galaxyproject / iwc

Galaxy Workflows maintained by the Intergalactic Workflow Commission
https://dockstore.org/organizations/iwc
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Updating workflows/epigenetics/atacseq from 0.16 to 0.17 #482

Closed gxydevbot closed 1 month ago

gxydevbot commented 3 months ago

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

The workflow release number has been updated from 0.16 to 0.17.

gxydevbot commented 1 month ago

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

github-actions[bot] commented 1 month ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ atacseq.ga_0
**Execution Problem:** * ``` Failed to run workflow, at least one job is in [error] state. ``` #### Workflow invocation details * Invocation Messages *
Steps - **Step 1: PE fastq input**: * step_state: scheduled - **Step 2: reference_genome**: * step_state: scheduled - **Step 11: convert BAM to BED to improve peak calling**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console ln -s '/tmp/tmplg07et_q/files/9/2/2/dataset_922a0de9-2ab3-4c9b-867a-a71a2dfc7257.dat' ./input.bam && bedtools bamtobed -i ./input.bam > '/tmp/tmplg07et_q/job_working_directory/000/9/outputs/dataset_06812ce1-f041-4841-87e6-ae7a5844afc2.dat' ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` | | dbkey | ` "hg19" ` | | ed\_score | ` false ` | | option | ` "" ` | | split | ` false ` | | tag | ` "" ` |
 - **Step 12: Compute fragment length histogram**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           ln -s '/tmp/tmplg07et_q/files/9/2/2/dataset_922a0de9-2ab3-4c9b-867a-a71a2dfc7257.dat' localbam.bam && ln -f -s '/tmp/tmplg07et_q/files/_metadata_files/5/5/8/metadata_558e6d2b-d27d-4eb7-9e1f-aaab05aa1175.dat' localbam.bam.bai && java -jar '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/bd1416eea1f0/pe_histogram/PEHistogram.jar' -B localbam.bam -I localbam.bam.bai -u 500 -p '/tmp/tmplg07et_q/job_working_directory/000/10/outputs/dataset_9456dfb7-cbac-4dd2-a8ba-85a4544ba1c5.dat' -t '/tmp/tmplg07et_q/job_working_directory/000/10/outputs/dataset_e0a9a692-3a7d-49d3-adeb-a40cb1bebd7f.dat' 1>/dev/null
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "bam" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | lower\_limit | ` None ` |
             | upper\_limit | ` "500" ` |

      </details>

 - **Step 13: number of reads**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmplg07et_q/files/9/2/2/dataset_922a0de9-2ab3-4c9b-867a-a71a2dfc7257.dat' infile && ln -s '/tmp/tmplg07et_q/files/_metadata_files/5/5/8/metadata_558e6d2b-d27d-4eb7-9e1f-aaab05aa1175.dat' infile.bai &&        samtools view -@ $addthreads -c    -o outfile     infile
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | mode | ` {"__current_case__": 0, "output_options": {"__current_case__": 1, "reads_report_type": "count"}, "outtype": "all_reads"} ` |

      </details>

 - **Step 14: Call Peak with MACS2**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           export PYTHON_EGG_CACHE=`pwd` &&   (macs2 callpeak   -t '/tmp/tmplg07et_q/files/0/6/8/dataset_06812ce1-f041-4841-87e6-ae7a5844afc2.dat'  --name SRR891268_chr22_enriched    --format BED   --gsize '2700000000'           --call-summits  --keep-dup 'all'  --d-min 20 --buffer-size 100000  --bdg  --qvalue '0.05'  --nomodel --extsize '200' --shift '-100'  2>&1 > macs2_stderr) && cp SRR891268_chr22_enriched_peaks.xls '/tmp/tmplg07et_q/job_working_directory/000/12/outputs/dataset_63c04351-b11f-4479-a666-ae55fa68b75d.dat'   && ( count=`ls -1 SRR891268_chr22_enriched* 2>/dev/null | wc -l`; if [ $count != 0 ]; then mkdir '/tmp/tmplg07et_q/job_working_directory/000/12/outputs/dataset_4be9bfb8-ccb8-4134-a615-edaf94244ae0_files' && cp -r SRR891268_chr22_enriched* '/tmp/tmplg07et_q/job_working_directory/000/12/outputs/dataset_4be9bfb8-ccb8-4134-a615-edaf94244ae0_files' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/macs2/86e2413cf3f8/macs2/dir2html.py' '/tmp/tmplg07et_q/job_working_directory/000/12/outputs/dataset_4be9bfb8-ccb8-4134-a615-edaf94244ae0_files' macs2_stderr > '/tmp/tmplg07et_q/job_working_directory/000/12/outputs/dataset_4be9bfb8-ccb8-4134-a615-edaf94244ae0.dat'; fi; ) && exit_code_for_galaxy=$? && cat macs2_stderr 2>&1 && (exit $exit_code_for_galaxy)
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Output:**

         * ```console
           INFO  @ Mon, 23 Sep 2024 15:01:44: 
           # Command line: callpeak -t /tmp/tmplg07et_q/files/0/6/8/dataset_06812ce1-f041-4841-87e6-ae7a5844afc2.dat --name SRR891268_chr22_enriched --format BED --gsize 2700000000 --call-summits --keep-dup all --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --nomodel --extsize 200 --shift -100
           # ARGUMENTS LIST:
           # name = SRR891268_chr22_enriched
           # format = BED
           # ChIP-seq file = ['/tmp/tmplg07et_q/files/0/6/8/dataset_06812ce1-f041-4841-87e6-ae7a5844afc2.dat']
           # control file = None
           # effective genome size = 2.70e+09
           # band width = 300
           # model fold = [5, 50]
           # qvalue cutoff = 5.00e-02
           # The maximum gap between significant sites is assigned as the read length/tag size.
           # The minimum length of peaks is assigned as the predicted fragment length "d".
           # Larger dataset will be scaled towards smaller dataset.
           # Range for calculating regional lambda is: 10000 bps
           # Broad region calling is off
           # Paired-End mode is off
           # Searching for subpeak summits is on

           INFO  @ Mon, 23 Sep 2024 15:01:44: #1 read tag files... 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #1 read treatment tags... 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #1 tag size is determined as 47 bps 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #1 tag size = 47.0 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #1  total tags in treatment: 232804 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #1 finished! 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #2 Build Peak Model... 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #2 Skipped... 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #2 Use 200 as fragment length 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #2 Sequencing ends will be shifted towards 5' by 100 bp(s) 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #3 Call peaks... 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #3 Going to call summits inside each peak ... 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #3 Pre-compute pvalue-qvalue table... 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #3 In the peak calling step, the following will be performed simultaneously: 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... SRR891268_chr22_enriched_treat_pileup.bdg 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #3   Write bedGraph files for control lambda (after scaling if necessary)... SRR891268_chr22_enriched_control_lambda.bdg 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #3   Pileup will be based on sequencing depth in treatment. 
           INFO  @ Mon, 23 Sep 2024 15:01:44: #3 Call peaks for each chromosome... 
           INFO  @ Mon, 23 Sep 2024 15:01:45: #4 Write output xls file... SRR891268_chr22_enriched_peaks.xls 
           INFO  @ Mon, 23 Sep 2024 15:01:45: #4 Write peak in narrowPeak format file... SRR891268_chr22_enriched_peaks.narrowPeak 
           INFO  @ Mon, 23 Sep 2024 15:01:45: #4 Write summits bed file... SRR891268_chr22_enriched_summits.bed 
           INFO  @ Mon, 23 Sep 2024 15:01:45: Done! 

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | advanced\_options | ` {"broad_options": {"__current_case__": 1, "broad_options_selector": "nobroad", "call_summits": true}, "buffer_size": "100000", "d_min": "20", "keep_dup_options": {"__current_case__": 2, "keep_dup_options_selector": "all"}, "llocal": null, "nolambda": false, "ratio": null, "slocal": null, "spmr": false, "to_large": false} ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | control | ` {"__current_case__": 1, "c_select": "No"} ` |
             | cutoff\_options | ` {"__current_case__": 1, "cutoff_options_selector": "qvalue", "qvalue": "0.05"} ` |
             | dbkey | ` "hg19" ` |
             | effective\_genome\_size\_options | ` {"__current_case__": 4, "effective_genome_size_options_selector": "user_defined", "gsize": "2700000000"} ` |
             | format | ` "BED" ` |
             | nomodel\_type | ` {"__current_case__": 1, "extsize": "200", "nomodel_type_selector": "nomodel", "shift": "-100"} ` |
             | outputs | ` ["peaks_tabular", "summits", "bdg", "html"] ` |
             | treatment | ` {"__current_case__": 0, "input_treatment_file": {"values": [{"id": 16, "src": "dce"}]}, "t_multi_select": "No"} ` |

      </details>

 - **Step 15: compute 1/million reads**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types int --avoid-scientific-notation --file '/tmp/tmplg07et_q/job_working_directory/000/13/configs/tmpra9jpg4l' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmplg07et_q/files/e/e/5/dataset_ee5adc42-f959-4ad0-9bc5-7037d9816f49.dat' '/tmp/tmplg07et_q/job_working_directory/000/13/outputs/dataset_1e8a5768-3f50-46ea-83f9-bc76b40700cb.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Output:**

         * ```console
           1000000/c1
           Computing 0 new columns with instructions ['1000000/c1;1R;']
           Computed new column values for 100.00% of 1 lines written.

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | avoid\_scientific\_notation | ` true ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | 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__": 2, "mode": "R", "pos": "1"}, "cond": "1000000/c1"}], "header_lines_select": "no"} ` |

      </details>

 - **Step 16: Bigwig from MACS2 (no norm)**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           grep -v "^track" '/tmp/tmplg07et_q/files/f/1/e/dataset_f1ed7a0e-69d9-479e-87fc-5716010e4fa5.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len' '/tmp/tmplg07et_q/job_working_directory/000/14/outputs/dataset_6de36ca3-12bd-4a62-a7d1-4fce5bd63b03.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "bedgraph" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | settings | ` {"__current_case__": 0, "settingsType": "preset"} ` |

      </details>

 - **Step 17: get summits +/-500kb**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           bedtools slop    -g '/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len'  -i '/tmp/tmplg07et_q/files/4/9/a/dataset_49a58f4b-c275-48f1-bec6-7ff67ff5d543.dat' -b 500  > '/tmp/tmplg07et_q/job_working_directory/000/15/outputs/dataset_624c3e02-9aaf-45d2-8aa8-cffc535fa5d4.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | addition | ` {"__current_case__": 0, "addition_select": "b", "b": "500"} ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | genome\_file\_opts | ` {"__current_case__": 0, "genome": "hg19", "genome_file_opts_selector": "loc"} ` |
             | header | ` false ` |
             | pct | ` false ` |
             | strand | ` false ` |

      </details>

 - **Step 18: summary of MACS2**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           grep -P -A 0 -B 0 --no-group-separator  -i -- '^#' '/tmp/tmplg07et_q/files/6/3/c/dataset_63c04351-b11f-4479-a666-ae55fa68b75d.dat' > '/tmp/tmplg07et_q/job_working_directory/000/16/outputs/dataset_38f4d72f-984d-4949-92b4-14c922d90255.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | case\_sensitive | ` "-i" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | color | ` "NOCOLOR" ` |
             | dbkey | ` "hg19" ` |
             | invert | ` "" ` |
             | lines\_after | ` "0" ` |
             | lines\_before | ` "0" ` |
             | regex\_type | ` "-P" ` |
             | url\_paste | ` "^#" ` |

      </details>

 - **Step 19: Convert 1/million reads to parameter**:

    * 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\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | param\_type | ` "text" ` |
             | remove\_newlines | ` true ` |

      </details>

 - **Step 20: Isolate each bigwig do normalize not average**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | input | ` {"values": [{"id": 23, "src": "hdca"}]} ` |
             | rules | ` {"mapping": [{"collapsible_value": {"__class__": "RuntimeValue"}, "columns": [0, 1], "connectable": true, "editing": false, "is_workflow": false, "type": "list_identifiers"}], "rules": [{"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"collapsible_value": {"__class__": "RuntimeValue"}, "connectable": true, "error": null, "is_workflow": false, "type": "add_column_metadata", "value": "identifier0", "warn": null}]} ` |

      </details>

 - **Step 3: effective_genome_size**:

    * step_state: scheduled

 - **Step 21: Merge summits +/-500kb**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           mergeBed -i '/tmp/tmplg07et_q/files/6/2/4/dataset_624c3e02-9aaf-45d2-8aa8-cffc535fa5d4.dat'  -d 0    > '/tmp/tmplg07et_q/job_working_directory/000/18/outputs/dataset_82ad138b-e620-47bf-8479-6bd5396c42c4.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | c\_and\_o\_argument\_repeat | ` [] ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | distance | ` "0" ` |
             | header | ` false ` |
             | strand | ` "" ` |

      </details>

 - **Step 22: normalize by million reads**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is running

        **Command Line:**

         * ```console
           bigwigAverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bigwigs /tmp/tmplg07et_q/files/6/d/e/dataset_6de36ca3-12bd-4a62-a7d1-4fce5bd63b03.dat --outFileName '/tmp/tmplg07et_q/job_working_directory/000/27/outputs/dataset_9c54add5-ee50-49bc-9d5b-62b01acf9594.dat' --outFileFormat 'bigwig'     --scaleFactors '4.295458840913386' --binSize 1000
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | advancedOpt | ` {"__current_case__": 1, "binSize": "1000", "blackListFileName": null, "scaleFactors": "4.295458840913386", "showAdvancedOpt": "yes", "skipNAs": false} ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | outFileFormat | ` "bigwig" ` |
             | region | ` "" ` |

      </details>

 - **Step 23: Compute coverage on summits +/-500kb**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           bedtools coverage        -a '/tmp/tmplg07et_q/files/8/2/a/dataset_82ad138b-e620-47bf-8479-6bd5396c42c4.dat' -b '/tmp/tmplg07et_q/files/9/2/2/dataset_922a0de9-2ab3-4c9b-867a-a71a2dfc7257.dat'      | sort -k1,1 -k2,2n > '/tmp/tmplg07et_q/job_working_directory/000/19/outputs/dataset_24487674-bd57-4acb-98e1-7ffcde692a6b.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | a\_or\_b | ` false ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | d | ` false ` |
             | dbkey | ` "hg19" ` |
             | hist | ` false ` |
             | mean | ` false ` |
             | overlap\_a | ` None ` |
             | overlap\_b | ` None ` |
             | reciprocal\_overlap | ` false ` |
             | reduce\_or\_iterate | ` {"__current_case__": 0, "inputB": {"values": [{"id": 14, "src": "dce"}]}, "reduce_or_iterate_selector": "iterate"} ` |
             | sorted | ` false ` |
             | split | ` false ` |
             | strandedness | ` false ` |

      </details>

 - **Step 24: number of reads in peaks**:

    * 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/tmplg07et_q/job_working_directory/000/20/configs/tmpnf08ggeh' '/tmp/tmplg07et_q/files/2/4/4/dataset_24487674-bd57-4acb-98e1-7ffcde692a6b.dat' > '/tmp/tmplg07et_q/job_working_directory/000/20/outputs/dataset_3c28d031-53ac-48cc-ae1f-aeb12435f4b7.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | code | ` "{S=S+$4}END{print S}" ` |
             | dbkey | ` "hg19" ` |

      </details>

 - **Step 25: compute 1/million reads in peaks**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types int --avoid-scientific-notation --file '/tmp/tmplg07et_q/job_working_directory/000/21/configs/tmpryvabeom' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmplg07et_q/files/3/c/2/dataset_3c28d031-53ac-48cc-ae1f-aeb12435f4b7.dat' '/tmp/tmplg07et_q/job_working_directory/000/21/outputs/dataset_a44d4794-2bca-480a-8100-d415ee759d6d.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Output:**

         * ```console
           1000000/c1
           Computing 0 new columns with instructions ['1000000/c1;1R;']
           Computed new column values for 100.00% of 1 lines written.

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | avoid\_scientific\_notation | ` true ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | 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__": 2, "mode": "R", "pos": "1"}, "cond": "1000000/c1"}], "header_lines_select": "no"} ` |

      </details>

 - **Step 26: Combine number of reads in peaks with total number of reads**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           python /tmp/tmplg07et_q/galaxy-dev/tools/filters/catWrapper.py '/tmp/tmplg07et_q/job_working_directory/000/22/outputs/dataset_d262816f-3382-4139-8ef9-1e0313fe317d.dat' '/tmp/tmplg07et_q/files/3/c/2/dataset_3c28d031-53ac-48cc-ae1f-aeb12435f4b7.dat' '/tmp/tmplg07et_q/files/e/e/5/dataset_ee5adc42-f959-4ad0-9bc5-7037d9816f49.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "tabular" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | queries | ` [{"__index__": 0, "input2": {"values": [{"id": 19, "src": "dce"}]}}] ` |

      </details>

 - **Step 27: Convert 1/million reads in peaks to parameter**:

    * 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\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | param\_type | ` "text" ` |
             | remove\_newlines | ` true ` |

      </details>

 - **Step 28: reads in peaks multiQC**:

    * 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/tmplg07et_q/job_working_directory/000/24/configs/tmpi72h41d1' '/tmp/tmplg07et_q/files/d/2/6/dataset_d262816f-3382-4139-8ef9-1e0313fe317d.dat' > '/tmp/tmplg07et_q/job_working_directory/000/24/outputs/dataset_3f220cc1-ff8c-43ab-9d00-d18239658190.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | code | ` " NR==1{print \"in peaks\",$1;inp=$1}NR==2{print \"outside peaks\",$1 - inp}" ` |
             | dbkey | ` "hg19" ` |

      </details>

 - **Step 29: normalize by million reads in peaks**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is running

        **Command Line:**

         * ```console
           bigwigAverage --numberOfProcessors "${GALAXY_SLOTS:-4}" --bigwigs /tmp/tmplg07et_q/files/6/d/e/dataset_6de36ca3-12bd-4a62-a7d1-4fce5bd63b03.dat --outFileName '/tmp/tmplg07et_q/job_working_directory/000/28/outputs/dataset_51369d65-e762-4ae5-a5e3-5b1a01507d33.dat' --outFileFormat 'bigwig'     --scaleFactors '114.96895838123707' --binSize 1000
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | advancedOpt | ` {"__current_case__": 1, "binSize": "1000", "blackListFileName": null, "scaleFactors": "114.96895838123707", "showAdvancedOpt": "yes", "skipNAs": false} ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |
             | outFileFormat | ` "bigwig" ` |
             | region | ` "" ` |

      </details>

 - **Step 30: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is error

        **Command Line:**

         * ```console
           die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/cutadapt_0 &&     ln -s '/tmp/tmplg07et_q/files/6/f/7/dataset_6f7d9739-56d4-4f8f-9293-e211963596c9.dat' 'multiqc_WDir/cutadapt_0/SRR891268_chr22_enriched.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/SRR891268_chr22_enriched.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/SRR891268_chr22_enriched.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" &&  mkdir multiqc_WDir/bowtie2_1 &&         grep -q '% overall alignment rate' /tmp/tmplg07et_q/files/4/5/0/dataset_450a5187-ddf8-42ae-a39a-3a39a34dd332.dat || die "Module 'bowtie2: '% overall alignment rate' not found in the file 'SRR891268_chr22_enriched'" && ln -s '/tmp/tmplg07et_q/files/4/5/0/dataset_450a5187-ddf8-42ae-a39a-3a39a34dd332.dat' 'multiqc_WDir/bowtie2_1/SRR891268_chr22_enriched'  &&    mkdir multiqc_WDir/custom_content_2 && ln -s '/tmp/tmplg07et_q/files/6/9/4/dataset_694b467f-a1fa-4e7c-8bcd-236df8495281.dat' 'multiqc_WDir/custom_content_2/file_2_0' && more /tmp/tmplg07et_q/files/6/9/4/dataset_694b467f-a1fa-4e7c-8bcd-236df8495281.dat && mkdir multiqc_WDir/picard_3 &&      mkdir 'multiqc_WDir/picard_3/markdups_0' &&    grep -q 'MarkDuplicates' /tmp/tmplg07et_q/files/3/6/d/dataset_36dd14cf-e40a-4819-a74d-73efeb75aa1c.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR891268_chr22_enriched'" && ln -s '/tmp/tmplg07et_q/files/3/6/d/dataset_36dd14cf-e40a-4819-a74d-73efeb75aa1c.dat' 'multiqc_WDir/picard_3/markdups_0/SRR891268_chr22_enriched'  &&    mkdir multiqc_WDir/custom_content_4 && ln -s '/tmp/tmplg07et_q/files/e/0/a/dataset_e0a9a692-3a7d-49d3-adeb-a40cb1bebd7f.dat' 'multiqc_WDir/custom_content_4/file_4_0' && more /tmp/tmplg07et_q/files/e/0/a/dataset_e0a9a692-3a7d-49d3-adeb-a40cb1bebd7f.dat && mkdir multiqc_WDir/macs2_5 &&    grep -q "# This file is generated by MACS" /tmp/tmplg07et_q/files/6/3/c/dataset_63c04351-b11f-4479-a666-ae55fa68b75d.dat || die "'# This file is generated by MACS' not found in the file" && ln -s '/tmp/tmplg07et_q/files/6/3/c/dataset_63c04351-b11f-4479-a666-ae55fa68b75d.dat' 'multiqc_WDir/macs2_5/SRR891268_chr22_enriched_peaks.xls' && mkdir multiqc_WDir/custom_content_6 && ln -s '/tmp/tmplg07et_q/files/3/f/2/dataset_3f220cc1-ff8c-43ab-9d00-d18239658190.dat' 'multiqc_WDir/custom_content_6/file_6_0' && more /tmp/tmplg07et_q/files/3/f/2/dataset_3f220cc1-ff8c-43ab-9d00-d18239658190.dat &&  multiqc multiqc_WDir --filename 'report'    --export  --config '/tmp/tmplg07et_q/job_working_directory/000/25/configs/tmpfrz0jg0j'  && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Error:**

         * ```console

           /// MultiQC 🔍 v1.24.1

                       config | Loading config settings from: /tmp/tmplg07et_q/job_working_directory/000/25/configs/tmpfrz0jg0j
                version_check | MultiQC Version v1.25 now available!
                  file_search | Search path: /tmp/tmplg07et_q/job_working_directory/000/25/working/multiqc_WDir

           ╭───────────── Oops! The 'custom_content' MultiQC module broke... ─────────────╮
           │ Please copy this log and report it at                                        │
           │ https://github.com/MultiQC/MultiQC/issues                                    │
           │ Please attach a file that triggers the error. The last file found was:       │
           │ multiqc_WDir/custom_content_4/file_4_0                                       │
           │                                                                              │
           │ Traceback (most recent call last):                                           │
           │   File "/usr/local/lib/python3.12/site-packages/multiqc/modules/custom_conte │
           │     hconfig = yaml.safe_load("\n".join(hlines))                              │
           │               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                              │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/__init__.py", line 125, │
           │     return load(stream, SafeLoader)                                          │
           │            ^^^^^^^^^^^^^^^^^^^^^^^^                                          │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/__init__.py", line 81,  │
           │     return loader.get_single_data()                                          │
           │            ^^^^^^^^^^^^^^^^^^^^^^^^                                          │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/constructor.py", line 4 │
           │     node = self.get_single_node()                                            │
           │            ^^^^^^^^^^^^^^^^^^^^^^                                            │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/composer.py", line 36,  │
           │     document = self.compose_document()                                       │
           │                ^^^^^^^^^^^^^^^^^^^^^^^                                       │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/composer.py", line 58,  │
           │     self.get_event()                                                         │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/parser.py", line 118, i │
           │     self.current_event = self.state()                                        │
           │                          ^^^^^^^^^^^^                                        │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/parser.py", line 193, i │
           │     token = self.peek_token()                                                │
           │             ^^^^^^^^^^^^^^^^^                                                │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/scanner.py", line 129,  │
           │     self.fetch_more_tokens()                                                 │
           │   File "/usr/local/lib/python3.12/site-packages/yaml/scanner.py", line 258,  │
           │     raise ScannerError("while scanning for the next token", None,            │
           │ yaml.scanner.ScannerError: while scanning for the next token                 │
           │ found character '\t' that cannot start any token                             │
           │   in "<unicode string>", line 2, column 15:                                  │
           │      Chromosome_ID  Chromosome_Size Aligned_Reads                            │
           │                   ^                                                          │
           │                                                                              │
           │ During handling of the above exception, another exception occurred:          │
           │                                                                              │
           │ Traceback (most recent call last):                                           │
           │   File "/usr/local/lib/python3.12/site-packages/multiqc/core/exec_modules.py │
           │     these_modules: Union[BaseMultiqcModule, List[BaseMultiqcModule]] = modul │
           │                                                                        ^^^^^ │
           │   File "/usr/local/lib/python3.12/site-packages/multiqc/modules/custom_conte │
           │     m_config, non_header_lines = _find_file_header(f)                        │
           │                                  ^^^^^^^^^^^^^^^^^^^^                        │
           │   File "/usr/local/lib/python3.12/site-packages/multiqc/modules/custom_conte │
           │     raise ConfigValidationError(                                             │
           │ multiqc.validation.ConfigValidationError                                     │
           │                                                                              │
           ╰──────────────────────────────────────────────────────────────────────────────╯
                        macs2 | Found 1 logs
                       picard | Found 1 MarkDuplicates reports
                      bowtie2 | Found 1 reports
                     cutadapt | Found 1 reports

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

           ```
        **Standard Output:**

         * ```console
           ::::::::::::::
           /tmp/tmplg07et_q/files/6/9/4/dataset_694b467f-a1fa-4e7c-8bcd-236df8495281.dat
           ::::::::::::::
           chrM 216347
           others   339454
           ::::::::::::::
           /tmp/tmplg07et_q/files/e/0/a/dataset_e0a9a692-3a7d-49d3-adeb-a40cb1bebd7f.dat
           ::::::::::::::
           # localbam.bam
           # Chromosome_ID  Chromosome_Size Aligned_Reads
           # chr10  135534747   5214.0
           # chr11  135006516   5674.0
           # chr11_gl000202_random  40103   0.0
           # chr12  133851895   5404.0
           # chr13  115169878   3794.0
           # chr14  107349540   3422.0
           # chr15  102531392   2518.0
           # chr16  90354753    3218.0
           # chr17_ctg5_hap1    1680828 0.0
           # chr17  81195210    2880.0
           # chr17_gl000203_random  37498   0.0
           # chr17_gl000204_random  81310   0.0
           # chr17_gl000205_random  174588  42.0
           # chr17_gl000206_random  41001   0.0
           # chr18  78077248    3012.0
           # chr18_gl000207_random  4262    0.0
           # chr19  59128983    2580.0
           # chr19_gl000208_random  92689   2.0
           # chr19_gl000209_random  159169  0.0
           # chr1   249250621   9842.0
           # chr1_gl000191_random   106433  2.0
           # chr1_gl000192_random   547496  4.0
           # chr20  63025520    2366.0
           # chr21  48129895    1214.0
           # chr21_gl000210_random  27682   0.0
           # chr22  51304566    116840.0
           # chr2   243199373   10050.0
           # chr3   198022430   8394.0
           # chr4_ctg9_hap1 590426  0.0
           # chr4   191154276   8172.0
           # chr4_gl000193_random   189789  2.0
           # chr4_gl000194_random   191469  4.0
           # chr5   180915260   7536.0
           # chr6_apd_hap1  4622290 0.0
           # chr6_cox_hap2  4795371 2.0
           # chr6_dbb_hap3  4610396 0.0
           # chr6   171115067   7054.0
           # chr6_mann_hap4 4683263 2.0
           # chr6_mcf_hap5  4833398 0.0
           # chr6_qbl_hap6  4611984 0.0
           # chr6_ssto_hap7 4928567 0.0
           # chr7   159138663   6548.0
           # chr7_gl000195_random   182896  16.0
           # chr8   146364022   6326.0
           # chr8_gl000196_random   38914   0.0
           # chr8_gl000197_random   37175   0.0
           # chr9   141213431   4420.0
           # chr9_gl000198_random   90085   22.0
           # chr9_gl000199_random   169874  2.0
           # chr9_gl000200_random   187035  0.0
           # chr9_gl000201_random   36148   0.0
           # chrM   16571   0.0
           # chrUn_gl000211 166566  6.0
           # chrUn_gl000212 186858  2.0
           # chrUn_gl000213 164239  0.0
           # chrUn_gl000214 137718  10.0
           # chrUn_gl000215 172545  0.0
           # chrUn_gl000216 172294  2.0
           # chrUn_gl000217 172149  24.0
           # chrUn_gl000218 161147  0.0
           # chrUn_gl000219 179198  10.0
           # chrUn_gl000220 161802  236.0
           # chrUn_gl000221 155397  2.0
           # chrUn_gl000222 186861  0.0
           # chrUn_gl000223 180455  0.0
           # chrUn_gl000224 179693  8.0
           # chrUn_gl000225 211173  8.0
           # chrUn_gl000226 15008   6.0
           # chrUn_gl000227 128374  0.0
           # chrUn_gl000228 129120  0.0
           # chrUn_gl000229 19913   82.0
           # chrUn_gl000230 43691   8.0
           # chrUn_gl000231 27386   84.0
           # chrUn_gl000232 40652   158.0
           # chrUn_gl000233 45941   32.0
           # chrUn_gl000234 40531   122.0
           # chrUn_gl000235 34474   50.0
           # chrUn_gl000236 41934   0.0
           # chrUn_gl000237 45867   66.0
           # chrUn_gl000238 39939   2.0
           # chrUn_gl000239 33824   2.0
           # chrUn_gl000240 41933   12.0
           # chrUn_gl000241 42152   118.0
           # chrUn_gl000242 43523   10.0
           # chrUn_gl000243 43341   12.0
           # chrUn_gl000244 39929   0.0
           # chrUn_gl000245 36651   2.0
           # chrUn_gl000246 38154   6.0
           # chrUn_gl000247 36422   0.0
           # chrUn_gl000248 39786   6.0
           # chrUn_gl000249 38502   0.0
           # chrX   155270560   5134.0
           # chrY   59373566    6.0
           # Total Genome Size: 3.137161264E9   Total Aligned Tags: 232804.0
           # bowtie2    # 2.5.3
           # "/usr/local/bin/bowtie2-align-s --wrapper basic-0 -p 1 -x /cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full --very-sensitive -1 input_f.fastq -2 input_r.fastq"
           # samtools   # 1.19.2
           # samtools sort -l 0 -T /tmp/tmplg07et_q/tmp -O bam
           # MarkDuplicates # Version:3.1.1
           # MarkDuplicates --TAGGING_POLICY All --INPUT SRR891268_chr22_enriched --OUTPUT /tmp/tmplg07et_q/job_working_directory/000/7/outputs/dataset_922a0de9-2ab3-4c9b-867a-a71a2dfc7257.dat --METRICS_FILE /tmp/tmplg07et_q/job_working_directory/000/7/outputs/dataset_36dd14cf-e40a-4819-a74d-73efeb75aa1c.dat --REMOVE_DUPLICATES true --ASSUME_SORTED true --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --VERBOSITY ERROR --QUIET true --VALIDATION_STRINGENCY LENIENT --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
           # Average Insert Size: 162.46371196371197
           # Median Insert Size: 126.0
           # Std deviation of Insert Size: 117.9037267671474
           # Number of ReadPairs: 116402.0
           # Histogram
           # Size (bp)  Frequency
           0    0.0
           1    0.0
           2    0.0
           3    0.0
           4    0.0
           5    0.0
           6    0.0
           7    0.0
           8    0.0
           9    0.0
           10   0.0
           11   0.0
           12   0.0
           13   0.0
           14   0.0
           15   0.0
           16   0.0
           17   0.0
           18   0.0
           19   0.0
           20   0.0
           21   0.0
           22   0.0
           23   1.0
           24   1.0
           25   11.0
           26   142.0
           27   117.0
           28   131.0
           29   130.0
           30   90.0
           31   88.0
           32   101.0
           33   116.0
           34   199.0
           35   385.0
           36   613.0
           37   761.0
           38   827.0
           39   1076.0
           40   1305.0
           41   1453.0
           42   1503.0
           43   1415.0
           44   1214.0
           45   1206.0
           46   1057.0
           47   969.0
           48   14.0
           49   19.0
           50   1190.0
           51   1450.0
           52   1335.0
           53   1142.0
           54   1041.0
           55   1022.0
           56   934.0
           57   779.0
           58   759.0
           59   711.0
           60   711.0
           61   880.0
           62   926.0
           63   835.0
           64   905.0
           65   885.0
           66   765.0
           67   697.0
           68   651.0
           69   598.0
           70   638.0
           71   717.0
           72   749.0
           73   770.0
           74   736.0
           75   677.0
           76   653.0
           77   578.0
           78   569.0
           79   530.0
           80   508.0
           81   594.0
           82   631.0
           83   584.0
           84   605.0
           85   579.0
           86   593.0
           87   544.0
           88   487.0
           89   439.0
           90   395.0
           91   420.0
           92   469.0
           93   512.0
           94   484.0
           95   502.0
           96   473.0
           97   431.0
           98   380.0
           99   348.0
           100  350.0
           101  380.0
           102  343.0
           103  371.0
           104  420.0
           105  410.0
           106  414.0
           107  364.0
           108  363.0
           109  301.0
           110  281.0
           111  314.0
           112  306.0
           113  337.0
           114  331.0
           115  321.0
           116  329.0
           117  352.0
           118  293.0
           119  276.0
           120  261.0
           121  261.0
           122  254.0
           123  266.0
           124  250.0
           125  263.0
           126  294.0
           127  265.0
           128  256.0
           129  261.0
           130  250.0
           131  234.0
           132  209.0
           133  245.0
           134  253.0
           135  238.0
           136  272.0
           137  304.0
           138  288.0
           139  287.0
           140  248.0
           141  238.0
           142  225.0
           143  193.0
           144  221.0
           145  219.0
           146  226.0
           147  266.0
           148  238.0
           149  240.0
           150  268.0
           151  267.0
           152  255.0
           153  258.0
           154  212.0
           155  221.0
           156  229.0
           157  249.0
           158  256.0
           159  267.0
           160  228.0
           161  239.0
           162  255.0
           163  221.0
           164  232.0
           165  300.0
           166  330.0
           167  387.0
           168  371.0
           169  345.0
           170  288.0
           171  299.0
           172  251.0
           173  251.0
           174  303.0
           175  353.0
           176  370.0
           177  383.0
           178  421.0
           179  351.0
           180  289.0
           181  321.0
           182  270.0
           183  270.0
           184  322.0
           185  315.0
           186  324.0
           187  339.0
           188  348.0
           189  334.0
           190  305.0
           191  309.0
           192  291.0
           193  303.0
           194  323.0
           195  374.0
           196  348.0
           197  343.0
           198  306.0
           199  317.0
           200  308.0
           201  314.0
           202  307.0
           203  340.0
           204  349.0
           205  336.0
           206  340.0
           207  342.0
           208  314.0
           209  287.0
           210  330.0
           211  340.0
           212  297.0
           213  318.0
           214  272.0
           215  321.0
           216  336.0
           217  324.0
           218  347.0
           219  297.0
           220  314.0
           221  285.0
           222  286.0
           223  270.0
           224  305.0
           225  307.0
           226  287.0
           227  283.0
           228  289.0
           229  256.0
           230  284.0
           231  275.0
           232  265.0
           233  250.0
           234  256.0
           235  239.0
           236  226.0
           237  237.0
           238  225.0
           239  232.0
           240  214.0
           241  221.0
           242  235.0
           243  211.0
           244  170.0
           245  202.0
           246  218.0
           247  214.0
           248  178.0
           249  158.0
           250  185.0
           251  175.0
           252  158.0
           253  181.0
           254  192.0
           255  172.0
           256  143.0
           257  140.0
           258  156.0
           259  159.0
           260  143.0
           261  126.0
           262  160.0
           263  126.0
           264  128.0
           265  132.0
           266  139.0
           267  109.0
           268  134.0
           269  110.0
           270  122.0
           271  116.0
           272  126.0
           273  96.0
           274  120.0
           275  119.0
           276  123.0
           277  120.0
           278  125.0
           279  95.0
           280  99.0
           281  124.0
           282  113.0
           283  121.0
           284  113.0
           285  79.0
           286  88.0
           287  89.0
           288  105.0
           289  105.0
           290  101.0
           291  82.0
           292  100.0
           293  104.0
           294  97.0
           295  102.0
           296  95.0
           297  102.0
           298  96.0
           299  98.0
           300  98.0
           301  109.0
           302  115.0
           303  96.0
           304  85.0
           305  75.0
           306  84.0
           307  94.0
           308  119.0
           309  81.0
           310  98.0
           311  94.0
           312  101.0
           313  95.0
           314  87.0
           315  93.0
           316  102.0
           317  77.0
           318  91.0
           319  104.0
           320  100.0
           321  92.0
           322  82.0
           323  76.0
           324  82.0
           325  106.0
           326  101.0
           327  92.0
           328  83.0
           329  86.0
           330  91.0
           331  98.0
           332  78.0
           333  79.0
           334  98.0
           335  79.0
           336  93.0
           337  92.0
           338  94.0
           339  88.0
           340  77.0
           341  95.0
           342  89.0
           343  112.0
           344  90.0
           345  119.0
           346  106.0
           347  108.0
           348  113.0
           349  77.0
           350  95.0
           351  95.0
           352  96.0
           353  99.0
           354  97.0
           355  118.0
           356  92.0
           357  101.0
           358  99.0
           359  90.0
           360  103.0
           361  103.0
           362  109.0
           363  119.0
           364  117.0
           365  105.0
           366  123.0
           367  115.0
           368  121.0
           369  123.0
           370  112.0
           371  121.0
           372  115.0
           373  94.0
           374  116.0
           375  113.0
           376  106.0
           377  112.0
           378  103.0
           379  113.0
           380  104.0
           381  105.0
           382  114.0
           383  109.0
           384  110.0
           385  107.0
           386  110.0
           387  113.0
           388  115.0
           389  128.0
           390  130.0
           391  112.0
           392  128.0
           393  95.0
           394  119.0
           395  111.0
           396  109.0
           397  111.0
           398  115.0
           399  103.0
           400  106.0
           401  113.0
           402  107.0
           403  118.0
           404  103.0
           405  93.0
           406  111.0
           407  113.0
           408  130.0
           409  106.0
           410  102.0
           411  97.0
           412  92.0
           413  112.0
           414  101.0
           415  96.0
           416  93.0
           417  89.0
           418  102.0
           419  96.0
           420  98.0
           421  108.0
           422  92.0
           423  95.0
           424  80.0
           425  76.0
           426  103.0
           427  90.0
           428  80.0
           429  82.0
           430  94.0
           431  93.0
           432  84.0
           433  77.0
           434  91.0
           435  90.0
           436  72.0
           437  78.0
           438  71.0
           439  66.0
           440  77.0
           441  80.0
           442  78.0
           443  68.0
           444  63.0
           445  71.0
           446  70.0
           447  78.0
           448  56.0
           449  61.0
           450  59.0
           451  60.0
           452  49.0
           453  59.0
           454  65.0
           455  73.0
           456  56.0
           457  50.0
           458  72.0
           459  52.0
           460  60.0
           461  67.0
           462  57.0
           463  61.0
           464  53.0
           465  50.0
           466  52.0
           467  58.0
           468  44.0
           469  64.0
           470  52.0
           471  57.0
           472  47.0
           473  63.0
           474  48.0
           475  53.0
           476  57.0
           477  41.0
           478  49.0
           479  50.0
           480  60.0
           481  46.0
           482  42.0
           483  51.0
           484  47.0
           485  35.0
           486  40.0
           487  41.0
           488  51.0
           489  44.0
           490  36.0
           491  37.0
           492  48.0
           493  52.0
           494  49.0
           495  52.0
           496  56.0
           497  50.0
           498  42.0
           499  49.0
           500  46.0
           ::::::::::::::
           /tmp/tmplg07et_q/files/3/f/2/dataset_3f220cc1-ff8c-43ab-9d00-d18239658190.dat
           ::::::::::::::
           in peaks 8698
           outside peaks    224106
           total 160
           -rw-r--r-- 1 1001 127    214 Sep 23 15:03 bowtie2_pe_plot.txt
           -rw-r--r-- 1 1001 127     92 Sep 23 15:03 cutadapt_filtered_reads_plot.txt
           -rw-r--r-- 1 1001 127   1063 Sep 23 15:03 cutadapt_trimmed_sequences_plot_3_Counts.txt
           -rw-r--r-- 1 1001 127   1425 Sep 23 15:03 cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt
           -rw-r--r-- 1 1001 127    422 Sep 23 15:03 multiqc_bowtie2.txt
           -rw-r--r-- 1 1001 127    425 Sep 23 15:03 multiqc_citations.txt
           -rw-r--r-- 1 1001 127    263 Sep 23 15:03 multiqc_cutadapt.txt
           -rw-r--r-- 1 1001 127 107051 Sep 23 15:03 multiqc_data.json
           -rw-r--r-- 1 1001 127    353 Sep 23 15:03 multiqc_general_stats.txt
           -rw-r--r-- 1 1001 127    109 Sep 23 15:03 multiqc_macs.txt
           -rw-r--r-- 1 1001 127    319 Sep 23 15:03 multiqc_picard_dups.txt
           -rw-r--r-- 1 1001 127     51 Sep 23 15:03 multiqc_software_versions.txt
           -rw-r--r-- 1 1001 127    663 Sep 23 15:03 multiqc_sources.txt
           -rw-r--r-- 1 1001 127    111 Sep 23 15:03 picard_deduplication.txt
           -rw-r--r-- 1 1001 127      0 Sep 23 15:03 picard_histogram.txt
           -rw-r--r-- 1 1001 127      0 Sep 23 15:03 picard_histogram_1.txt
           -rw-r--r-- 1 1001 127      0 Sep 23 15:03 picard_histogram_2.txt

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | comment | ` "" ` |
             | dbkey | ` "hg19" ` |
             | export | ` true ` |
             | flat | ` false ` |
             | results | ` [{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}, {"__index__": 1, "software_cond": {"__current_case__": 3, "input": {"values": [{"id": 5, "src": "hdca"}]}, "software": "bowtie2"}}, {"__index__": 2, "software_cond": {"__current_case__": 32, "description": "", "input": {"values": [{"id": 11, "src": "hdca"}]}, "plot_type": "bargraph", "section_name": "chrM", "software": "custom_content", "title": "reads mapping on chrM", "xlab": "", "ylab": ""}}, {"__index__": 3, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}, {"__index__": 4, "software_cond": {"__current_case__": 32, "description": "", "input": {"values": [{"id": 14, "src": "hdca"}]}, "plot_type": "linegraph", "section_name": "Fragment size", "software": "custom_content", "title": "Fragment size distribution", "xlab": "", "ylab": ""}}, {"__index__": 5, "software_cond": {"__current_case__": 16, "input": {"values": [{"id": 16, "src": "hdca"}]}, "software": "macs2"}}, {"__index__": 6, "software_cond": {"__current_case__": 32, "description": "Number of reads falling 500bp from a summit", "input": {"values": [{"id": 33, "src": "hdca"}]}, "plot_type": "bargraph", "section_name": "Reads in peaks", "software": "custom_content", "title": "Number of reads in peaks", "xlab": "", "ylab": ""}}] ` |
             | saveLog | ` "false" ` |
             | title | ` "" ` |

      </details>

 - **Step 4: bin_size**:

    * step_state: scheduled

 - **Step 5: Cutadapt (remove adapter + bad quality bases)**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           ln -f -s '/tmp/tmplg07et_q/files/3/9/4/dataset_3945eba8-cfed-49aa-8f49-65c023664138.dat' 'SRR891268_chr22_enriched_1.fq' && ln -f -s '/tmp/tmplg07et_q/files/f/e/9/dataset_fe92420b-f266-4e9b-b956-8a6549945214.dat' 'SRR891268_chr22_enriched_2.fq' &&  cutadapt  -j=${GALAXY_SLOTS:-4}   -a 'Nextera R1'='CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'    -A 'Nextera R2'='CTGTCTCTTATACACATCTGACGCTGCCGACGA'    --error-rate=0.1 --times=1 --overlap=3    --action=trim   --quality-cutoff=30       --minimum-length=15      -o 'out1.fq' -p 'out2.fq'  'SRR891268_chr22_enriched_1.fq' 'SRR891268_chr22_enriched_2.fq'  > report.txt
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"} ` |
             | chromInfo | ` "/tmp/tmplg07et_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | filter\_options | ` {"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "15", "minimum_length2": null, "pair_filter": "any"} ` |
             | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC", "adapter_name": "Nextera R1", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CTGTCTCTTATACACATCTGACGCTGCCGACGA", "adapter_name": "Nextera R2", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"} ` |
             | other\_trimming\_options | ` {"cut": "0", "cut2": "0", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "30", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false} ` |
             | output\_selector | ` ["report"] ` |
             | read\_mod\_options | ` {"length_tag": "", "rename": "", "strip_suffix": "", "zero_cap": false} ` |

      </details>

 - **Step 6: Bowtie2 map on reference**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           set -o | grep -q pipefail && set -o pipefail;   ln -f -s '/tmp/tmplg07et_q/files/5/e/0/dataset_5e0cceab-28bf-4cc1-8c1c-1c4545bc71ff.dat' input_f.fastq &&  ln -f -s '/tmp/tmplg07et_q/files/9/3/d/dataset_93df7438-072f-44c2-b1ec-017b3bd679ec.dat' input_r.fastq &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full'   -1 'input_f.fastq' -2 'input_r.fastq'              --very-sensitive   2> >(tee '/tmp/tmplg07et_q/job_working_directory/000/4/outputs/dataset_450a5187-ddf8-42ae-a39a-3a39a34dd332.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmplg07et_q/job_working_directory/000/4/outputs/dataset_0c3d05d7-0cd8-404f-b771-0e31bace8fa3.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Error:**

         * ```console
           280964 reads; of these:
             280964 (100.00%) were paired; of these:
               30410 (10.82%) aligned concordantly 0 times
               109333 (38.91%) aligned concordantly exactly 1 time
               141221 (50.26%) aligned concordantly >1 times
               ----
               30410 pairs aligned concordantly 0 times; of these:
                 13319 (43.80%) aligned discordantly 1 time
               ----
               17091 pairs aligned 0 times concordantly or discordantly; of these:
                 34182 mates make up the pairs; of these:
                   6127 (17.92%) aligned 0 times
                   6515 (19.06%) aligned exactly 1 time
                   21540 (63.02%) aligned >1 times
           98.91% overall alignment rate

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | analysis\_type | ` {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "--very-sensitive"} ` |
             | chromInfo | ` "/tmp/tmplg07et_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | library | ` {"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 4, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false} ` |
             | reference\_genome | ` {"__current_case__": 0, "index": "hg19", "source": "indexed"} ` |
             | rg | ` {"__current_case__": 3, "rg_selector": "do_not_set"} ` |
             | sam\_options | ` {"__current_case__": 1, "sam_options_selector": "no"} ` |
             | save\_mapping\_stats | ` true ` |

      </details>

 - **Step 7: filter MAPQ30 concordant pairs and not mitochondrial pairs**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           cp '/tmp/tmplg07et_q/job_working_directory/000/5/configs/tmps2bew_s0' '/tmp/tmplg07et_q/job_working_directory/000/5/outputs/dataset_e122cd8e-d120-43f6-bc9d-14d953143f90.dat' && ln -s '/tmp/tmplg07et_q/files/0/c/3/dataset_0c3d05d7-0cd8-404f-b771-0e31bace8fa3.dat' localbam.bam && ln -s '/tmp/tmplg07et_q/files/_metadata_files/e/2/b/metadata_e2bd7897-a28c-4d2f-8205-ecaa4c667ce3.dat' localbam.bam.bai && cat '/tmp/tmplg07et_q/job_working_directory/000/5/configs/tmps2bew_s0' && bamtools filter -script '/tmp/tmplg07et_q/job_working_directory/000/5/configs/tmps2bew_s0' -in localbam.bam -out '/tmp/tmplg07et_q/job_working_directory/000/5/outputs/dataset_6bc7ddd8-ec8d-4e5f-92a5-344bcd9ddae1.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Output:**

         * ```console

           {
               "filters": [
                   {
                       "id": "1",
                       "mapQuality": ">=30",
                       "isProperPair": "true",
                       "reference": "!chrM",
                       "mateReference": "!MT"
                   }
               ],
               "rule": ""
           }

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "bam" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | conditions | ` [{"__index__": 0, "filters": [{"__index__": 0, "bam_property": {"__current_case__": 14, "bam_property_selector": "mapQuality", "bam_property_value": ">=30"}}, {"__index__": 1, "bam_property": {"__current_case__": 11, "bam_property_selector": "isProperPair", "bam_property_value": true}}, {"__index__": 2, "bam_property": {"__current_case__": 20, "bam_property_selector": "reference", "bam_property_value": "!chrM"}}, {"__index__": 3, "bam_property": {"__current_case__": 16, "bam_property_selector": "mateReference", "bam_property_value": "!MT"}}]}] ` |
             | dbkey | ` "hg19" ` |
             | rule\_configuration | ` {"__current_case__": 1, "rules": null, "rules_selector": "true"} ` |

      </details>

 - **Step 8: Get number of reads per chromosome**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmplg07et_q/files/0/c/3/dataset_0c3d05d7-0cd8-404f-b771-0e31bace8fa3.dat' infile && ln -s '/tmp/tmplg07et_q/files/_metadata_files/e/2/b/metadata_e2bd7897-a28c-4d2f-8205-ecaa4c667ce3.dat' infile.bai &&  samtools idxstats -@ $addthreads infile  > '/tmp/tmplg07et_q/job_working_directory/000/6/outputs/dataset_de4a19af-1b79-4bf8-a7e5-377b17a3d276.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | dbkey | ` "hg19" ` |

      </details>

 - **Step 9: remove PCR duplicates**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           _JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmplg07et_q/files/6/b/c/dataset_6bc7ddd8-ec8d-4e5f-92a5-344bcd9ddae1.dat' 'SRR891268_chr22_enriched' &&  picard MarkDuplicates  --INPUT 'SRR891268_chr22_enriched' --OUTPUT '/tmp/tmplg07et_q/job_working_directory/000/7/outputs/dataset_922a0de9-2ab3-4c9b-867a-a71a2dfc7257.dat'  --METRICS_FILE '/tmp/tmplg07et_q/job_working_directory/000/7/outputs/dataset_36dd14cf-e40a-4819-a74d-73efeb75aa1c.dat'  --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Error:**

         * ```console
           /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
           Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmplg07et_q/tmp
           Sep 23, 2024 3:00:59 PM com.intel.gkl.NativeLibraryLoader load
           INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | assume\_sorted | ` true ` |
             | barcode\_tag | ` "" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | comments | ` [] ` |
             | dbkey | ` "hg19" ` |
             | duplicate\_scoring\_strategy | ` "SUM_OF_BASE_QUALITIES" ` |
             | optical\_duplicate\_pixel\_distance | ` "100" ` |
             | read\_name\_regex | ` "" ` |
             | remove\_duplicates | ` true ` |
             | validation\_stringency | ` "LENIENT" ` |

      </details>

 - **Step 10: reads in chrM/MT for multiQC**:

    * 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/tmplg07et_q/job_working_directory/000/8/configs/tmp815dlole' '/tmp/tmplg07et_q/files/d/e/4/dataset_de4a19af-1b79-4bf8-a7e5-377b17a3d276.dat' > '/tmp/tmplg07et_q/job_working_directory/000/8/outputs/dataset_694b467f-a1fa-4e7c-8bcd-236df8495281.dat'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "0b3175a079bb11ef9383e1adc2f1e5e9" ` |
             | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg19.len" ` |
             | code | ` " ($1==\"chrM\" || $1 == \"MT\"){print $1, $3}($1!=\"chrM\" && $1!=\"MT\"){SUM+=$3}END{print \"others\", SUM} " ` |
             | dbkey | ` "hg19" ` |

      </details>
  </details>
  • Other invocation details - **error_message** * Failed to run workflow, at least one job is in [error] state. - **history_id** * 7b68da00f749b68c - **history_state** * error - **invocation_id** * 7b68da00f749b68c - **invocation_state** * scheduled - **workflow_id** * 7b68da00f749b68c