3f43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/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 5: 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/tmpwrj4k1w9/files/9/2/8/dataset_9286db39-eaa9-4737-bb4b-c1ed04a33ab5.dat" "/tmp/tmpwrj4k1w9/job_working_directory/000/33/outputs/dataset_6f40bfec-8176-45d4-87f3-3131b3af9443.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3f43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 6: 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\_\_ | ` "e574fd3f43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 7: 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\_\_ | ` "e574fd3f43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/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": "1008829", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpwrj4k1w9/job_working_directory/000/55/configs/tmp9n0pnqci' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpwrj4k1w9/files/6/f/4/dataset_6f40bfec-8176-45d4-87f3-3131b3af9443.dat' '/tmp/tmpwrj4k1w9/job_working_directory/000/55/outputs/dataset_7cd2a14f-c7a0-4ceb-a37f-2f8e8656499b.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 3 new columns with instructions ['c3/1008829;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 35 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3f43b211efbfc95f3c64deef26" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/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": "c3/1008829"}, {"__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>
</details>
- **Step 37: Data Prep Hap1**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: gfa_stats**:
* step_state: scheduled
- **Step 2: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpwrj4k1w9/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpwrj4k1w9/files/e/4/7/dataset_e47da8bf-08cd-4738-8b31-db97d5736859.dat' --output='/tmp/tmpwrj4k1w9/job_working_directory/000/35/outputs/dataset_b9ccf7f4-883f-4330-98be-12f43207712a.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4043b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 3: 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/tmpwrj4k1w9/job_working_directory/000/36/configs/tmp1kyxmbok' '/tmp/tmpwrj4k1w9/files/b/9/c/dataset_b9ccf7f4-883f-4330-98be-12f43207712a.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/36/outputs/dataset_ab0cdb46-f20c-456a-9702-615095c1d6e1.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4043b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 4: 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/tmpwrj4k1w9/files/a/b/0/dataset_ab0cdb46-f20c-456a-9702-615095c1d6e1.dat > '/tmp/tmpwrj4k1w9/job_working_directory/000/37/outputs/dataset_ccfc8232-5540-425c-abfa-d107a0fef3a6.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4043b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/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 5: 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/tmpwrj4k1w9/files/a/b/0/dataset_ab0cdb46-f20c-456a-9702-615095c1d6e1.dat" "/tmp/tmpwrj4k1w9/job_working_directory/000/38/outputs/dataset_3f9c2e5c-a759-4e82-a610-3e31e5108760.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4043b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 6: 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\_\_ | ` "e574fd4043b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 7: 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\_\_ | ` "e574fd4043b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/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": "1778748", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpwrj4k1w9/job_working_directory/000/56/configs/tmp_6dp2x60' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpwrj4k1w9/files/3/f/9/dataset_3f9c2e5c-a759-4e82-a610-3e31e5108760.dat' '/tmp/tmpwrj4k1w9/job_working_directory/000/56/outputs/dataset_4a58b2ca-42e4-4726-bf8f-aa249d88ec7f.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 3 new columns with instructions ['c3/1778748;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 72 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4043b211efbfc95f3c64deef26" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/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": "c3/1778748"}, {"__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>
</details>
- **Step 38: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpwrj4k1w9/job_working_directory/000/40/configs/tmp9jz16cmq' '/tmp/tmpwrj4k1w9/files/2/a/e/dataset_2aece2f6-ca1b-4130-9436-388176370f73.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/40/outputs/dataset_c3a3ea3d-5da0-4ec5-84f1-6ab0bb5375c5.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/_path//g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 39: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpwrj4k1w9/job_working_directory/000/41/configs/tmp8zhevgk_' '/tmp/tmpwrj4k1w9/files/6/d/9/dataset_6d9cec78-1bee-439b-96d0-bdc5979e9e29.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/41/outputs/dataset_09dfca66-a933-4585-8cbd-914b3824f49b.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/_path//g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 40: join1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpwrj4k1w9/galaxy-dev/tools/filters/join.py' '/tmp/tmpwrj4k1w9/files/a/4/a/dataset_a4a3d42e-d2ad-4a6a-9452-3030b50f081d.dat' '/tmp/tmpwrj4k1w9/files/0/e/c/dataset_0ec35f04-286b-43db-9147-7614b783b2d4.dat' 1 1 '/tmp/tmpwrj4k1w9/job_working_directory/000/42/outputs/dataset_c7005a7e-b823-4d7a-9fca-88fd31f94c57.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpwrj4k1w9/job_working_directory/000/42/configs/tmpco5jal47
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| field1 | ` "1" ` |
| field2 | ` "1" ` |
| fill\_empty\_columns | ` {"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"} ` |
| header | ` "" ` |
| partial | ` "-p" ` |
| unmatched | ` "-u" ` |
</details>
- **Step 5: Meryl Database**:
* step_state: scheduled
- **Step 41: Plot Data**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: Primary data**:
* step_state: scheduled
- **Step 2: Alternate data**:
* step_state: scheduled
- **Step 11: Size Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpwrj4k1w9/job_working_directory/000/63/configs/tmp_ibqf5rt' && Rscript '/tmp/tmpwrj4k1w9/job_working_directory/000/63/configs/tmp_ibqf5rt'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library(ggplot2)
#Choose between automatically scaled x and y axis or user defined
gg_scalex = NULL
gg_scaley = NULL
gg_theme = theme_bw()
gg_legend = theme(legend.position="right")
input <- read.csv('/tmp/tmpwrj4k1w9/files/8/9/2/dataset_89206b4c-b42f-4b66-b363-5459740d095a.dat', sep='\t', header=TRUE)
names(input)[2] <- "xcol"
names(input)[3] <- "ycol"
gg_facet = NULL
gg_factor = aes(colour=factor(factor))
gg_line = geom_line(size=1, alpha=1, gg_factor)
color_scale = scale_color_brewer(palette='Set1', direction='1')
names(input)[1] <- "factor"
gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
gg_gridline = NULL
gg_point = NULL
#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('6.0')
gg_height <- as.double('4.0')
gg_unit <- 'in'
gg_dpi <- as.double('300.0')
gg_add_device <- 'none'
output1 <- '/tmp/tmpwrj4k1w9/job_working_directory/000/63/outputs/dataset_628d685d-9947-4507-97b4-0a24f7f7dcff.dat'
output2 <- 'XXXX'
ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
if(gg_add_device != "none"){
ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
}
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4143b211efbfc95f3c64deef26" ` |
| 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/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` |
| title | ` "" ` |
| xlab | ` "Scaffold number" ` |
| xplot | ` "2" ` |
| ylab | ` "Cumulative Size (Mb)" ` |
| yplot | ` "3" ` |
</details>
- **Step 3: Name of primary assembly**:
* step_state: scheduled
- **Step 4: Name of alternate assembly**:
* step_state: scheduled
- **Step 5: 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/tmpwrj4k1w9/files/4/a/5/dataset_4a58b2ca-42e4-4726-bf8f-aa249d88ec7f.dat" "/tmp/tmpwrj4k1w9/job_working_directory/000/57/outputs/dataset_4466aacd-1f57-440e-a218-7a16f41b6c74.dat" "Hap1" "no"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4143b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "Hap1" ` |
| iterate | ` "no" ` |
</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/tmpwrj4k1w9/files/7/c/d/dataset_7cd2a14f-c7a0-4ceb-a37f-2f8e8656499b.dat" "/tmp/tmpwrj4k1w9/job_working_directory/000/58/outputs/dataset_9fa8be7d-6604-43a0-8dc6-c14055469ce0.dat" "Hap2" "no"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4143b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "Hap2" ` |
| iterate | ` "no" ` |
</details>
- **Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cat/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpwrj4k1w9/files/4/4/6/dataset_4466aacd-1f57-440e-a218-7a16f41b6c74.dat' >> '/tmp/tmpwrj4k1w9/job_working_directory/000/59/outputs/dataset_cf2c7514-ff26-4b73-bf74-02b9ac6059b5.dat' && cat '/tmp/tmpwrj4k1w9/files/9/f/a/dataset_9fa8be7d-6604-43a0-8dc6-c14055469ce0.dat' >> '/tmp/tmpwrj4k1w9/job_working_directory/000/59/outputs/dataset_cf2c7514-ff26-4b73-bf74-02b9ac6059b5.dat' && exit 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4143b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| queries | ` [{"__index__": 0, "inputs2": {"values": [{"id": 106, "src": "hda"}]}}] ` |
</details>
- **Step 8: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpwrj4k1w9/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwrj4k1w9/files/c/f/2/dataset_cf2c7514-ff26-4b73-bf74-02b9ac6059b5.dat' 'c8,c5,c6' T '/tmp/tmpwrj4k1w9/job_working_directory/000/60/outputs/dataset_2977f044-e9af-4b8c-9cb9-b6f0590321db.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4143b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c5,c6" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 9: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpwrj4k1w9/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwrj4k1w9/files/c/f/2/dataset_cf2c7514-ff26-4b73-bf74-02b9ac6059b5.dat' 'c8,c4,c7' T '/tmp/tmpwrj4k1w9/job_working_directory/000/61/outputs/dataset_89206b4c-b42f-4b66-b363-5459740d095a.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4143b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c4,c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 10: Nx Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpwrj4k1w9/job_working_directory/000/62/configs/tmpwuz8gap5' && Rscript '/tmp/tmpwrj4k1w9/job_working_directory/000/62/configs/tmpwuz8gap5'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library(ggplot2)
#Choose between automatically scaled x and y axis or user defined
gg_scalex = NULL
gg_scaley = NULL
gg_theme = theme_bw()
gg_legend = theme(legend.position="right")
input <- read.csv('/tmp/tmpwrj4k1w9/files/2/9/7/dataset_2977f044-e9af-4b8c-9cb9-b6f0590321db.dat', sep='\t', header=TRUE)
names(input)[2] <- "xcol"
names(input)[3] <- "ycol"
gg_facet = NULL
gg_factor = aes(colour=factor(factor))
gg_line = geom_line(size=1, alpha=1, gg_factor)
color_scale = scale_color_brewer(palette='Set1', direction='1')
names(input)[1] <- "factor"
gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
gg_gridline = NULL
gg_point = NULL
#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('6.0')
gg_height <- as.double('4.0')
gg_unit <- 'in'
gg_dpi <- as.double('300.0')
gg_add_device <- 'none'
output1 <- '/tmp/tmpwrj4k1w9/job_working_directory/000/62/outputs/dataset_3f0a874d-d86e-4259-aa29-6ac90159c427.dat'
output2 <- 'XXXX'
ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
if(gg_add_device != "none"){
ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
}
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd4143b211efbfc95f3c64deef26" ` |
| 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/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` |
| title | ` "" ` |
| xlab | ` "x" ` |
| xplot | ` "2" ` |
| ylab | ` "Nx (Mb)" ` |
| yplot | ` "3" ` |
</details>
</details>
- **Step 42: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
busco --in '/tmp/tmpwrj4k1w9/files/c/3/a/dataset_c3a3ea3d-5da0-4ec5-84f1-6ab0bb5375c5.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --update-data --lineage_dataset 'vertebrata_odb10' && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
2024-07-16 20:54:21 ERROR:
Warning message:
package ‘ggplot2’ was built under R version 4.2.3
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
```
**Standard Output:**
* ```console
2024-07-16 20:43:06 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 07/16/2024 20:43:06 *****
2024-07-16 20:43:06 INFO: Configuring BUSCO with local environment
2024-07-16 20:43:06 INFO: Mode is genome
2024-07-16 20:43:06 INFO: Downloading information on latest versions of BUSCO data...
2024-07-16 20:43:12 INFO: Input file is /tmp/tmpwrj4k1w9/files/c/3/a/dataset_c3a3ea3d-5da0-4ec5-84f1-6ab0bb5375c5.dat
2024-07-16 20:43:12 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/vertebrata_odb10.2024-01-08.tar.gz'
2024-07-16 20:43:25 INFO: Decompressing file '/tmp/tmpwrj4k1w9/job_working_directory/000/43/working/busco_downloads/lineages/vertebrata_odb10.tar.gz'
2024-07-16 20:43:53 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-16 20:43:53 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-16 20:43:53 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2024-01-08)
2024-07-16 20:43:53 INFO: Running 1 job(s) on bbtools, starting at 07/16/2024 20:43:53
2024-07-16 20:43:55 INFO: [bbtools] 1 of 1 task(s) completed
2024-07-16 20:44:00 INFO: Running 1 job(s) on metaeuk, starting at 07/16/2024 20:44:00
2024-07-16 20:46:56 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-16 20:46:57 INFO: ***** Run HMMER on gene sequences *****
2024-07-16 20:46:57 INFO: Running 3354 job(s) on hmmsearch, starting at 07/16/2024 20:46:57
2024-07-16 20:47:02 INFO: [hmmsearch] 336 of 3354 task(s) completed
2024-07-16 20:47:07 INFO: [hmmsearch] 671 of 3354 task(s) completed
2024-07-16 20:47:11 INFO: [hmmsearch] 1007 of 3354 task(s) completed
2024-07-16 20:47:15 INFO: [hmmsearch] 1342 of 3354 task(s) completed
2024-07-16 20:47:19 INFO: [hmmsearch] 1677 of 3354 task(s) completed
2024-07-16 20:47:22 INFO: [hmmsearch] 2013 of 3354 task(s) completed
2024-07-16 20:47:25 INFO: [hmmsearch] 2348 of 3354 task(s) completed
2024-07-16 20:47:28 INFO: [hmmsearch] 2684 of 3354 task(s) completed
2024-07-16 20:47:32 INFO: [hmmsearch] 3019 of 3354 task(s) completed
2024-07-16 20:47:37 INFO: [hmmsearch] 3354 of 3354 task(s) completed
2024-07-16 20:47:40 INFO: Validating exons and removing overlapping matches
2024-07-16 20:47:41 INFO: 0 candidate overlapping regions found
2024-07-16 20:47:41 INFO: 26 exons in total
2024-07-16 20:47:41 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-07-16 20:49:22 INFO: Running 1 job(s) on metaeuk, starting at 07/16/2024 20:49:22
2024-07-16 20:53:35 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-16 20:53:36 INFO: ***** Run HMMER on gene sequences *****
2024-07-16 20:53:36 INFO: Running 3337 job(s) on hmmsearch, starting at 07/16/2024 20:53:36
2024-07-16 20:53:40 INFO: [hmmsearch] 334 of 3337 task(s) completed
2024-07-16 20:53:44 INFO: [hmmsearch] 668 of 3337 task(s) completed
2024-07-16 20:53:48 INFO: [hmmsearch] 1002 of 3337 task(s) completed
2024-07-16 20:53:52 INFO: [hmmsearch] 1335 of 3337 task(s) completed
2024-07-16 20:53:56 INFO: [hmmsearch] 1669 of 3337 task(s) completed
2024-07-16 20:54:00 INFO: [hmmsearch] 2003 of 3337 task(s) completed
2024-07-16 20:54:04 INFO: [hmmsearch] 2336 of 3337 task(s) completed
2024-07-16 20:54:08 INFO: [hmmsearch] 2670 of 3337 task(s) completed
2024-07-16 20:54:11 INFO: [hmmsearch] 3004 of 3337 task(s) completed
2024-07-16 20:54:15 INFO: [hmmsearch] 3337 of 3337 task(s) completed
2024-07-16 20:54:18 INFO: Validating exons and removing overlapping matches
2024-07-16 20:54:19 INFO: 0 candidate overlapping regions found
2024-07-16 20:54:19 INFO: 24 exons in total
2024-07-16 20:54:19 INFO: Results: C:0.5%[S:0.5%,D:0.0%],F:0.2%,M:99.3%,n:3354
2024-07-16 20:54:19 INFO:
---------------------------------------------------
|Results from dataset vertebrata_odb10 |
---------------------------------------------------
|C:0.5%[S:0.5%,D:0.0%],F:0.2%,M:99.3%,n:3354 |
|17 Complete BUSCOs (C) |
|16 Complete and single-copy BUSCOs (S) |
|1 Complete and duplicated BUSCOs (D) |
|6 Fragmented BUSCOs (F) |
|3331 Missing BUSCOs (M) |
|3354 Total BUSCO groups searched |
---------------------------------------------------
2024-07-16 20:54:19 INFO: BUSCO analysis done with WARNING(s). Total running time: 667 seconds
***** Summary of warnings: *****
2024-07-16 20:43:53 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-16 20:43:53 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-16 20:54:19 INFO: Results written in /tmp/tmpwrj4k1w9/job_working_directory/000/43/working/busco_galaxy
2024-07-16 20:54:19 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
2024-07-16 20:54:19 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 136
drwxr-xr-x 5 1001 127 4096 Jul 16 20:43 busco_sequences
-rw-r--r-- 1 1001 127 72957 Jul 16 20:54 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Jul 16 20:47 hmmer_output
drwxr-xr-x 4 1001 127 4096 Jul 16 20:54 metaeuk_output
-rw-r--r-- 1 1001 127 42736 Jul 16 20:54 missing_busco_list.tsv
-rw-r--r-- 1 1001 127 2298 Jul 16 20:54 short_summary.json
-rw-r--r-- 1 1001 127 882 Jul 16 20:54 short_summary.txt
2024-07-16 20:54:19 INFO: ****************** Start plot generation at 07/16/2024 20:54:19 ******************
2024-07-16 20:54:19 INFO: Load data ...
2024-07-16 20:54:19 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-07-16 20:54:19 INFO: Generate the R code ...
2024-07-16 20:54:19 INFO: Run the R code ...
2024-07-16 20:54:21 INFO:
[1] "Plotting the figure ..."
[1] "Done"
2024-07-16 20:54:21 INFO: Plot generation done. Total running time: 2.27154278755188 seconds
2024-07-16 20:54:21 INFO: Results written in BUSCO_summaries/
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| adv | ` {"contig_break": "10", "evalue": "0.001", "limit": "3"} ` |
| busco\_mode | ` {"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}} ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| lineage | ` {"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"} ` |
| lineage\_conditional | ` {"__current_case__": 1, "selector": "download"} ` |
| outputs | ` ["short_summary", "missing", "image", "gff"] ` |
</details>
- **Step 43: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpwrj4k1w9/files/6/b/a/dataset_6bae683e-cfc1-4e56-b544-133fcc6cf1a8.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpwrj4k1w9/files/0/9/d/dataset_09dfca66-a933-4585-8cbd-914b3824f49b.dat' assembly_01.fasta && ln -s '/tmp/tmpwrj4k1w9/files/c/3/a/dataset_c3a3ea3d-5da0-4ec5-84f1-6ab0bb5375c5.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpwrj4k1w9/job_working_directory/000/44/outputs/dataset_a64b777b-14db-4111-9780-a5d986b5aa51.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files && sed -i '1s/^/assembly\tk-mer set\tsolid k-mers in assembly\tsolid k-mers in reads\tcompleteness %\n/' 'output_files/output_merqury.completeness.stats' && sed -i '1s/^/assembly\tunique k-mers\tcommon k-mers\tQV\terror rate\n/' 'output_files/output_merqury.qv'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| label | ` "output_merqury" ` |
| mode | ` {"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 51, "src": "hda"}]}, "assembly_02": {"values": [{"id": 50, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"} ` |
| output\_add\_headers | ` true ` |
| output\_selector | ` ["qv", "plots", "stats", "log", "hist"] ` |
</details>
- **Step 44: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
busco --in '/tmp/tmpwrj4k1w9/files/0/9/d/dataset_09dfca66-a933-4585-8cbd-914b3824f49b.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --update-data --lineage_dataset 'vertebrata_odb10' && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
2024-07-16 20:57:08 ERROR:
Warning message:
package ‘ggplot2’ was built under R version 4.2.3
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
```
**Standard Output:**
* ```console
2024-07-16 20:43:06 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 07/16/2024 20:43:06 *****
2024-07-16 20:43:06 INFO: Configuring BUSCO with local environment
2024-07-16 20:43:06 INFO: Mode is genome
2024-07-16 20:43:06 INFO: Downloading information on latest versions of BUSCO data...
2024-07-16 20:43:11 INFO: Input file is /tmp/tmpwrj4k1w9/files/0/9/d/dataset_09dfca66-a933-4585-8cbd-914b3824f49b.dat
2024-07-16 20:43:11 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/vertebrata_odb10.2024-01-08.tar.gz'
2024-07-16 20:43:24 INFO: Decompressing file '/tmp/tmpwrj4k1w9/job_working_directory/000/45/working/busco_downloads/lineages/vertebrata_odb10.tar.gz'
2024-07-16 20:43:51 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-16 20:43:51 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-16 20:43:51 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2024-01-08)
2024-07-16 20:43:51 INFO: Running 1 job(s) on bbtools, starting at 07/16/2024 20:43:51
2024-07-16 20:43:53 INFO: [bbtools] 1 of 1 task(s) completed
2024-07-16 20:43:58 INFO: Running 1 job(s) on metaeuk, starting at 07/16/2024 20:43:58
2024-07-16 20:47:35 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-16 20:47:36 INFO: ***** Run HMMER on gene sequences *****
2024-07-16 20:47:36 INFO: Running 3354 job(s) on hmmsearch, starting at 07/16/2024 20:47:36
2024-07-16 20:47:42 INFO: [hmmsearch] 336 of 3354 task(s) completed
2024-07-16 20:47:47 INFO: [hmmsearch] 671 of 3354 task(s) completed
2024-07-16 20:47:52 INFO: [hmmsearch] 1007 of 3354 task(s) completed
2024-07-16 20:47:57 INFO: [hmmsearch] 1342 of 3354 task(s) completed
2024-07-16 20:48:01 INFO: [hmmsearch] 1677 of 3354 task(s) completed
2024-07-16 20:48:05 INFO: [hmmsearch] 2013 of 3354 task(s) completed
2024-07-16 20:48:09 INFO: [hmmsearch] 2348 of 3354 task(s) completed
2024-07-16 20:48:12 INFO: [hmmsearch] 2684 of 3354 task(s) completed
2024-07-16 20:48:17 INFO: [hmmsearch] 3019 of 3354 task(s) completed
2024-07-16 20:48:23 INFO: [hmmsearch] 3354 of 3354 task(s) completed
2024-07-16 20:48:26 INFO: Validating exons and removing overlapping matches
2024-07-16 20:48:27 INFO: 0 candidate overlapping regions found
2024-07-16 20:48:27 INFO: 50 exons in total
2024-07-16 20:48:27 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-07-16 20:50:07 INFO: Running 1 job(s) on metaeuk, starting at 07/16/2024 20:50:07
2024-07-16 20:56:16 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-16 20:56:17 INFO: ***** Run HMMER on gene sequences *****
2024-07-16 20:56:17 INFO: Running 3320 job(s) on hmmsearch, starting at 07/16/2024 20:56:17
2024-07-16 20:56:22 INFO: [hmmsearch] 332 of 3320 task(s) completed
2024-07-16 20:56:26 INFO: [hmmsearch] 664 of 3320 task(s) completed
2024-07-16 20:56:30 INFO: [hmmsearch] 996 of 3320 task(s) completed
2024-07-16 20:56:35 INFO: [hmmsearch] 1328 of 3320 task(s) completed
2024-07-16 20:56:39 INFO: [hmmsearch] 1660 of 3320 task(s) completed
2024-07-16 20:56:44 INFO: [hmmsearch] 1992 of 3320 task(s) completed
2024-07-16 20:56:48 INFO: [hmmsearch] 2324 of 3320 task(s) completed
2024-07-16 20:56:53 INFO: [hmmsearch] 2656 of 3320 task(s) completed
2024-07-16 20:56:57 INFO: [hmmsearch] 2988 of 3320 task(s) completed
2024-07-16 20:57:02 INFO: [hmmsearch] 3320 of 3320 task(s) completed
2024-07-16 20:57:05 INFO: Validating exons and removing overlapping matches
2024-07-16 20:57:05 INFO: 0 candidate overlapping regions found
2024-07-16 20:57:05 INFO: 52 exons in total
2024-07-16 20:57:05 INFO: Results: C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354
2024-07-16 20:57:05 INFO:
---------------------------------------------------
|Results from dataset vertebrata_odb10 |
---------------------------------------------------
|C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354 |
|34 Complete BUSCOs (C) |
|33 Complete and single-copy BUSCOs (S) |
|1 Complete and duplicated BUSCOs (D) |
|13 Fragmented BUSCOs (F) |
|3307 Missing BUSCOs (M) |
|3354 Total BUSCO groups searched |
---------------------------------------------------
2024-07-16 20:57:05 INFO: BUSCO analysis done with WARNING(s). Total running time: 835 seconds
***** Summary of warnings: *****
2024-07-16 20:43:51 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-16 20:43:51 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-16 20:57:05 INFO: Results written in /tmp/tmpwrj4k1w9/job_working_directory/000/45/working/busco_galaxy
2024-07-16 20:57:05 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
2024-07-16 20:57:05 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 140
drwxr-xr-x 5 1001 127 4096 Jul 16 20:43 busco_sequences
-rw-r--r-- 1 1001 127 76099 Jul 16 20:57 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Jul 16 20:48 hmmer_output
drwxr-xr-x 4 1001 127 4096 Jul 16 20:57 metaeuk_output
-rw-r--r-- 1 1001 127 42431 Jul 16 20:57 missing_busco_list.tsv
-rw-r--r-- 1 1001 127 2298 Jul 16 20:57 short_summary.json
-rw-r--r-- 1 1001 127 883 Jul 16 20:57 short_summary.txt
2024-07-16 20:57:06 INFO: ****************** Start plot generation at 07/16/2024 20:57:06 ******************
2024-07-16 20:57:06 INFO: Load data ...
2024-07-16 20:57:06 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-07-16 20:57:06 INFO: Generate the R code ...
2024-07-16 20:57:06 INFO: Run the R code ...
2024-07-16 20:57:08 INFO:
[1] "Plotting the figure ..."
[1] "Done"
2024-07-16 20:57:08 INFO: Plot generation done. Total running time: 2.179131507873535 seconds
2024-07-16 20:57:08 INFO: Results written in BUSCO_summaries/
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| adv | ` {"contig_break": "10", "evalue": "0.001", "limit": "3"} ` |
| busco\_mode | ` {"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}} ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| lineage | ` {"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"} ` |
| lineage\_conditional | ` {"__current_case__": 1, "selector": "download"} ` |
| outputs | ` ["short_summary", "missing", "image", "gff"] ` |
</details>
- **Step 45: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cut\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cut --complement -f '3' '/tmp/tmpwrj4k1w9/files/c/7/0/dataset_c7005a7e-b823-4d7a-9fca-88fd31f94c57.dat' > '/tmp/tmpwrj4k1w9/job_working_directory/000/46/outputs/dataset_e35a3bf4-7ffb-4fe8-950f-b4da7202cdb5.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| chromInfo | ` "/tmp/tmpwrj4k1w9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| complement | ` "--complement" ` |
| cut\_type\_options | ` {"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""} ` |
| dbkey | ` "?" ` |
</details>
- **Step 46: output_merqury.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 47: output_merqury.spectra-asm.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 48: merqury_qv**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| input | ` {"values": [{"id": 7, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"} ` |
</details>
- **Step 49: output_merqury.assembly_01.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 50: merqury_stats**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| input | ` {"values": [{"id": 9, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.completeness", "which_dataset": "by_identifier"} ` |
</details>
- **Step 6: Lineage**:
* step_state: scheduled
- **Step 51: output_merqury.assembly_02.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "e574fd3e43b211efbfc95f3c64deef26" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 7: Name for Haplotype 1**:
* step_state: scheduled
- **Step 8: Name for Haplotype 2**:
* step_state: scheduled
- **Step 9: Bits for bloom filter**:
* step_state: scheduled
- **Step 10: SAK input file**:
* step_state: scheduled
</details>| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 1 |
| Error | 0 |
| Failure | 0 |
| Skipped | 0 |
- **Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_grep\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
grep -G -A 0 -B 0 --no-group-separator -i -- 'Haploid' '/tmp/tmpaomw2_y7/files/e/8/1/dataset_e81b0199-626f-4667-a7da-0cd96e4cb092.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/8/outputs/dataset_af4c5da9-5188-4ebf-a980-15a31efc2cd1.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| case\_sensitive | ` "-i" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| color | ` "NOCOLOR" ` |
| dbkey | ` "?" ` |
| invert | ` "" ` |
| lines\_after | ` "0" ` |
| lines\_before | ` "0" ` |
| regex\_type | ` "-G" ` |
| url\_paste | ` "Haploid" ` |
</details>
- **Step 15: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int --file '/tmp/tmpaomw2_y7/job_working_directory/000/9/configs/tmpit7c_k7g' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpaomw2_y7/files/7/8/4/dataset_7842bac0-36c9-4f50-9ffc-b398c13f4550.dat' '/tmp/tmpaomw2_y7/job_working_directory/000/9/outputs/dataset_81e9fee3-091a-496e-a7d2-30451ec29a9b.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 1 new columns with instructions ['c3*2;;']
Computed new column values for 100.00% of 1 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/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*2"}], "header_lines_select": "no"} ` |
</details>
- **Step 16: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmpaomw2_y7/files/5/d/5/dataset_5d5dcf84-1852-4ab2-babd-9fada093d8e2.dat' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && multiqc multiqc_WDir --filename 'report'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
/// MultiQC 🔍 | v1.11
| multiqc | MultiQC Version v1.23 now available!
| multiqc | Search path : /tmp/tmpaomw2_y7/job_working_directory/000/10/working/multiqc_WDir
| cutadapt | Found 1 reports
| multiqc | Compressing plot data
| multiqc | Report : report.html
| multiqc | Data : report_data
| multiqc | MultiQC complete
```
**Standard Output:**
* ```console
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 2/2
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| comment | ` "" ` |
| dbkey | ` "?" ` |
| export | ` false ` |
| flat | ` false ` |
| results | ` [{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}] ` |
| saveLog | ` false ` |
| title | ` "" ` |
</details>
- **Step 17: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_replace\_in\_line/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpaomw2_y7/files/a/f/4/dataset_af4c5da9-5188-4ebf-a980-15a31efc2cd1.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/11/outputs/dataset_21ac72cf-6f64-41b9-bf02-12e5681cff6d.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| replacements | ` [{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}] ` |
</details>
- **Step 18: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpaomw2_y7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpaomw2_y7/files/8/1/e/dataset_81e9fee3-091a-496e-a7d2-30451ec29a9b.dat' 'c7' T '/tmp/tmpaomw2_y7/job_working_directory/000/12/outputs/dataset_c0ff20f3-2a51-436e-8338-0d03fef41463.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 19: Convert characters1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python /tmp/tmpaomw2_y7/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpaomw2_y7/files/2/1/a/dataset_21ac72cf-6f64-41b9-bf02-12e5681cff6d.dat s /tmp/tmpaomw2_y7/job_working_directory/000/13/outputs/dataset_2938e438-3b10-4cca-bbc9-8e4c45aa563e.dat
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "txt" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| condense | ` true ` |
| convert\_from | ` "s" ` |
| dbkey | ` "?" ` |
| strip | ` true ` |
</details>
- **Step 20: Estimated homozygous read coverage**:
* 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\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 3: HiC reverse reads**:
* step_state: scheduled
- **Step 21: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpaomw2_y7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpaomw2_y7/files/2/9/3/dataset_2938e438-3b10-4cca-bbc9-8e4c45aa563e.dat' 'c3' T '/tmp/tmpaomw2_y7/job_working_directory/000/15/outputs/dataset_8f2687fa-27ec-4248-a924-f076f3b98c43.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c3" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 22: Homozygous read coverage for Hifiasm**:
* 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\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": null}, {"__index__": 1, "value": "21"}]}} ` |
</details>
- **Step 23: Estimated genome size**:
* 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\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmpaomw2_y7/files/e/c/d/dataset_ecdeed42-3326-4607-a345-324e7456be3e.dat' input_0.fastq.gz && mkdir HiCF HiCR && ln -s '/tmp/tmpaomw2_y7/files/4/2/9/dataset_429751d0-e294-4019-a2b9-5dba236dadca.dat' ./HiCF/input_0.fastqsanger.gz && ln -s '/tmp/tmpaomw2_y7/files/e/3/4/dataset_e34dab52-1ba3-4506-a735-b01833b006b3.dat' ./HiCR/input_0.fastqsanger.gz && hifiasm -t ${GALAXY_SLOTS:-1} -o output -f 32 -a 4 -z 0 -m 10000000 -p 100000 -n 3 -x 0.8 -y 0.2 --hom-cov 21 --h1 './HiCF/input_0.fastqsanger.gz' --h2 './HiCR/input_0.fastqsanger.gz' --l-msjoin 500000 --primary input_0.fastq.gz 2> output.log && mkdir noseq_files && mv *.noseq.gfa noseq_files
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "fastq.gz" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| advanced\_options | ` {"__current_case__": 0, "advanced_selector": "blank"} ` |
| assembly\_options | ` {"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"} ` |
| bins\_out | ` false ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| filter\_bits | ` "32" ` |
| hic\_partition | ` {"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null} ` |
| log\_out | ` true ` |
| mode | ` {"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}} ` |
| ont\_integration | ` {"__current_case__": 0, "ont_integration_selector": "blank"} ` |
| purge\_options | ` {"__current_case__": 0, "purge_selector": "blank"} ` |
| scaffolding\_options | ` {"__current_case__": 0, "scaffold_selector": "blank"} ` |
</details>
- **Step 25: Raw Unitig Image**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
ln -s '/tmp/tmpaomw2_y7/files/d/c/a/dataset_dcaefcd3-4086-451e-bf5a-78e7d5a2b503.dat' input.gfa && export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.png' --height '2000' --nodewidth '25.0'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| fontsize | ` None ` |
| height | ` "2000" ` |
| lengths | ` false ` |
| names | ` false ` |
| nodewidth | ` "25.0" ` |
| output\_format | ` "png" ` |
| width | ` None ` |
</details>
- **Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpaomw2_y7/files/e/6/8/dataset_e68ddb35-3d58-46f2-b44d-84fc4785e866.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpaomw2_y7/job_working_directory/000/20/outputs/dataset_dec9b23a-6373-4000-887e-5366138d7fa1.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpaomw2_y7/files/b/d/1/dataset_bd156e82-10df-4e20-a62e-53305f7e45c4.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpaomw2_y7/job_working_directory/000/21/outputs/dataset_42cdab25-e057-4504-ba72-707de96b365a.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpaomw2_y7/files/e/6/8/dataset_e68ddb35-3d58-46f2-b44d-84fc4785e866.dat' --out-size c --discover-paths --tabular > '/tmp/tmpaomw2_y7/job_working_directory/000/22/outputs/dataset_056195f0-641f-4608-9099-9e2ef7a26435.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpaomw2_y7/files/e/6/8/dataset_e68ddb35-3d58-46f2-b44d-84fc4785e866.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 35
Total scaffold length: 1008829
Average scaffold length: 28823.69
Scaffold N50: 24719
Scaffold auN: 47664.45
Scaffold L50: 10
Largest scaffold: 132637
Smallest scaffold: 11730
# contigs: 35
Total contig length: 1008829
Average contig length: 28823.69
Contig N50: 24719
Contig auN: 47664.45
Contig L50: 10
Largest contig: 132637
Smallest contig: 11730
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 303859:199058:199884:306028
GC content %: 39.55
# soft-masked bases: 0
# segments: 35
Total segment length: 1008829
Average segment length: 28823.69
# gaps: 0
# paths: 35
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpaomw2_y7/files/b/d/1/dataset_bd156e82-10df-4e20-a62e-53305f7e45c4.dat' --out-size c --discover-paths --tabular > '/tmp/tmpaomw2_y7/job_working_directory/000/24/outputs/dataset_e9871bcd-1e36-42db-a2a0-e7c28ac9e8e6.dat' --threads ${GALAXY_SLOTS:-8}
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 4: Genomescope Summary**:
* step_state: scheduled
- **Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpaomw2_y7/files/b/d/1/dataset_bd156e82-10df-4e20-a62e-53305f7e45c4.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 72
Total scaffold length: 1778748
Average scaffold length: 24704.83
Scaffold N50: 22121
Scaffold auN: 35945.06
Scaffold L50: 25
Largest scaffold: 132637
Smallest scaffold: 11410
# contigs: 72
Total contig length: 1778748
Average contig length: 24704.83
Contig N50: 22121
Contig auN: 35945.06
Contig L50: 25
Largest contig: 132637
Smallest contig: 11410
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 543138:342989:347557:545064
GC content %: 38.82
# soft-masked bases: 0
# segments: 72
Total segment length: 1778748
Average segment length: 24704.83
# gaps: 0
# paths: 72
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpaomw2_y7/files/e/6/8/dataset_e68ddb35-3d58-46f2-b44d-84fc4785e866.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 35
Total scaffold length: 1008829
Average scaffold length: 28823.69
Scaffold N50: 24719
Scaffold auN: 47664.45
Scaffold L50: 10
Largest scaffold: 132637
Smallest scaffold: 11730
# contigs: 35
Total contig length: 1008829
Average contig length: 28823.69
Contig N50: 24719
Contig auN: 47664.45
Contig L50: 10
Largest contig: 132637
Smallest contig: 11730
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 303859:199058:199884:306028
GC content %: 39.55
# soft-masked bases: 0
# segments: 35
Total segment length: 1008829
Average segment length: 28823.69
# gaps: 0
# paths: 35
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
gfastats '/tmp/tmpaomw2_y7/files/b/d/1/dataset_bd156e82-10df-4e20-a62e-53305f7e45c4.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
+++Assembly summary+++:
# scaffolds: 72
Total scaffold length: 1778748
Average scaffold length: 24704.83
Scaffold N50: 22121
Scaffold auN: 35945.06
Scaffold L50: 25
Largest scaffold: 132637
Smallest scaffold: 11410
# contigs: 72
Total contig length: 1778748
Average contig length: 24704.83
Contig N50: 22121
Contig auN: 35945.06
Contig L50: 25
Largest contig: 132637
Smallest contig: 11410
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 543138:342989:347557:545064
GC content %: 38.82
# soft-masked bases: 0
# segments: 72
Total segment length: 1778748
Average segment length: 24704.83
# gaps: 0
# paths: 72
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` |
| target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` |
</details>
- **Step 34: 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/tmpaomw2_y7/job_working_directory/000/28/configs/tmpr0phkar8' '/tmp/tmpaomw2_y7/files/d/e/c/dataset_dec9b23a-6373-4000-887e-5366138d7fa1.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/28/outputs/dataset_c0ed1d16-f55e-46af-b8b2-8d6c105f8e87.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "BEGIN{print \"Metric\\thap2\"}; {print}; " ` |
| dbkey | ` "?" ` |
</details>
- **Step 35: 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/tmpaomw2_y7/job_working_directory/000/29/configs/tmpxpr_mnra' '/tmp/tmpaomw2_y7/files/4/2/c/dataset_42cdab25-e057-4504-ba72-707de96b365a.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/29/outputs/dataset_24dbd01f-d62e-4c11-9693-07d10276f5e2.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "BEGIN{print \"Metric\\thap1\"}; {print}; " ` |
| dbkey | ` "?" ` |
</details>
- **Step 36: Data Prep Hap2**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: gfa_stats**:
* step_state: scheduled
- **Step 2: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpaomw2_y7/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpaomw2_y7/files/0/5/6/dataset_056195f0-641f-4608-9099-9e2ef7a26435.dat' --output='/tmp/tmpaomw2_y7/job_working_directory/000/30/outputs/dataset_6cf5cf71-7017-49cf-aa8b-230dca6c3d1a.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8deb452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 3: 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/tmpaomw2_y7/job_working_directory/000/31/configs/tmprvaw3e9c' '/tmp/tmpaomw2_y7/files/6/c/f/dataset_6cf5cf71-7017-49cf-aa8b-230dca6c3d1a.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/31/outputs/dataset_7c0b0059-4d75-4377-b6e8-610bb88dc7e8.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8deb452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 4: 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/tmpaomw2_y7/files/7/c/0/dataset_7c0b0059-4d75-4377-b6e8-610bb88dc7e8.dat > '/tmp/tmpaomw2_y7/job_working_directory/000/32/outputs/dataset_c449320b-8cba-4aae-b731-3670b4a3b7d4.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8deb452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/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 5: 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/tmpaomw2_y7/files/7/c/0/dataset_7c0b0059-4d75-4377-b6e8-610bb88dc7e8.dat" "/tmp/tmpaomw2_y7/job_working_directory/000/33/outputs/dataset_34739b00-0b26-4ea4-92bb-835fa91bdb10.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8deb452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 6: 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\_\_ | ` "6f1f8deb452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 7: 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\_\_ | ` "6f1f8deb452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/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": "1008829", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpaomw2_y7/job_working_directory/000/56/configs/tmp_vwljnye' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpaomw2_y7/files/3/4/7/dataset_34739b00-0b26-4ea4-92bb-835fa91bdb10.dat' '/tmp/tmpaomw2_y7/job_working_directory/000/56/outputs/dataset_426ea208-5ab8-4dfc-b001-a7dd3bb02c67.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 3 new columns with instructions ['c3/1008829;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 35 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8deb452711ef8e7417cd12271348" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/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": "c3/1008829"}, {"__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>
</details>
- **Step 37: Data Prep Hap1**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: gfa_stats**:
* step_state: scheduled
- **Step 2: sort1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpaomw2_y7/galaxy-dev/tools/filters/sorter.py' --input='/tmp/tmpaomw2_y7/files/e/9/8/dataset_e9871bcd-1e36-42db-a2a0-e7c28ac9e8e6.dat' --output='/tmp/tmpaomw2_y7/job_working_directory/000/35/outputs/dataset_10da8b68-a9ae-4fc2-ab52-2cb8ea5289a8.dat' --key=2,2nr --header 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dec452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| column | ` "2" ` |
| column\_set | ` [] ` |
| dbkey | ` "?" ` |
| header\_lines | ` "0" ` |
| order | ` "DESC" ` |
| style | ` "num" ` |
</details>
- **Step 3: 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/tmpaomw2_y7/job_working_directory/000/36/configs/tmpksfcoxk5' '/tmp/tmpaomw2_y7/files/1/0/d/dataset_10da8b68-a9ae-4fc2-ab52-2cb8ea5289a8.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/36/outputs/dataset_1d623504-6360-469b-baa4-44cf7a5ac86c.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dec452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "{total += $2; $3 = total}1" ` |
| dbkey | ` "?" ` |
</details>
- **Step 4: 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/tmpaomw2_y7/files/1/d/6/dataset_1d623504-6360-469b-baa4-44cf7a5ac86c.dat > '/tmp/tmpaomw2_y7/job_working_directory/000/37/outputs/dataset_dc2bb9c8-d0e4-4b0c-b1ec-ff8c1d38ac64.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dec452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/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 5: 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/tmpaomw2_y7/files/1/d/6/dataset_1d623504-6360-469b-baa4-44cf7a5ac86c.dat" "/tmp/tmpaomw2_y7/job_working_directory/000/38/outputs/dataset_b96e10d0-2849-4610-9e22-4cf7ae70a796.dat" "1" "yes"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dec452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "1" ` |
| iterate | ` "yes" ` |
</details>
- **Step 6: 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\_\_ | ` "6f1f8dec452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "integer" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 7: 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\_\_ | ` "6f1f8dec452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/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": "1778748", "select_param_type": "integer"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.0**:
* 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/6595517c2dd8/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpaomw2_y7/job_working_directory/000/57/configs/tmpsuppwyhh' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpaomw2_y7/files/b/9/6/dataset_b96e10d0-2849-4610-9e22-4cf7ae70a796.dat' '/tmp/tmpaomw2_y7/job_working_directory/000/57/outputs/dataset_903f44db-8401-4cee-b750-36772cec81cf.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Computing 3 new columns with instructions ['c3/1778748;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 72 lines written.
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dec452711ef8e7417cd12271348" ` |
| avoid\_scientific\_notation | ` false ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/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": "c3/1778748"}, {"__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>
</details>
- **Step 38: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpaomw2_y7/job_working_directory/000/40/configs/tmpahozv6pt' '/tmp/tmpaomw2_y7/files/f/a/7/dataset_fa7785c6-f1a9-4a04-b5ab-98f4566a4290.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/40/outputs/dataset_b9e82b17-21d3-4b1d-a88d-fc5e9d1b1801.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/_path//g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 39: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpaomw2_y7/job_working_directory/000/41/configs/tmpwq8bic3u' '/tmp/tmpaomw2_y7/files/8/4/0/dataset_84035572-e69a-44fa-ad24-3d818ca9e0d6.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/41/outputs/dataset_baab54b7-0ef8-4ba1-ab65-57bbd498deb4.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/_path//g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 40: join1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpaomw2_y7/galaxy-dev/tools/filters/join.py' '/tmp/tmpaomw2_y7/files/2/4/d/dataset_24dbd01f-d62e-4c11-9693-07d10276f5e2.dat' '/tmp/tmpaomw2_y7/files/c/0/e/dataset_c0ed1d16-f55e-46af-b8b2-8d6c105f8e87.dat' 1 1 '/tmp/tmpaomw2_y7/job_working_directory/000/42/outputs/dataset_f2c03c8d-6522-4a59-94ef-b967b30e9ef7.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpaomw2_y7/job_working_directory/000/42/configs/tmpkqxtux99
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| field1 | ` "1" ` |
| field2 | ` "1" ` |
| fill\_empty\_columns | ` {"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"} ` |
| header | ` "" ` |
| partial | ` "-p" ` |
| unmatched | ` "-u" ` |
</details>
- **Step 5: Meryl Database**:
* step_state: scheduled
- **Step 41: Plot Data**:
* step_state: scheduled
* <details><summary>Subworkflow Steps</summary>
- **Step 1: Primary data**:
* step_state: scheduled
- **Step 2: Alternate data**:
* step_state: scheduled
- **Step 11: Size Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpaomw2_y7/job_working_directory/000/64/configs/tmpibsvquvv' && Rscript '/tmp/tmpaomw2_y7/job_working_directory/000/64/configs/tmpibsvquvv'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library(ggplot2)
#Choose between automatically scaled x and y axis or user defined
gg_scalex = NULL
gg_scaley = NULL
gg_theme = theme_bw()
gg_legend = theme(legend.position="right")
input <- read.csv('/tmp/tmpaomw2_y7/files/6/3/d/dataset_63d024d9-dd6a-406d-8b90-12ce3cb4ece8.dat', sep='\t', header=TRUE)
names(input)[2] <- "xcol"
names(input)[3] <- "ycol"
gg_facet = NULL
gg_factor = aes(colour=factor(factor))
gg_line = geom_line(size=1, alpha=1, gg_factor)
color_scale = scale_color_brewer(palette='Set1', direction='1')
names(input)[1] <- "factor"
gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
gg_gridline = NULL
gg_point = NULL
#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('6.0')
gg_height <- as.double('4.0')
gg_unit <- 'in'
gg_dpi <- as.double('300.0')
gg_add_device <- 'none'
output1 <- '/tmp/tmpaomw2_y7/job_working_directory/000/64/outputs/dataset_2e30c44a-6dfb-4379-8c9f-536a61302e05.dat'
output2 <- 'XXXX'
ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
if(gg_add_device != "none"){
ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
}
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8ded452711ef8e7417cd12271348" ` |
| 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/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` |
| title | ` "" ` |
| xlab | ` "Scaffold number" ` |
| xplot | ` "2" ` |
| ylab | ` "Cumulative Size (Mb)" ` |
| yplot | ` "3" ` |
</details>
- **Step 3: Name of primary assembly**:
* step_state: scheduled
- **Step 4: Name of alternate assembly**:
* step_state: scheduled
- **Step 5: 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/tmpaomw2_y7/files/9/0/3/dataset_903f44db-8401-4cee-b750-36772cec81cf.dat" "/tmp/tmpaomw2_y7/job_working_directory/000/58/outputs/dataset_bafb1d8f-eb09-424b-8d2f-e9505c476de8.dat" "Hap1" "no"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8ded452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "Hap1" ` |
| iterate | ` "no" ` |
</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/tmpaomw2_y7/files/4/2/6/dataset_426ea208-5ab8-4dfc-b001-a7dd3bb02c67.dat" "/tmp/tmpaomw2_y7/job_working_directory/000/59/outputs/dataset_c8032c99-f53f-400d-9adb-971b14ec6e72.dat" "Hap2" "no"
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8ded452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| exp | ` "Hap2" ` |
| iterate | ` "no" ` |
</details>
- **Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cat/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpaomw2_y7/files/b/a/f/dataset_bafb1d8f-eb09-424b-8d2f-e9505c476de8.dat' >> '/tmp/tmpaomw2_y7/job_working_directory/000/60/outputs/dataset_3d748aea-f672-44ab-8d3b-c13011463694.dat' && cat '/tmp/tmpaomw2_y7/files/c/8/0/dataset_c8032c99-f53f-400d-9adb-971b14ec6e72.dat' >> '/tmp/tmpaomw2_y7/job_working_directory/000/60/outputs/dataset_3d748aea-f672-44ab-8d3b-c13011463694.dat' && exit 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8ded452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| queries | ` [{"__index__": 0, "inputs2": {"values": [{"id": 107, "src": "hda"}]}}] ` |
</details>
- **Step 8: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpaomw2_y7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpaomw2_y7/files/3/d/7/dataset_3d748aea-f672-44ab-8d3b-c13011463694.dat' 'c8,c5,c6' T '/tmp/tmpaomw2_y7/job_working_directory/000/61/outputs/dataset_1bc075af-a127-4fb1-b01a-a8dc6f204b93.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8ded452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c5,c6" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 9: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpaomw2_y7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpaomw2_y7/files/3/d/7/dataset_3d748aea-f672-44ab-8d3b-c13011463694.dat' 'c8,c4,c7' T '/tmp/tmpaomw2_y7/job_working_directory/000/62/outputs/dataset_63d024d9-dd6a-406d-8b90-12ce3cb4ece8.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8ded452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c8,c4,c7" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 10: Nx Plot**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpaomw2_y7/job_working_directory/000/63/configs/tmpr67req1g' && Rscript '/tmp/tmpaomw2_y7/job_working_directory/000/63/configs/tmpr67req1g'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library(ggplot2)
#Choose between automatically scaled x and y axis or user defined
gg_scalex = NULL
gg_scaley = NULL
gg_theme = theme_bw()
gg_legend = theme(legend.position="right")
input <- read.csv('/tmp/tmpaomw2_y7/files/1/b/c/dataset_1bc075af-a127-4fb1-b01a-a8dc6f204b93.dat', sep='\t', header=TRUE)
names(input)[2] <- "xcol"
names(input)[3] <- "ycol"
gg_facet = NULL
gg_factor = aes(colour=factor(factor))
gg_line = geom_line(size=1, alpha=1, gg_factor)
color_scale = scale_color_brewer(palette='Set1', direction='1')
names(input)[1] <- "factor"
gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
gg_gridline = NULL
gg_point = NULL
#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('6.0')
gg_height <- as.double('4.0')
gg_unit <- 'in'
gg_dpi <- as.double('300.0')
gg_add_device <- 'none'
output1 <- '/tmp/tmpaomw2_y7/job_working_directory/000/63/outputs/dataset_8f02c9a3-8f56-428b-b3d8-2116a7d43eac.dat'
output2 <- 'XXXX'
ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
if(gg_add_device != "none"){
ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
}
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8ded452711ef8e7417cd12271348" ` |
| 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/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` |
| title | ` "" ` |
| xlab | ` "x" ` |
| xplot | ` "2" ` |
| ylab | ` "Nx (Mb)" ` |
| yplot | ` "3" ` |
</details>
</details>
- **Step 42: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
busco --in '/tmp/tmpaomw2_y7/files/b/9/e/dataset_b9e82b17-21d3-4b1d-a88d-fc5e9d1b1801.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --update-data --lineage_dataset 'vertebrata_odb10' && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
2024-07-18 17:21:00 ERROR:
Warning message:
package ‘ggplot2’ was built under R version 4.2.3
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
```
**Standard Output:**
* ```console
2024-07-18 17:09:49 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 07/18/2024 17:09:49 *****
2024-07-18 17:09:49 INFO: Configuring BUSCO with local environment
2024-07-18 17:09:49 INFO: Mode is genome
2024-07-18 17:09:49 INFO: Downloading information on latest versions of BUSCO data...
2024-07-18 17:09:54 INFO: Input file is /tmp/tmpaomw2_y7/files/b/9/e/dataset_b9e82b17-21d3-4b1d-a88d-fc5e9d1b1801.dat
2024-07-18 17:09:54 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/vertebrata_odb10.2024-01-08.tar.gz'
2024-07-18 17:10:05 INFO: Decompressing file '/tmp/tmpaomw2_y7/job_working_directory/000/43/working/busco_downloads/lineages/vertebrata_odb10.tar.gz'
2024-07-18 17:10:34 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-18 17:10:34 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-18 17:10:34 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2024-01-08)
2024-07-18 17:10:34 INFO: Running 1 job(s) on bbtools, starting at 07/18/2024 17:10:34
2024-07-18 17:10:36 INFO: [bbtools] 1 of 1 task(s) completed
2024-07-18 17:10:41 INFO: Running 1 job(s) on metaeuk, starting at 07/18/2024 17:10:40
2024-07-18 17:13:32 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-18 17:13:33 INFO: ***** Run HMMER on gene sequences *****
2024-07-18 17:13:33 INFO: Running 3354 job(s) on hmmsearch, starting at 07/18/2024 17:13:33
2024-07-18 17:13:38 INFO: [hmmsearch] 336 of 3354 task(s) completed
2024-07-18 17:13:43 INFO: [hmmsearch] 671 of 3354 task(s) completed
2024-07-18 17:13:47 INFO: [hmmsearch] 1007 of 3354 task(s) completed
2024-07-18 17:13:51 INFO: [hmmsearch] 1342 of 3354 task(s) completed
2024-07-18 17:13:55 INFO: [hmmsearch] 1677 of 3354 task(s) completed
2024-07-18 17:13:58 INFO: [hmmsearch] 2013 of 3354 task(s) completed
2024-07-18 17:14:02 INFO: [hmmsearch] 2348 of 3354 task(s) completed
2024-07-18 17:14:05 INFO: [hmmsearch] 2684 of 3354 task(s) completed
2024-07-18 17:14:09 INFO: [hmmsearch] 3019 of 3354 task(s) completed
2024-07-18 17:14:14 INFO: [hmmsearch] 3354 of 3354 task(s) completed
2024-07-18 17:14:17 INFO: Validating exons and removing overlapping matches
2024-07-18 17:14:18 INFO: 0 candidate overlapping regions found
2024-07-18 17:14:18 INFO: 26 exons in total
2024-07-18 17:14:18 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-07-18 17:16:01 INFO: Running 1 job(s) on metaeuk, starting at 07/18/2024 17:16:01
2024-07-18 17:20:14 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-18 17:20:14 INFO: ***** Run HMMER on gene sequences *****
2024-07-18 17:20:14 INFO: Running 3337 job(s) on hmmsearch, starting at 07/18/2024 17:20:14
2024-07-18 17:20:19 INFO: [hmmsearch] 334 of 3337 task(s) completed
2024-07-18 17:20:22 INFO: [hmmsearch] 668 of 3337 task(s) completed
2024-07-18 17:20:26 INFO: [hmmsearch] 1002 of 3337 task(s) completed
2024-07-18 17:20:30 INFO: [hmmsearch] 1335 of 3337 task(s) completed
2024-07-18 17:20:34 INFO: [hmmsearch] 1669 of 3337 task(s) completed
2024-07-18 17:20:38 INFO: [hmmsearch] 2003 of 3337 task(s) completed
2024-07-18 17:20:42 INFO: [hmmsearch] 2336 of 3337 task(s) completed
2024-07-18 17:20:46 INFO: [hmmsearch] 2670 of 3337 task(s) completed
2024-07-18 17:20:50 INFO: [hmmsearch] 3004 of 3337 task(s) completed
2024-07-18 17:20:54 INFO: [hmmsearch] 3337 of 3337 task(s) completed
2024-07-18 17:20:57 INFO: Validating exons and removing overlapping matches
2024-07-18 17:20:57 INFO: 0 candidate overlapping regions found
2024-07-18 17:20:57 INFO: 24 exons in total
2024-07-18 17:20:57 INFO: Results: C:0.5%[S:0.5%,D:0.0%],F:0.2%,M:99.3%,n:3354
2024-07-18 17:20:57 INFO:
---------------------------------------------------
|Results from dataset vertebrata_odb10 |
---------------------------------------------------
|C:0.5%[S:0.5%,D:0.0%],F:0.2%,M:99.3%,n:3354 |
|17 Complete BUSCOs (C) |
|16 Complete and single-copy BUSCOs (S) |
|1 Complete and duplicated BUSCOs (D) |
|6 Fragmented BUSCOs (F) |
|3331 Missing BUSCOs (M) |
|3354 Total BUSCO groups searched |
---------------------------------------------------
2024-07-18 17:20:57 INFO: BUSCO analysis done with WARNING(s). Total running time: 663 seconds
***** Summary of warnings: *****
2024-07-18 17:10:34 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-18 17:10:34 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-18 17:20:57 INFO: Results written in /tmp/tmpaomw2_y7/job_working_directory/000/43/working/busco_galaxy
2024-07-18 17:20:57 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
2024-07-18 17:20:57 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 136
drwxr-xr-x 5 1001 127 4096 Jul 18 17:10 busco_sequences
-rw-r--r-- 1 1001 127 72957 Jul 18 17:20 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Jul 18 17:14 hmmer_output
drwxr-xr-x 4 1001 127 4096 Jul 18 17:20 metaeuk_output
-rw-r--r-- 1 1001 127 42736 Jul 18 17:20 missing_busco_list.tsv
-rw-r--r-- 1 1001 127 2298 Jul 18 17:20 short_summary.json
-rw-r--r-- 1 1001 127 882 Jul 18 17:20 short_summary.txt
2024-07-18 17:20:57 INFO: ****************** Start plot generation at 07/18/2024 17:20:57 ******************
2024-07-18 17:20:57 INFO: Load data ...
2024-07-18 17:20:57 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-07-18 17:20:57 INFO: Generate the R code ...
2024-07-18 17:20:57 INFO: Run the R code ...
2024-07-18 17:21:00 INFO:
[1] "Plotting the figure ..."
[1] "Done"
2024-07-18 17:21:00 INFO: Plot generation done. Total running time: 2.3523128032684326 seconds
2024-07-18 17:21:00 INFO: Results written in BUSCO_summaries/
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| adv | ` {"contig_break": "10", "evalue": "0.001", "limit": "3"} ` |
| busco\_mode | ` {"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}} ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| lineage | ` {"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"} ` |
| lineage\_conditional | ` {"__current_case__": 1, "selector": "download"} ` |
| outputs | ` ["short_summary", "missing", "image", "gff"] ` |
</details>
- **Step 43: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpaomw2_y7/files/9/4/1/dataset_9419279f-0524-4363-a1aa-60ed0f7f4c99.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpaomw2_y7/files/b/a/a/dataset_baab54b7-0ef8-4ba1-ab65-57bbd498deb4.dat' assembly_01.fasta && ln -s '/tmp/tmpaomw2_y7/files/b/9/e/dataset_b9e82b17-21d3-4b1d-a88d-fc5e9d1b1801.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpaomw2_y7/job_working_directory/000/44/outputs/dataset_61309f44-777d-443c-afea-dc2dd8f3af17.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files && sed -i '1s/^/assembly\tk-mer set\tsolid k-mers in assembly\tsolid k-mers in reads\tcompleteness %\n/' 'output_files/output_merqury.completeness.stats' && sed -i '1s/^/assembly\tunique k-mers\tcommon k-mers\tQV\terror rate\n/' 'output_files/output_merqury.qv'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| label | ` "output_merqury" ` |
| mode | ` {"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 51, "src": "hda"}]}, "assembly_02": {"values": [{"id": 50, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"} ` |
| output\_add\_headers | ` true ` |
| output\_selector | ` ["qv", "plots", "stats", "log", "hist"] ` |
</details>
- **Step 44: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
busco --in '/tmp/tmpaomw2_y7/files/b/a/a/dataset_baab54b7-0ef8-4ba1-ab65-57bbd498deb4.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --update-data --lineage_dataset 'vertebrata_odb10' && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
2024-07-18 17:23:35 ERROR:
Warning message:
package ‘ggplot2’ was built under R version 4.2.3
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
```
**Standard Output:**
* ```console
2024-07-18 17:09:49 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 07/18/2024 17:09:49 *****
2024-07-18 17:09:49 INFO: Configuring BUSCO with local environment
2024-07-18 17:09:49 INFO: Mode is genome
2024-07-18 17:09:49 INFO: Downloading information on latest versions of BUSCO data...
2024-07-18 17:09:55 INFO: Input file is /tmp/tmpaomw2_y7/files/b/a/a/dataset_baab54b7-0ef8-4ba1-ab65-57bbd498deb4.dat
2024-07-18 17:09:55 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/vertebrata_odb10.2024-01-08.tar.gz'
2024-07-18 17:10:06 INFO: Decompressing file '/tmp/tmpaomw2_y7/job_working_directory/000/45/working/busco_downloads/lineages/vertebrata_odb10.tar.gz'
2024-07-18 17:10:34 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-18 17:10:34 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-18 17:10:35 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2024-01-08)
2024-07-18 17:10:35 INFO: Running 1 job(s) on bbtools, starting at 07/18/2024 17:10:35
2024-07-18 17:10:36 INFO: [bbtools] 1 of 1 task(s) completed
2024-07-18 17:10:40 INFO: Running 1 job(s) on metaeuk, starting at 07/18/2024 17:10:40
2024-07-18 17:14:04 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-18 17:14:04 INFO: ***** Run HMMER on gene sequences *****
2024-07-18 17:14:04 INFO: Running 3354 job(s) on hmmsearch, starting at 07/18/2024 17:14:04
2024-07-18 17:14:11 INFO: [hmmsearch] 336 of 3354 task(s) completed
2024-07-18 17:14:16 INFO: [hmmsearch] 671 of 3354 task(s) completed
2024-07-18 17:14:21 INFO: [hmmsearch] 1007 of 3354 task(s) completed
2024-07-18 17:14:26 INFO: [hmmsearch] 1342 of 3354 task(s) completed
2024-07-18 17:14:30 INFO: [hmmsearch] 1677 of 3354 task(s) completed
2024-07-18 17:14:34 INFO: [hmmsearch] 2013 of 3354 task(s) completed
2024-07-18 17:14:38 INFO: [hmmsearch] 2348 of 3354 task(s) completed
2024-07-18 17:14:42 INFO: [hmmsearch] 2684 of 3354 task(s) completed
2024-07-18 17:14:47 INFO: [hmmsearch] 3019 of 3354 task(s) completed
2024-07-18 17:14:53 INFO: [hmmsearch] 3354 of 3354 task(s) completed
2024-07-18 17:14:56 INFO: Validating exons and removing overlapping matches
2024-07-18 17:14:57 INFO: 0 candidate overlapping regions found
2024-07-18 17:14:57 INFO: 50 exons in total
2024-07-18 17:14:57 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-07-18 17:16:36 INFO: Running 1 job(s) on metaeuk, starting at 07/18/2024 17:16:36
2024-07-18 17:22:45 INFO: [metaeuk] 1 of 1 task(s) completed
2024-07-18 17:22:46 INFO: ***** Run HMMER on gene sequences *****
2024-07-18 17:22:46 INFO: Running 3320 job(s) on hmmsearch, starting at 07/18/2024 17:22:46
2024-07-18 17:22:51 INFO: [hmmsearch] 332 of 3320 task(s) completed
2024-07-18 17:22:55 INFO: [hmmsearch] 664 of 3320 task(s) completed
2024-07-18 17:22:59 INFO: [hmmsearch] 996 of 3320 task(s) completed
2024-07-18 17:23:03 INFO: [hmmsearch] 1328 of 3320 task(s) completed
2024-07-18 17:23:08 INFO: [hmmsearch] 1660 of 3320 task(s) completed
2024-07-18 17:23:12 INFO: [hmmsearch] 1992 of 3320 task(s) completed
2024-07-18 17:23:17 INFO: [hmmsearch] 2324 of 3320 task(s) completed
2024-07-18 17:23:21 INFO: [hmmsearch] 2656 of 3320 task(s) completed
2024-07-18 17:23:25 INFO: [hmmsearch] 2988 of 3320 task(s) completed
2024-07-18 17:23:29 INFO: [hmmsearch] 3320 of 3320 task(s) completed
2024-07-18 17:23:32 INFO: Validating exons and removing overlapping matches
2024-07-18 17:23:33 INFO: 0 candidate overlapping regions found
2024-07-18 17:23:33 INFO: 52 exons in total
2024-07-18 17:23:33 INFO: Results: C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354
2024-07-18 17:23:33 INFO:
---------------------------------------------------
|Results from dataset vertebrata_odb10 |
---------------------------------------------------
|C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354 |
|34 Complete BUSCOs (C) |
|33 Complete and single-copy BUSCOs (S) |
|1 Complete and duplicated BUSCOs (D) |
|13 Fragmented BUSCOs (F) |
|3307 Missing BUSCOs (M) |
|3354 Total BUSCO groups searched |
---------------------------------------------------
2024-07-18 17:23:33 INFO: BUSCO analysis done with WARNING(s). Total running time: 818 seconds
***** Summary of warnings: *****
2024-07-18 17:10:34 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met
2024-07-18 17:10:34 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met
2024-07-18 17:23:33 INFO: Results written in /tmp/tmpaomw2_y7/job_working_directory/000/45/working/busco_galaxy
2024-07-18 17:23:33 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
2024-07-18 17:23:33 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 140
drwxr-xr-x 5 1001 127 4096 Jul 18 17:10 busco_sequences
-rw-r--r-- 1 1001 127 76099 Jul 18 17:23 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Jul 18 17:14 hmmer_output
drwxr-xr-x 4 1001 127 4096 Jul 18 17:23 metaeuk_output
-rw-r--r-- 1 1001 127 42431 Jul 18 17:23 missing_busco_list.tsv
-rw-r--r-- 1 1001 127 2298 Jul 18 17:23 short_summary.json
-rw-r--r-- 1 1001 127 883 Jul 18 17:23 short_summary.txt
2024-07-18 17:23:33 INFO: ****************** Start plot generation at 07/18/2024 17:23:33 ******************
2024-07-18 17:23:33 INFO: Load data ...
2024-07-18 17:23:33 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-07-18 17:23:33 INFO: Generate the R code ...
2024-07-18 17:23:33 INFO: Run the R code ...
2024-07-18 17:23:35 INFO:
[1] "Plotting the figure ..."
[1] "Done"
2024-07-18 17:23:35 INFO: Plot generation done. Total running time: 2.0762593746185303 seconds
2024-07-18 17:23:35 INFO: Results written in BUSCO_summaries/
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| adv | ` {"contig_break": "10", "evalue": "0.001", "limit": "3"} ` |
| busco\_mode | ` {"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}} ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| lineage | ` {"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"} ` |
| lineage\_conditional | ` {"__current_case__": 1, "selector": "download"} ` |
| outputs | ` ["short_summary", "missing", "image", "gff"] ` |
</details>
- **Step 45: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cut\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cut --complement -f '3' '/tmp/tmpaomw2_y7/files/f/2/c/dataset_f2c03c8d-6522-4a59-94ef-b967b30e9ef7.dat' > '/tmp/tmpaomw2_y7/job_working_directory/000/46/outputs/dataset_2faba0ec-ac64-455b-9897-dad8566713d6.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| complement | ` "--complement" ` |
| cut\_type\_options | ` {"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""} ` |
| dbkey | ` "?" ` |
</details>
- **Step 46: output_merqury.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 47: output_merqury.spectra-asm.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 48: merqury_qv**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| input | ` {"values": [{"id": 7, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"} ` |
</details>
- **Step 49: output_merqury.assembly_01.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 50: merqury_stats**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| input | ` {"values": [{"id": 9, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.completeness", "which_dataset": "by_identifier"} ` |
</details>
- **Step 6: Lineage**:
* step_state: scheduled
- **Step 51: output_merqury.assembly_02.spectra-cn.fl**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| input | ` {"values": [{"id": 8, "src": "hdca"}]} ` |
| which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"} ` |
</details>
- **Step 52: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_find\_and\_replace/9.3+galaxy1**:
* 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/bgruening/text_processing/fbf99087e067/text_processing/find_and_replace' -o '/tmp/tmpaomw2_y7/job_working_directory/000/47/outputs/dataset_7abe2142-6399-43dd-b496-3e00b82b22f4.dat' -g '#' 'Number of' '/tmp/tmpaomw2_y7/files/2/f/a/dataset_2faba0ec-ac64-455b-9897-dad8566713d6.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "6f1f8dea452711ef8e7417cd12271348" ` |
| chromInfo | ` "/tmp/tmpaomw2_y7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| find\_and\_replace | ` [{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}] ` |
</details>
- **Step 7: Name for Haplotype 1**:
* step_state: scheduled
- **Step 8: Name for Haplotype 2**:
* step_state: scheduled
- **Step 9: Bits for bloom filter**:
* step_state: scheduled
- **Step 10: SAK input file**:
* step_state: scheduled
</details>