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Updating workflows/transcriptomics/rnaseq-pe from 0.5 to 0.6 #336

Merged
merged 6 commits into from
Mar 14, 2024
Merged

Updating workflows/transcriptomics/rnaseq-pe from 0.5 to 0.6 #336

merged 6 commits into from
Mar 14, 2024

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

  • toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1
  • toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0

The workflow release number has been updated from 0.5 to 0.6.

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github-actions bot commented Feb 5, 2024

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 1
Failure 0
Skipped 0
Errored Tests
  • ❌ rnaseq-pe.ga_0

    Execution Problem:

    • Final state of invocation 2c05f2cc9ab2dc58 is [failed]

    Workflow invocation details

    • Invocation Messages

      • Invocation scheduling failed because step 19 contains an expression that could not be evaluated.
    • Steps

      • Step 1: PE fastq input:

        • step_state: scheduled

      • Step 2: forward_adapter:

        • step_state: scheduled

      • Step 11: get reference_genome as text parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "793b1cfdc43c11ee8d69dbeee7925256"
              chromInfo "/tmp/tmp99x4ez98/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              components [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "dm6", "select_param_type": "text"}}]
              dbkey "?"

      • Step 12: awk command from strand:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "793b1cfdc43c11ee8d69dbeee7925256"
              chromInfo "/tmp/tmp99x4ez98/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "NR>4{print $1\"\\t\"$3}"}, {"__index__": 1, "from": "stranded - reverse", "to": "NR>4{print $1\"\\t\"$4}"}, {"__index__": 2, "from": "unstranded", "to": "NR>4{print $1\"\\t\"$2}"}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 13: Get cufflinks strandess parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "793b1cfdc43c11ee8d69dbeee7925256"
              chromInfo "/tmp/tmp99x4ez98/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "fr-secondstrand"}, {"__index__": 1, "from": "stranded - reverse", "to": "fr-firststrand"}, {"__index__": 2, "from": "unstranded", "to": "fr-unstranded"}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 14: Get Stringtie strandedness parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "793b1cfdc43c11ee8d69dbeee7925256"
              chromInfo "/tmp/tmp99x4ez98/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "--fr"}, {"__index__": 1, "from": "stranded - reverse", "to": "--rf"}, {"__index__": 2, "from": "unstranded", "to": ""}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 15: STAR: map and count and coverage splitted:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • STAR  --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir '/cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files' --sjdbOverhang 100 --sjdbGTFfile '/tmp/tmp99x4ez98/files/2/6/4/dataset_2648eeff-a8b2-47bf-82cf-44a305724e46.dat' --sjdbGTFfeatureExon 'exon'   --readFilesIn '/tmp/tmp99x4ez98/files/1/c/f/dataset_1cf8d94b-52a2-435f-840e-07f9d77bdd67.dat' '/tmp/tmp99x4ez98/files/3/5/9/dataset_35953125-8255-4324-b4ea-477768fb6dec.dat'   --outSAMtype BAM SortedByCoordinate  --twopassMode None ''  --quantMode GeneCounts   --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM  --outSAMprimaryFlag OneBestScore  --outSAMmapqUnique 255    --outSAMunmapped None  --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1   --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10  --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01   --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000   --outBAMsortingThreadN ${GALAXY_SLOTS:-4} --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM $((${GALAXY_MEMORY_MB:-0}*1000000))    --outWigType 'bedGraph' '' --outWigStrand 'Stranded' --outWigReferencesPrefix '-' --outWigNorm 'RPM'  && samtools view -b -o '/tmp/tmp99x4ez98/job_working_directory/000/9/outputs/dataset_b51127fa-7844-49df-bd03-f3237ee6bde1.dat' Aligned.sortedByCoord.out.bam  && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out

            Exit Code:

            • 0

            Standard Output:

            • 	STAR --runThreadN 1 --genomeLoad NoSharedMemory --genomeDir /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files --sjdbOverhang 100 --sjdbGTFfile /tmp/tmp99x4ez98/files/2/6/4/dataset_2648eeff-a8b2-47bf-82cf-44a305724e46.dat --sjdbGTFfeatureExon exon --readFilesIn /tmp/tmp99x4ez98/files/1/c/f/dataset_1cf8d94b-52a2-435f-840e-07f9d77bdd67.dat /tmp/tmp99x4ez98/files/3/5/9/dataset_35953125-8255-4324-b4ea-477768fb6dec.dat --outSAMtype BAM SortedByCoordinate --twopassMode None  --quantMode GeneCounts --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 255 --outSAMunmapped None --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1 --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000 --outBAMsortingThreadN 1 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 0 --outWigType bedGraph  --outWigStrand Stranded --outWigReferencesPrefix - --outWigNorm RPM
	STAR version: 2.7.10b   compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Feb 05 15:38:18 ..... started STAR run
Feb 05 15:38:18 ..... loading genome
Feb 05 15:45:35 ..... processing annotations GTF
Feb 05 15:45:36 ..... inserting junctions into the genome indices
Feb 05 15:46:50 ..... started mapping
Feb 05 15:48:52 ..... finished mapping
Feb 05 15:48:52 ..... started sorting BAM
Feb 05 15:48:58 ..... started wiggle output
Feb 05 15:49:04 ..... finished successfully

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "793b1cfdc43c11ee8d69dbeee7925256"
              algo {"params": {"__current_case__": 3, "align": {"alignEndsType": "Local", "alignIntronMax": "1000000", "alignIntronMin": "20", "alignMatesGapMax": "1000000", "alignSJDBoverhangMin": "1", "alignSJoverhangMin": "8", "alignSJstitchMismatchNmax": {"alignSJstitchMismatchNmax1": "0", "alignSJstitchMismatchNmax2": "-1", "alignSJstitchMismatchNmax3": "0", "alignSJstitchMismatchNmax4": "0"}, "alignSplicedMateMapLmin": "0", "alignSplicedMateMapLminOverLmate": "0.66", "alignTranscriptsPerReadNmax": "10000", "alignTranscriptsPerWindowNmax": "100", "alignWindowsPerReadNmax": "10000", "peOverlapMMp": "0.01", "peOverlapNbasesMin": "0"}, "chim_settings": {"chimFilter": true, "chimJunctionOverhangMin": "20", "chimMainSegmentMultNmax": "10", "chimMultimapNmax": "1", "chimMultimapScoreRange": "1", "chimScoreDropMax": "20", "chimScoreJunctionNonGTAG": "-1", "chimScoreMin": "0", "chimScoreSeparation": "10", "chimSegmentMin": "12", "chimSegmentReadGapMax": "0"}, "junction_limits": {"limitOutSJcollapsed": "1000000", "limitOutSJoneRead": "1000", "limitSjdbInsertNsj": "1000000"}, "seed": {"seedMultimapNmax": "10000", "seedNoneLociPerWindow": "10", "seedPerReadNmax": "1000", "seedPerWindowNmax": "50", "seedSearchLmax": "0", "seedSearchStartLmax": "50", "seedSearchStartLmaxOverLread": "1.0"}, "settingsType": "full"}}
              chimOutType ""
              chromInfo "/tmp/tmp99x4ez98/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              filter {"basic_filters": ["exclude_unmapped"], "output_params2": {"__current_case__": 0, "outFilterMatchNmin": "0", "outFilterMatchNminOverLread": "0.66", "outFilterMismatchNmax": "999", "outFilterMismatchNoverLmax": "0.3", "outFilterMismatchNoverReadLmax": "0.04", "outFilterMultimapNmax": "20", "outFilterMultimapScoreRange": "1", "outFilterScoreMin": "0", "outFilterScoreMinOverLread": "0.66", "outFilterType": true, "outSAMmultNmax": "-1", "outSAMtlen": "1", "output_select2": "yes"}}
              oformat {"HI_offset": "1", "outSAMattributes": ["NH", "HI", "AS", "nM"], "outSAMmapqUnique": "255", "outSAMprimaryFlag": "OneBestScore"}
              outWig {"__current_case__": 1, "outWigNorm": true, "outWigReferencesPrefix": "-", "outWigStrand": true, "outWigType": "bedGraph", "outWigTypeSecondWord": ""}
              perf {"outBAMsortingBinsN": "50", "winAnchorMultimapNmax": "50"}
              refGenomeSource {"GTFconditional": {"GTFselect": "without-gtf-with-gtf", "__current_case__": 1, "genomeDir": "dm6", "quantmode_output": {"__current_case__": 1, "quantMode": "GeneCounts"}, "sjdbGTFfeatureExon": "exon", "sjdbGTFfile": {"values": [{"id": 1, "src": "hda"}]}, "sjdbOverhang": "100"}, "__current_case__": 0, "geneSource": "indexed"}
              singlePaired {"__current_case__": 2, "input": {"values": [{"id": 4, "src": "dce"}]}, "sPaired": "paired_collection"}
              twopass {"__current_case__": 0, "sj_precalculated": "", "twopassMode": "None", "twopass_read_subset": ""}

      • Step 16: MultiQC:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/cutadapt_0 &&    ln -s '/tmp/tmp99x4ez98/files/b/4/a/dataset_b4a1806e-5bef-4d11-bea7-fdf710dec504.dat' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/GSM461177.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && mkdir multiqc_WDir/star_1 &&    mkdir 'multiqc_WDir/star_1/log_0' &&     ln -s '/tmp/tmp99x4ez98/files/8/d/f/dataset_8dfa5ccd-f90e-4617-8825-1de05d800c09.dat' 'multiqc_WDir/star_1/log_0/GSM461177_Log.final.out' &&   mkdir 'multiqc_WDir/star_1/genecounts_1' &&     ln -s '/tmp/tmp99x4ez98/files/0/5/0/dataset_05026048-6822-4253-ab24-5de9d17010e7.dat' 'multiqc_WDir/star_1/genecounts_1/GSM461177_ReadsPerGene.out.tab' &&   multiqc multiqc_WDir --filename 'report'    --export

            Exit Code:

            • 0

            Standard Error:

            •   /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.19 now available!
|           multiqc | Search path : /tmp/tmp99x4ez98/job_working_directory/000/10/working/multiqc_WDir
|              star | Found 1 reports and 1 gene count files
|          cutadapt | Found 1 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | Plots       : report_plots
|           multiqc | MultiQC complete

            Standard Output:

            • |         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "793b1cfdc43c11ee8d69dbeee7925256"
              chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
              comment ""
              dbkey "dm6"
              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__": 28, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 4, "src": "hdca"}]}, "type": "log"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "genecounts"}}], "software": "star"}}]
              saveLog false
              title ""

      • Step 17: Unlabelled step:

        • step_state: new

        • Subworkflow Steps

          • Step 1: STAR BAM:

            • step_state: scheduled

          • Step 2: STAR log:

            • step_state: scheduled

          • Step 3: keep uniquely mapped reads:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cp '/tmp/tmp99x4ez98/job_working_directory/000/11/configs/tmpmanelmer' '/tmp/tmp99x4ez98/job_working_directory/000/11/outputs/dataset_79ab6a3a-7d34-4911-8256-1e7a5f890f87.dat' && ln -s '/tmp/tmp99x4ez98/files/b/5/1/dataset_b51127fa-7844-49df-bd03-f3237ee6bde1.dat' localbam.bam && ln -s '/tmp/tmp99x4ez98/files/_metadata_files/8/d/7/metadata_8d718c58-fecf-4fa2-b098-1326337014cf.dat' localbam.bam.bai && cat '/tmp/tmp99x4ez98/job_working_directory/000/11/configs/tmpmanelmer' && bamtools filter -script '/tmp/tmp99x4ez98/job_working_directory/000/11/configs/tmpmanelmer' -in localbam.bam -out '/tmp/tmp99x4ez98/job_working_directory/000/11/outputs/dataset_9cc029b3-5882-4b60-840c-bf51907c5b4f.dat'

                Exit Code:

                • 0

                Standard Output:

                •         
{
    "filters": [
        {
            "id": "1",
            "tag": "NH=1"
        }
    ]
}

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bam"
                  __workflow_invocation_uuid__ "793b1cfec43c11ee8d69dbeee7925256"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  conditions [{"__index__": 0, "filters": [{"__index__": 0, "bam_property": {"__current_case__": 21, "bam_property_selector": "tag", "bam_property_value": "NH=1"}}]}]
                  dbkey "dm6"
                  rule_configuration {"__current_case__": 0, "rules_selector": false}

          • Step 4: get scaling factor:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f "/tmp/tmp99x4ez98/job_working_directory/000/12/configs/tmphpy56c21" "/tmp/tmp99x4ez98/files/8/d/f/dataset_8dfa5ccd-f90e-4617-8825-1de05d800c09.dat" > "/tmp/tmp99x4ez98/job_working_directory/000/12/outputs/dataset_84beeffc-e43a-48f2-874a-8615b5b088e5.dat"

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "793b1cfec43c11ee8d69dbeee7925256"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  code "$0~\"Uniquely mapped reads number\"{print 1000000/$NF}"
                  dbkey "dm6"

          • Step 5: param_value_from_file:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "793b1cfec43c11ee8d69dbeee7925256"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  param_type "float"
                  remove_newlines true

          • Step 6: Scaled Coverage both strands combined:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • bedtools genomecov  -ibam '/tmp/tmp99x4ez98/files/9/c/c/dataset_9cc029b3-5882-4b60-840c-bf51907c5b4f.dat'   -split   -bg  -scale 1.17005     > '/tmp/tmp99x4ez98/job_working_directory/000/20/outputs/dataset_8dfeaddc-b8c8-48b2-bb57-00156c1431a3.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "793b1cfec43c11ee8d69dbeee7925256"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  d false
                  dbkey "dm6"
                  dz false
                  five false
                  input_type {"__current_case__": 1, "input": {"values": [{"id": 17, "src": "dce"}]}, "input_type_select": "bam"}
                  report {"__current_case__": 0, "report_select": "bg", "scale": "1.17005", "zero_regions": false}
                  split true
                  strand ""
                  three false

          • Step 7: convert both strands coverage to bigwig:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • grep -v "^track" '/tmp/tmp99x4ez98/files/8/d/f/dataset_8dfeaddc-b8c8-48b2-bb57-00156c1431a3.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len' '/tmp/tmp99x4ez98/job_working_directory/000/21/outputs/dataset_60c21d52-0fa8-432e-b85d-3fb3f3331d9d.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bedgraph"
                  __workflow_invocation_uuid__ "793b1cfec43c11ee8d69dbeee7925256"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  settings {"__current_case__": 0, "settingsType": "preset"}

      • Step 18: Unlabelled step:

        • step_state: new

        • Subworkflow Steps

          • Step 1: strandedness:

            • step_state: scheduled

          • Step 2: Bedgraph strand 1:

            • step_state: scheduled

          • Step 11: Unlabelled step:

            • step_state: new

          • Step 12: convert to bigwig:

            • step_state: new

          • Step 3: Bedgraph strand 2:

            • step_state: scheduled

          • Step 4: Get replacement for strand1:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "793b1cffc43c11ee8d69dbeee7925256"
                  chromInfo "/tmp/tmp99x4ez98/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                  dbkey "?"
                  input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_forward"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_reverse"}, {"__index__": 2, "from": "unstranded", "to": "$1_forward"}], "type": "text"}
                  output_param_type "text"
                  unmapped {"__current_case__": 1, "on_unmapped": "fail"}

          • Step 5: Get replacement for strand2:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "793b1cffc43c11ee8d69dbeee7925256"
                  chromInfo "/tmp/tmp99x4ez98/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                  dbkey "?"
                  input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_reverse"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_forward"}, {"__index__": 2, "from": "unstranded", "to": "$1_reverse"}], "type": "text"}
                  output_param_type "text"
                  unmapped {"__current_case__": 1, "on_unmapped": "fail"}

          • Step 6: get identifiers:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • mv '/tmp/tmp99x4ez98/job_working_directory/000/16/configs/tmpx2e5l197' '/tmp/tmp99x4ez98/job_working_directory/000/16/outputs/dataset_d537ee71-14e0-4f70-9456-c69e8b6a1130.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bedgraph"
                  __workflow_invocation_uuid__ "793b1cffc43c11ee8d69dbeee7925256"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  input_collection {"values": [{"id": 8, "src": "hdca"}]}

          • Step 7: New labels strand 1:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp99x4ez98/job_working_directory/000/18/outputs/dataset_18b6f08e-1adf-43a9-b19f-b6d0920d2c63.dat' -g    -r '^(.+)$' '$1_forward' '/tmp/tmp99x4ez98/files/d/5/3/dataset_d537ee71-14e0-4f70-9456-c69e8b6a1130.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "793b1cffc43c11ee8d69dbeee7925256"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  find_and_replace [{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_forward", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

          • Step 8: New labels strand 2:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp99x4ez98/job_working_directory/000/19/outputs/dataset_1f4d6986-8037-4d16-a51a-b8c873043a8a.dat' -g    -r '^(.+)$' '$1_reverse' '/tmp/tmp99x4ez98/files/d/5/3/dataset_d537ee71-14e0-4f70-9456-c69e8b6a1130.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "793b1cffc43c11ee8d69dbeee7925256"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  find_and_replace [{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_reverse", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

          • Step 9: Relabelled strand 1:

            • step_state: new

          • Step 10: Relabelled strand 2:

            • step_state: new

      • Step 19: Compute FPKM with cufflinks:

        • step_state: new

      • Step 20: Extract gene counts:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f "/tmp/tmp99x4ez98/job_working_directory/000/17/configs/tmph2xfaym5" "/tmp/tmp99x4ez98/files/0/5/0/dataset_05026048-6822-4253-ab24-5de9d17010e7.dat" > "/tmp/tmp99x4ez98/job_working_directory/000/17/outputs/dataset_127a83dc-e80a-43f5-8c88-09c3feb5fb98.dat"

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "tabular"
              __workflow_invocation_uuid__ "793b1cfdc43c11ee8d69dbeee7925256"
              chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
              code "NR>4{print $1\"\\t\"$2}"
              dbkey "dm6"

      • Step 3: reverse_adapter:

        • step_state: scheduled

      • Step 21: Compute FPKM with StringTie:

        • step_state: new

      • Step 4: reference_genome:

        • step_state: scheduled

      • Step 5: gtf:

        • step_state: scheduled

      • Step 6: strandedness:

        • step_state: scheduled

      • Step 7: cufflinks_FPKM:

        • step_state: scheduled

      • Step 8: gtf with regions to exclude from FPKM normalization with Cufflinks:

        • step_state: scheduled

      • Step 9: stringtie_FPKM:

        • step_state: scheduled

      • Step 10: Cutadapt (remove adapter + bad quality bases):

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • ln -f -s '/tmp/tmp99x4ez98/files/8/3/1/dataset_8313f3a2-5c71-4684-a492-19fc1600b069.dat' 'GSM461177_1.fq' &&  ln -f -s '/tmp/tmp99x4ez98/files/5/8/2/dataset_58226046-19ac-4ed9-a5a8-821a923c909b.dat' 'GSM461177_2.fq' &&    cutadapt  -j=${GALAXY_SLOTS:-4}       -a 'Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'             -A 'Dummy-Adapter (do not use me)'='TGTAGGCC'       --output='out1.fq' --paired-output='out2.fq'  --error-rate=0.1 --times=1 --overlap=3    --action=trim      --minimum-length=15 --pair-filter=any    --quality-cutoff=30      'GSM461177_1.fq' 'GSM461177_2.fq'  > report.txt

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __job_resource {"__current_case__": 0, "__job_resource__select": "no"}
              __workflow_invocation_uuid__ "793b1cfdc43c11ee8d69dbeee7925256"
              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/tmp99x4ez98/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              filter_options {"discard_cassava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": "15", "pair_filter": "any"}
              library {"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_name": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source": {"__current_case__": 1, "adapter": "TGTAGGCC", "adapter_source_list": "builtin"}, "single_noindels": false}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "maximum_length2": null, "minimum_length2": null, "quality_cutoff2": null}, "type": "paired_collection"}
              output_selector ["report"]
              read_mod_options {"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "30", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}
    • Other invocation details

      • error_message

        • Final state of invocation 2c05f2cc9ab2dc58 is [failed]

      • history_id

        • c497c3168fc77de5

      • history_state

        • ok

      • invocation_id

        • c497c3168fc77de5

      • invocation_state

        • failed

      • messages

        • [{'details': None, 'reason': 'expression_evaluation_failed', 'workflow_step_id': 18}]

      • workflow_id

        • 2c05f2cc9ab2dc58

@gxydevbot gxydevbot changed the title Updating workflows/transcriptomics/rnaseq-pe from 0.5 to 0.6 Updating workflows/transcriptomics/rnaseq-pe from 0.5 to 0.6 Feb 12, 2024
@github-actions GitHub Actions
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Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 1
Failure 0
Skipped 0
Errored Tests
  • ❌ rnaseq-pe.ga_0

    Execution Problem:

    • Final state of invocation c0d4991e672fd404 is [failed]

    Workflow invocation details

    • Invocation Messages

      • Invocation scheduling failed because step 19 contains an expression that could not be evaluated.
    • Steps

      • Step 1: PE fastq input:

        • step_state: scheduled

      • Step 2: forward_adapter:

        • step_state: scheduled

      • Step 11: get reference_genome as text parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "bbf5acdbc96211ee855e2743ef507876"
              chromInfo "/tmp/tmp5s8uq5dm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              components [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "dm6", "select_param_type": "text"}}]
              dbkey "?"

      • Step 12: awk command from strand:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "bbf5acdbc96211ee855e2743ef507876"
              chromInfo "/tmp/tmp5s8uq5dm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "NR>4{print $1\"\\t\"$3}"}, {"__index__": 1, "from": "stranded - reverse", "to": "NR>4{print $1\"\\t\"$4}"}, {"__index__": 2, "from": "unstranded", "to": "NR>4{print $1\"\\t\"$2}"}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 13: Get cufflinks strandess parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "bbf5acdbc96211ee855e2743ef507876"
              chromInfo "/tmp/tmp5s8uq5dm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "fr-secondstrand"}, {"__index__": 1, "from": "stranded - reverse", "to": "fr-firststrand"}, {"__index__": 2, "from": "unstranded", "to": "fr-unstranded"}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 14: Get Stringtie strandedness parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "bbf5acdbc96211ee855e2743ef507876"
              chromInfo "/tmp/tmp5s8uq5dm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "--fr"}, {"__index__": 1, "from": "stranded - reverse", "to": "--rf"}, {"__index__": 2, "from": "unstranded", "to": ""}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 15: STAR: map and count and coverage splitted:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • STAR  --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir '/cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files' --sjdbOverhang 100 --sjdbGTFfile '/tmp/tmp5s8uq5dm/files/4/4/b/dataset_44bbe5a0-674c-4390-9826-7684259fb2f6.dat' --sjdbGTFfeatureExon 'exon'   --readFilesIn '/tmp/tmp5s8uq5dm/files/7/1/c/dataset_71cf38b1-9e71-4ea7-9842-752306b2d6ae.dat' '/tmp/tmp5s8uq5dm/files/7/e/4/dataset_7e4669fe-161e-4179-be77-f8aa30120a33.dat'   --outSAMtype BAM SortedByCoordinate  --twopassMode None ''  --quantMode GeneCounts   --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM  --outSAMprimaryFlag OneBestScore  --outSAMmapqUnique 255     --outSAMunmapped None  --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1   --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10  --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01   --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000   --outBAMsortingThreadN ${GALAXY_SLOTS:-4} --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM $((${GALAXY_MEMORY_MB:-0}*1000000))    --outWigType 'bedGraph' '' --outWigStrand 'Stranded' --outWigReferencesPrefix '-' --outWigNorm 'RPM'  && samtools view -b -o '/tmp/tmp5s8uq5dm/job_working_directory/000/9/outputs/dataset_703e7d3f-873b-4f37-acc5-2714340a5366.dat' Aligned.sortedByCoord.out.bam  && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out

            Exit Code:

            • 0

            Standard Output:

            • 	/usr/local/bin/STAR-avx2 --runThreadN 1 --genomeLoad NoSharedMemory --genomeDir /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files --sjdbOverhang 100 --sjdbGTFfile /tmp/tmp5s8uq5dm/files/4/4/b/dataset_44bbe5a0-674c-4390-9826-7684259fb2f6.dat --sjdbGTFfeatureExon exon --readFilesIn /tmp/tmp5s8uq5dm/files/7/1/c/dataset_71cf38b1-9e71-4ea7-9842-752306b2d6ae.dat /tmp/tmp5s8uq5dm/files/7/e/4/dataset_7e4669fe-161e-4179-be77-f8aa30120a33.dat --outSAMtype BAM SortedByCoordinate --twopassMode None  --quantMode GeneCounts --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 255 --outSAMunmapped None --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1 --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000 --outBAMsortingThreadN 1 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 0 --outWigType bedGraph  --outWigStrand Stranded --outWigReferencesPrefix - --outWigNorm RPM
	STAR version: 2.7.11a   compiled: 2023-09-15T02:58:53+0000 :/opt/conda/conda-bld/star_1694746407721/work/source
Feb 12 04:54:50 ..... started STAR run
Feb 12 04:54:51 ..... loading genome
Feb 12 05:07:40 ..... processing annotations GTF
Feb 12 05:07:41 ..... inserting junctions into the genome indices
Feb 12 05:09:05 ..... started mapping
Feb 12 05:11:01 ..... finished mapping
Feb 12 05:11:01 ..... started sorting BAM
Feb 12 05:11:04 ..... started wiggle output
Feb 12 05:11:10 ..... finished successfully

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "bbf5acdbc96211ee855e2743ef507876"
              algo {"params": {"__current_case__": 3, "align": {"alignEndsType": "Local", "alignIntronMax": "1000000", "alignIntronMin": "20", "alignMatesGapMax": "1000000", "alignSJDBoverhangMin": "1", "alignSJoverhangMin": "8", "alignSJstitchMismatchNmax": {"alignSJstitchMismatchNmax1": "0", "alignSJstitchMismatchNmax2": "-1", "alignSJstitchMismatchNmax3": "0", "alignSJstitchMismatchNmax4": "0"}, "alignSplicedMateMapLmin": "0", "alignSplicedMateMapLminOverLmate": "0.66", "alignTranscriptsPerReadNmax": "10000", "alignTranscriptsPerWindowNmax": "100", "alignWindowsPerReadNmax": "10000", "peOverlapMMp": "0.01", "peOverlapNbasesMin": "0"}, "chim_settings": {"chimFilter": true, "chimJunctionOverhangMin": "20", "chimMainSegmentMultNmax": "10", "chimMultimapNmax": "1", "chimMultimapScoreRange": "1", "chimScoreDropMax": "20", "chimScoreJunctionNonGTAG": "-1", "chimScoreMin": "0", "chimScoreSeparation": "10", "chimSegmentMin": "12", "chimSegmentReadGapMax": "0"}, "junction_limits": {"limitOutSJcollapsed": "1000000", "limitOutSJoneRead": "1000", "limitSjdbInsertNsj": "1000000"}, "seed": {"seedMultimapNmax": "10000", "seedNoneLociPerWindow": "10", "seedPerReadNmax": "1000", "seedPerWindowNmax": "50", "seedSearchLmax": "0", "seedSearchStartLmax": "50", "seedSearchStartLmaxOverLread": "1.0"}, "settingsType": "full"}}
              chimOutType ""
              chromInfo "/tmp/tmp5s8uq5dm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              filter {"basic_filters": ["exclude_unmapped"], "output_params2": {"__current_case__": 0, "outFilterMatchNmin": "0", "outFilterMatchNminOverLread": "0.66", "outFilterMismatchNmax": "999", "outFilterMismatchNoverLmax": "0.3", "outFilterMismatchNoverReadLmax": "0.04", "outFilterMultimapNmax": "20", "outFilterMultimapScoreRange": "1", "outFilterScoreMin": "0", "outFilterScoreMinOverLread": "0.66", "outFilterType": true, "outSAMmultNmax": "-1", "outSAMtlen": "1", "output_select2": "yes"}}
              oformat {"HI_offset": "1", "outSAMattributes": ["NH", "HI", "AS", "nM"], "outSAMmapqUnique": "255", "outSAMprimaryFlag": "OneBestScore"}
              outWig {"__current_case__": 1, "outWigNorm": true, "outWigReferencesPrefix": "-", "outWigStrand": true, "outWigType": "bedGraph", "outWigTypeSecondWord": ""}
              perf {"outBAMsortingBinsN": "50", "winAnchorMultimapNmax": "50"}
              refGenomeSource {"GTFconditional": {"GTFselect": "without-gtf-with-gtf", "__current_case__": 1, "genomeDir": "dm6", "quantmode_output": {"__current_case__": 1, "quantMode": "GeneCounts"}, "sjdbGTFfeatureExon": "exon", "sjdbGTFfile": {"values": [{"id": 1, "src": "hda"}]}, "sjdbOverhang": "100"}, "__current_case__": 0, "geneSource": "indexed"}
              singlePaired {"__current_case__": 2, "input": {"values": [{"id": 4, "src": "dce"}]}, "sPaired": "paired_collection"}
              twopass {"__current_case__": 0, "sj_precalculated": "", "twopassMode": "None", "twopass_read_subset": ""}

      • Step 16: MultiQC:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/cutadapt_0 &&    ln -s '/tmp/tmp5s8uq5dm/files/3/7/8/dataset_37801dc7-0c01-4e8a-8f71-8ed29371c853.dat' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/GSM461177.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && mkdir multiqc_WDir/star_1 &&    mkdir 'multiqc_WDir/star_1/log_0' &&     ln -s '/tmp/tmp5s8uq5dm/files/4/1/5/dataset_415c2eb9-02c3-4189-a329-d7da7e5f7d35.dat' 'multiqc_WDir/star_1/log_0/GSM461177_Log.final.out' &&   mkdir 'multiqc_WDir/star_1/genecounts_1' &&     ln -s '/tmp/tmp5s8uq5dm/files/9/8/7/dataset_987690d9-2405-434c-8e71-ae047967d746.dat' 'multiqc_WDir/star_1/genecounts_1/GSM461177_ReadsPerGene.out.tab' &&   multiqc multiqc_WDir --filename 'report'    --export

            Exit Code:

            • 0

            Standard Error:

            •   /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.19 now available!
|           multiqc | Search path : /tmp/tmp5s8uq5dm/job_working_directory/000/10/working/multiqc_WDir
|              star | Found 1 reports and 1 gene count files
|          cutadapt | Found 1 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | Plots       : report_plots
|           multiqc | MultiQC complete

            Standard Output:

            • |         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "bbf5acdbc96211ee855e2743ef507876"
              chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
              comment ""
              dbkey "dm6"
              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__": 28, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 4, "src": "hdca"}]}, "type": "log"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "genecounts"}}], "software": "star"}}]
              saveLog false
              title ""

      • Step 17: Unlabelled step:

        • step_state: new

        • Subworkflow Steps

          • Step 1: STAR BAM:

            • step_state: scheduled

          • Step 2: STAR log:

            • step_state: scheduled

          • Step 3: keep uniquely mapped reads:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cp '/tmp/tmp5s8uq5dm/job_working_directory/000/11/configs/tmp4dflaqo5' '/tmp/tmp5s8uq5dm/job_working_directory/000/11/outputs/dataset_6b23edd9-c816-428b-9863-f0314de0e119.dat' && ln -s '/tmp/tmp5s8uq5dm/files/7/0/3/dataset_703e7d3f-873b-4f37-acc5-2714340a5366.dat' localbam.bam && ln -s '/tmp/tmp5s8uq5dm/files/_metadata_files/9/7/9/metadata_9796bee8-9043-4d5a-b59a-a802c2e1d786.dat' localbam.bam.bai && cat '/tmp/tmp5s8uq5dm/job_working_directory/000/11/configs/tmp4dflaqo5' && bamtools filter -script '/tmp/tmp5s8uq5dm/job_working_directory/000/11/configs/tmp4dflaqo5' -in localbam.bam -out '/tmp/tmp5s8uq5dm/job_working_directory/000/11/outputs/dataset_f358ebd6-aad8-4f9e-9b8d-52fbb88beeb0.dat'

                Exit Code:

                • 0

                Standard Output:

                •         
{
    "filters": [
        {
            "id": "1",
            "tag": "NH=1"
        }
    ]
}

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bam"
                  __workflow_invocation_uuid__ "bbf5acdcc96211ee855e2743ef507876"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  conditions [{"__index__": 0, "filters": [{"__index__": 0, "bam_property": {"__current_case__": 21, "bam_property_selector": "tag", "bam_property_value": "NH=1"}}]}]
                  dbkey "dm6"
                  rule_configuration {"__current_case__": 0, "rules_selector": false}

          • Step 4: get scaling factor:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f "/tmp/tmp5s8uq5dm/job_working_directory/000/12/configs/tmp33zgvjc3" "/tmp/tmp5s8uq5dm/files/4/1/5/dataset_415c2eb9-02c3-4189-a329-d7da7e5f7d35.dat" > "/tmp/tmp5s8uq5dm/job_working_directory/000/12/outputs/dataset_43a01cf1-c3f7-4160-9693-2b239d85f386.dat"

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "bbf5acdcc96211ee855e2743ef507876"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  code "$0~\"Uniquely mapped reads number\"{print 1000000/$NF}"
                  dbkey "dm6"

          • Step 5: param_value_from_file:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "bbf5acdcc96211ee855e2743ef507876"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  param_type "float"
                  remove_newlines true

          • Step 6: Scaled Coverage both strands combined:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • bedtools genomecov  -ibam '/tmp/tmp5s8uq5dm/files/f/3/5/dataset_f358ebd6-aad8-4f9e-9b8d-52fbb88beeb0.dat'   -split   -bg  -scale 1.17005     > '/tmp/tmp5s8uq5dm/job_working_directory/000/20/outputs/dataset_6eab00a4-feec-4b6f-bfd2-b24af5b70d67.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "bbf5acdcc96211ee855e2743ef507876"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  d false
                  dbkey "dm6"
                  dz false
                  five false
                  input_type {"__current_case__": 1, "input": {"values": [{"id": 17, "src": "dce"}]}, "input_type_select": "bam"}
                  report {"__current_case__": 0, "report_select": "bg", "scale": "1.17005", "zero_regions": false}
                  split true
                  strand ""
                  three false

          • Step 7: convert both strands coverage to bigwig:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • grep -v "^track" '/tmp/tmp5s8uq5dm/files/6/e/a/dataset_6eab00a4-feec-4b6f-bfd2-b24af5b70d67.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len' '/tmp/tmp5s8uq5dm/job_working_directory/000/21/outputs/dataset_bb2b98c4-f7e4-4ac5-8992-21b3f244c30d.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bedgraph"
                  __workflow_invocation_uuid__ "bbf5acdcc96211ee855e2743ef507876"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  settings {"__current_case__": 0, "settingsType": "preset"}

      • Step 18: Unlabelled step:

        • step_state: new

        • Subworkflow Steps

          • Step 1: strandedness:

            • step_state: scheduled

          • Step 2: Bedgraph strand 1:

            • step_state: scheduled

          • Step 11: Unlabelled step:

            • step_state: new

          • Step 12: convert to bigwig:

            • step_state: new

          • Step 3: Bedgraph strand 2:

            • step_state: scheduled

          • Step 4: Get replacement for strand1:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "bbf5acddc96211ee855e2743ef507876"
                  chromInfo "/tmp/tmp5s8uq5dm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                  dbkey "?"
                  input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_forward"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_reverse"}, {"__index__": 2, "from": "unstranded", "to": "$1_forward"}], "type": "text"}
                  output_param_type "text"
                  unmapped {"__current_case__": 1, "on_unmapped": "fail"}

          • Step 5: Get replacement for strand2:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "bbf5acddc96211ee855e2743ef507876"
                  chromInfo "/tmp/tmp5s8uq5dm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                  dbkey "?"
                  input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_reverse"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_forward"}, {"__index__": 2, "from": "unstranded", "to": "$1_reverse"}], "type": "text"}
                  output_param_type "text"
                  unmapped {"__current_case__": 1, "on_unmapped": "fail"}

          • Step 6: get identifiers:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • mv '/tmp/tmp5s8uq5dm/job_working_directory/000/16/configs/tmp0naef_84' '/tmp/tmp5s8uq5dm/job_working_directory/000/16/outputs/dataset_b4fcffc1-23f3-4aa1-b731-4047948b0c2e.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bedgraph"
                  __workflow_invocation_uuid__ "bbf5acddc96211ee855e2743ef507876"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  input_collection {"values": [{"id": 8, "src": "hdca"}]}

          • Step 7: New labels strand 1:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp5s8uq5dm/job_working_directory/000/18/outputs/dataset_cfa12edf-71a5-4c2e-98f2-53285f226388.dat' -g    -r '^(.+)$' '$1_forward' '/tmp/tmp5s8uq5dm/files/b/4/f/dataset_b4fcffc1-23f3-4aa1-b731-4047948b0c2e.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "bbf5acddc96211ee855e2743ef507876"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  find_and_replace [{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_forward", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

          • Step 8: New labels strand 2:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/d698c222f354/text_processing/find_and_replace' -o '/tmp/tmp5s8uq5dm/job_working_directory/000/19/outputs/dataset_b41224a4-76df-447f-a09c-c8f6936ce252.dat' -g    -r '^(.+)$' '$1_reverse' '/tmp/tmp5s8uq5dm/files/b/4/f/dataset_b4fcffc1-23f3-4aa1-b731-4047948b0c2e.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "bbf5acddc96211ee855e2743ef507876"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  find_and_replace [{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_reverse", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

          • Step 9: Relabelled strand 1:

            • step_state: new

          • Step 10: Relabelled strand 2:

            • step_state: new

      • Step 19: Compute FPKM with cufflinks:

        • step_state: new

      • Step 20: Extract gene counts:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f "/tmp/tmp5s8uq5dm/job_working_directory/000/17/configs/tmp1egt5jbw" "/tmp/tmp5s8uq5dm/files/9/8/7/dataset_987690d9-2405-434c-8e71-ae047967d746.dat" > "/tmp/tmp5s8uq5dm/job_working_directory/000/17/outputs/dataset_05b7044a-4914-49d5-9e4d-c5ff0183566b.dat"

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "tabular"
              __workflow_invocation_uuid__ "bbf5acdbc96211ee855e2743ef507876"
              chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
              code "NR>4{print $1\"\\t\"$2}"
              dbkey "dm6"

      • Step 3: reverse_adapter:

        • step_state: scheduled

      • Step 21: Compute FPKM with StringTie:

        • step_state: new

      • Step 4: reference_genome:

        • step_state: scheduled

      • Step 5: gtf:

        • step_state: scheduled

      • Step 6: strandedness:

        • step_state: scheduled

      • Step 7: cufflinks_FPKM:

        • step_state: scheduled

      • Step 8: gtf with regions to exclude from FPKM normalization with Cufflinks:

        • step_state: scheduled

      • Step 9: stringtie_FPKM:

        • step_state: scheduled

      • Step 10: Cutadapt (remove adapter + bad quality bases):

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • ln -f -s '/tmp/tmp5s8uq5dm/files/2/3/1/dataset_2310197f-c4d9-4273-aa0e-fd124c04abbf.dat' 'GSM461177_1.fq' &&  ln -f -s '/tmp/tmp5s8uq5dm/files/4/f/5/dataset_4f5ad857-c7e6-4fea-bb1d-0336efe0f2f5.dat' 'GSM461177_2.fq' &&    cutadapt  -j=${GALAXY_SLOTS:-4}       -a 'Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'             -A 'Dummy-Adapter (do not use me)'='TGTAGGCC'       --output='out1.fq' --paired-output='out2.fq'  --error-rate=0.1 --times=1 --overlap=3    --action=trim      --minimum-length=15 --pair-filter=any    --quality-cutoff=30      'GSM461177_1.fq' 'GSM461177_2.fq'  > report.txt

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __job_resource {"__current_case__": 0, "__job_resource__select": "no"}
              __workflow_invocation_uuid__ "bbf5acdbc96211ee855e2743ef507876"
              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/tmp5s8uq5dm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              filter_options {"discard_cassava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": "15", "pair_filter": "any"}
              library {"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_name": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source": {"__current_case__": 1, "adapter": "TGTAGGCC", "adapter_source_list": "builtin"}, "single_noindels": false}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "maximum_length2": null, "minimum_length2": null, "quality_cutoff2": null}, "type": "paired_collection"}
              output_selector ["report"]
              read_mod_options {"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "30", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}
    • Other invocation details

      • error_message

        • Final state of invocation c0d4991e672fd404 is [failed]

      • history_id

        • 91b461542d7ae630

      • history_state

        • ok

      • invocation_id

        • 91b461542d7ae630

      • invocation_state

        • failed

      • messages

        • [{'details': None, 'reason': 'expression_evaluation_failed', 'workflow_step_id': 18}]

      • workflow_id

        • c0d4991e672fd404

@mvdbeek
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mvdbeek commented Feb 12, 2024 •
edited
Loading 

galaxy.workflow.run ERROR 2024-02-12 05:08:27,012 [pN:main.1,p:5403,tN:WorkflowRequestMonitor.monitor_thread] Failed to schedule Workflow[id=2,name=Re-arrange Stranded RNA-seq coverage], problem occurred on WorkflowStep[index=8,type=tool,label=Relabelled strand 1,uuid=6a3f57c0-f6d6-468f-8ac9-b6882f754eed,id=12].
Traceback (most recent call last):
  File "/tmp/tmp5s8uq5dm/galaxy-dev/lib/galaxy/workflow/run.py", line 463, in replacement_for_connection
    replacement = step_outputs[output_name]
                  ~~~~~~~~~~~~^^^^^^^^^^^^^
KeyError: 'output'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmp5s8uq5dm/galaxy-dev/lib/galaxy/workflow/run.py", line 234, in invoke
    incomplete_or_none = self._invoke_step(workflow_invocation_step)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp5s8uq5dm/galaxy-dev/lib/galaxy/workflow/run.py", line 318, in _invoke_step
    incomplete_or_none = invocation_step.workflow_step.module.execute(
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp5s8uq5dm/galaxy-dev/lib/galaxy/workflow/modules.py", line 2159, in execute
    collection_info = self.compute_collection_info(progress, step, all_inputs)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp5s8uq5dm/galaxy-dev/lib/galaxy/workflow/modules.py", line 520, in compute_collection_info
    collections_to_match = self._find_collections_to_match(progress, step, all_inputs)
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp5s8uq5dm/galaxy-dev/lib/galaxy/workflow/modules.py", line 540, in _find_collections_to_match
    data = progress.replacement_for_input(self.trans, step, input_dict)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp5s8uq5dm/galaxy-dev/lib/galaxy/workflow/run.py", line 438, in replacement_for_input
    replacement = self.replacement_for_connection(connection[0], is_data=is_data)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp5s8uq5dm/galaxy-dev/lib/galaxy/workflow/run.py", line 465, in replacement_for_connection
    raise modules.FailWorkflowEvaluation(
galaxy.workflow.modules.FailWorkflowEvaluation

definitely need to improve the error reporting there. The report says that the expression evaluation failed, but I think an output name change is the real issue.

@bgruening
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Outputs look ok to me. I can load the workflow to 23.1 without any warning, or error.

@github-actions GitHub Actions
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github-actions bot commented Mar 5, 2024

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 1
Failure 0
Skipped 0
Errored Tests
  • ❌ rnaseq-pe.ga_0

    Execution Problem:

    • Final state of invocation 518bb681ddc45917 is [failed]

    Workflow invocation details

    • Invocation Messages

      • Invocation scheduling failed because step 19 contains an expression that could not be evaluated.
    • Steps

      • Step 1: PE fastq input:

        • step_state: scheduled

      • Step 2: forward_adapter:

        • step_state: scheduled

      • Step 11: get reference_genome as text parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "10f88df1db2f11ee94fbe3bd9700bdd3"
              chromInfo "/tmp/tmpiqoz1m1_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              components [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "dm6", "select_param_type": "text"}}]
              dbkey "?"

      • Step 12: awk command from strand:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "10f88df1db2f11ee94fbe3bd9700bdd3"
              chromInfo "/tmp/tmpiqoz1m1_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "NR>4{print $1\"\\t\"$3}"}, {"__index__": 1, "from": "stranded - reverse", "to": "NR>4{print $1\"\\t\"$4}"}, {"__index__": 2, "from": "unstranded", "to": "NR>4{print $1\"\\t\"$2}"}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 13: Get cufflinks strandess parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "10f88df1db2f11ee94fbe3bd9700bdd3"
              chromInfo "/tmp/tmpiqoz1m1_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "fr-secondstrand"}, {"__index__": 1, "from": "stranded - reverse", "to": "fr-firststrand"}, {"__index__": 2, "from": "unstranded", "to": "fr-unstranded"}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 14: Get Stringtie strandedness parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "10f88df1db2f11ee94fbe3bd9700bdd3"
              chromInfo "/tmp/tmpiqoz1m1_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "--fr"}, {"__index__": 1, "from": "stranded - reverse", "to": "--rf"}, {"__index__": 2, "from": "unstranded", "to": ""}], "type": "text"}
              output_param_type "text"
              unmapped {"__current_case__": 1, "on_unmapped": "fail"}

      • Step 15: STAR: map and count and coverage splitted:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • STAR  --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir '/cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files' --sjdbOverhang 100 --sjdbGTFfile '/tmp/tmpiqoz1m1_/files/b/d/1/dataset_bd154a61-8dc8-406c-ac7e-393617eea733.dat' --sjdbGTFfeatureExon 'exon'   --readFilesIn '/tmp/tmpiqoz1m1_/files/6/a/6/dataset_6a6a3331-6744-4a03-b393-280319e2ad39.dat' '/tmp/tmpiqoz1m1_/files/d/d/8/dataset_dd8b9e8e-43f6-45b9-a979-6ad264cb4d6d.dat'   --outSAMtype BAM SortedByCoordinate  --twopassMode None ''  --quantMode GeneCounts   --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM  --outSAMprimaryFlag OneBestScore  --outSAMmapqUnique 255     --outSAMunmapped None  --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1   --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10  --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01   --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000   --outBAMsortingThreadN ${GALAXY_SLOTS:-4} --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM $((${GALAXY_MEMORY_MB:-0}*1000000))    --outWigType 'bedGraph' '' --outWigStrand 'Stranded' --outWigReferencesPrefix '-' --outWigNorm 'RPM'  && samtools view -b -o '/tmp/tmpiqoz1m1_/job_working_directory/000/9/outputs/dataset_0e538981-f949-460e-8fdf-22c55c94af4d.dat' Aligned.sortedByCoord.out.bam  && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out

            Exit Code:

            • 0

            Standard Output:

            • 	/usr/local/bin/STAR-avx2 --runThreadN 1 --genomeLoad NoSharedMemory --genomeDir /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files --sjdbOverhang 100 --sjdbGTFfile /tmp/tmpiqoz1m1_/files/b/d/1/dataset_bd154a61-8dc8-406c-ac7e-393617eea733.dat --sjdbGTFfeatureExon exon --readFilesIn /tmp/tmpiqoz1m1_/files/6/a/6/dataset_6a6a3331-6744-4a03-b393-280319e2ad39.dat /tmp/tmpiqoz1m1_/files/d/d/8/dataset_dd8b9e8e-43f6-45b9-a979-6ad264cb4d6d.dat --outSAMtype BAM SortedByCoordinate --twopassMode None  --quantMode GeneCounts --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 255 --outSAMunmapped None --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1 --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000 --outBAMsortingThreadN 1 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 0 --outWigType bedGraph  --outWigStrand Stranded --outWigReferencesPrefix - --outWigNorm RPM
	STAR version: 2.7.11a   compiled: 2023-09-15T02:58:53+0000 :/opt/conda/conda-bld/star_1694746407721/work/source
Mar 05 20:30:47 ..... started STAR run
Mar 05 20:30:47 ..... loading genome
Mar 05 20:40:26 ..... processing annotations GTF
Mar 05 20:40:27 ..... inserting junctions into the genome indices
Mar 05 20:41:37 ..... started mapping
Mar 05 20:43:22 ..... finished mapping
Mar 05 20:43:23 ..... started sorting BAM
Mar 05 20:43:25 ..... started wiggle output
Mar 05 20:43:30 ..... finished successfully

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "10f88df1db2f11ee94fbe3bd9700bdd3"
              algo {"params": {"__current_case__": 3, "align": {"alignEndsType": "Local", "alignIntronMax": "1000000", "alignIntronMin": "20", "alignMatesGapMax": "1000000", "alignSJDBoverhangMin": "1", "alignSJoverhangMin": "8", "alignSJstitchMismatchNmax": {"alignSJstitchMismatchNmax1": "0", "alignSJstitchMismatchNmax2": "-1", "alignSJstitchMismatchNmax3": "0", "alignSJstitchMismatchNmax4": "0"}, "alignSplicedMateMapLmin": "0", "alignSplicedMateMapLminOverLmate": "0.66", "alignTranscriptsPerReadNmax": "10000", "alignTranscriptsPerWindowNmax": "100", "alignWindowsPerReadNmax": "10000", "peOverlapMMp": "0.01", "peOverlapNbasesMin": "0"}, "chim_settings": {"chimFilter": true, "chimJunctionOverhangMin": "20", "chimMainSegmentMultNmax": "10", "chimMultimapNmax": "1", "chimMultimapScoreRange": "1", "chimScoreDropMax": "20", "chimScoreJunctionNonGTAG": "-1", "chimScoreMin": "0", "chimScoreSeparation": "10", "chimSegmentMin": "12", "chimSegmentReadGapMax": "0"}, "junction_limits": {"limitOutSJcollapsed": "1000000", "limitOutSJoneRead": "1000", "limitSjdbInsertNsj": "1000000"}, "seed": {"seedMultimapNmax": "10000", "seedNoneLociPerWindow": "10", "seedPerReadNmax": "1000", "seedPerWindowNmax": "50", "seedSearchLmax": "0", "seedSearchStartLmax": "50", "seedSearchStartLmaxOverLread": "1.0"}, "settingsType": "full"}}
              chimOutType ""
              chromInfo "/tmp/tmpiqoz1m1_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              filter {"basic_filters": ["exclude_unmapped"], "output_params2": {"__current_case__": 0, "outFilterMatchNmin": "0", "outFilterMatchNminOverLread": "0.66", "outFilterMismatchNmax": "999", "outFilterMismatchNoverLmax": "0.3", "outFilterMismatchNoverReadLmax": "0.04", "outFilterMultimapNmax": "20", "outFilterMultimapScoreRange": "1", "outFilterScoreMin": "0", "outFilterScoreMinOverLread": "0.66", "outFilterType": true, "outSAMmultNmax": "-1", "outSAMtlen": "1", "output_select2": "yes"}}
              oformat {"HI_offset": "1", "outSAMattributes": ["NH", "HI", "AS", "nM"], "outSAMmapqUnique": "255", "outSAMprimaryFlag": "OneBestScore"}
              outWig {"__current_case__": 1, "outWigNorm": true, "outWigReferencesPrefix": "-", "outWigStrand": true, "outWigType": "bedGraph", "outWigTypeSecondWord": ""}
              perf {"outBAMsortingBinsN": "50", "winAnchorMultimapNmax": "50"}
              refGenomeSource {"GTFconditional": {"GTFselect": "without-gtf-with-gtf", "__current_case__": 1, "genomeDir": "dm6", "quantmode_output": {"__current_case__": 1, "quantMode": "GeneCounts"}, "sjdbGTFfeatureExon": "exon", "sjdbGTFfile": {"values": [{"id": 1, "src": "hda"}]}, "sjdbOverhang": "100"}, "__current_case__": 0, "geneSource": "indexed"}
              singlePaired {"__current_case__": 2, "input": {"values": [{"id": 4, "src": "dce"}]}, "sPaired": "paired_collection"}
              twopass {"__current_case__": 0, "sj_precalculated": "", "twopassMode": "None", "twopass_read_subset": ""}

      • Step 16: MultiQC:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/cutadapt_0 &&    ln -s '/tmp/tmpiqoz1m1_/files/c/4/a/dataset_c4a0ef85-0fa5-48b3-8485-1c279a106ff4.dat' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/GSM461177.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && mkdir multiqc_WDir/star_1 &&    mkdir 'multiqc_WDir/star_1/log_0' &&     ln -s '/tmp/tmpiqoz1m1_/files/4/4/d/dataset_44d545e4-e089-468b-9ec5-b38cdd6743ff.dat' 'multiqc_WDir/star_1/log_0/GSM461177_Log.final.out' &&   mkdir 'multiqc_WDir/star_1/genecounts_1' &&     ln -s '/tmp/tmpiqoz1m1_/files/b/a/7/dataset_ba7cd7e8-c901-4bae-aa55-e849d7ac89d1.dat' 'multiqc_WDir/star_1/genecounts_1/GSM461177_ReadsPerGene.out.tab' &&   multiqc multiqc_WDir --filename 'report'    --export

            Exit Code:

            • 0

            Standard Error:

            •   /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpiqoz1m1_/job_working_directory/000/10/working/multiqc_WDir
|              star | Found 1 reports and 1 gene count files
|          cutadapt | Found 1 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | Plots       : report_plots
|           multiqc | MultiQC complete

            Standard Output:

            • |         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "10f88df1db2f11ee94fbe3bd9700bdd3"
              chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
              comment ""
              dbkey "dm6"
              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__": 28, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 4, "src": "hdca"}]}, "type": "log"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "genecounts"}}], "software": "star"}}]
              saveLog false
              title ""

      • Step 17: Unlabelled step:

        • step_state: new

        • Subworkflow Steps

          • Step 1: STAR BAM:

            • step_state: scheduled

          • Step 2: STAR log:

            • step_state: scheduled

          • Step 3: keep uniquely mapped reads:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cp '/tmp/tmpiqoz1m1_/job_working_directory/000/11/configs/tmpxdrqahvn' '/tmp/tmpiqoz1m1_/job_working_directory/000/11/outputs/dataset_fc3d9b4d-9a77-4c83-a84b-d7c7df0d9c34.dat' && ln -s '/tmp/tmpiqoz1m1_/files/0/e/5/dataset_0e538981-f949-460e-8fdf-22c55c94af4d.dat' localbam.bam && ln -s '/tmp/tmpiqoz1m1_/files/_metadata_files/f/4/5/metadata_f4524b55-e02c-47a8-9e4f-5c69dd6da194.dat' localbam.bam.bai && cat '/tmp/tmpiqoz1m1_/job_working_directory/000/11/configs/tmpxdrqahvn' && bamtools filter -script '/tmp/tmpiqoz1m1_/job_working_directory/000/11/configs/tmpxdrqahvn' -in localbam.bam -out '/tmp/tmpiqoz1m1_/job_working_directory/000/11/outputs/dataset_e27ec5af-b117-4cf7-8ff0-9c90699fe9fc.dat'

                Exit Code:

                • 0

                Standard Output:

                •         
{
    "filters": [
        {
            "id": "1",
            "tag": "NH=1"
        }
    ]
}

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bam"
                  __workflow_invocation_uuid__ "10f88df2db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  conditions [{"__index__": 0, "filters": [{"__index__": 0, "bam_property": {"__current_case__": 21, "bam_property_selector": "tag", "bam_property_value": "NH=1"}}]}]
                  dbkey "dm6"
                  rule_configuration {"__current_case__": 0, "rules_selector": false}

          • Step 4: get scaling factor:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpiqoz1m1_/job_working_directory/000/12/configs/tmp7efpcr6n' '/tmp/tmpiqoz1m1_/files/4/4/d/dataset_44d545e4-e089-468b-9ec5-b38cdd6743ff.dat' > '/tmp/tmpiqoz1m1_/job_working_directory/000/12/outputs/dataset_ee4402e9-bcb1-440e-b51e-056c0644a8cc.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "10f88df2db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  code "$0~\"Uniquely mapped reads number\"{print 1000000/$NF}"
                  dbkey "dm6"

          • Step 5: param_value_from_file:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "txt"
                  __workflow_invocation_uuid__ "10f88df2db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  param_type "float"
                  remove_newlines true

          • Step 6: Scaled Coverage both strands combined:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • bedtools genomecov  -ibam '/tmp/tmpiqoz1m1_/files/e/2/7/dataset_e27ec5af-b117-4cf7-8ff0-9c90699fe9fc.dat'   -split   -bg  -scale 1.17005     > '/tmp/tmpiqoz1m1_/job_working_directory/000/20/outputs/dataset_73d08203-1875-4978-8c70-a196f6637df3.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "10f88df2db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  d false
                  dbkey "dm6"
                  dz false
                  five false
                  input_type {"__current_case__": 1, "input": {"values": [{"id": 17, "src": "dce"}]}, "input_type_select": "bam"}
                  report {"__current_case__": 0, "report_select": "bg", "scale": "1.17005", "zero_regions": false}
                  split true
                  strand ""
                  three false

          • Step 7: convert both strands coverage to bigwig:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • grep -v "^track" '/tmp/tmpiqoz1m1_/files/7/3/d/dataset_73d08203-1875-4978-8c70-a196f6637df3.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len' '/tmp/tmpiqoz1m1_/job_working_directory/000/21/outputs/dataset_9917fb96-4e7b-412d-81c3-9929b63e9e7c.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bedgraph"
                  __workflow_invocation_uuid__ "10f88df2db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  settings {"__current_case__": 0, "settingsType": "preset"}

      • Step 18: Unlabelled step:

        • step_state: new

        • Subworkflow Steps

          • Step 1: strandedness:

            • step_state: scheduled

          • Step 2: Bedgraph strand 1:

            • step_state: scheduled

          • Step 11: Unlabelled step:

            • step_state: new

          • Step 12: convert to bigwig:

            • step_state: new

          • Step 3: Bedgraph strand 2:

            • step_state: scheduled

          • Step 4: Get replacement for strand1:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "10f88df3db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/tmp/tmpiqoz1m1_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                  dbkey "?"
                  input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_forward"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_reverse"}, {"__index__": 2, "from": "unstranded", "to": "$1_forward"}], "type": "text"}
                  output_param_type "text"
                  unmapped {"__current_case__": 1, "on_unmapped": "fail"}

          • Step 5: Get replacement for strand2:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • cd ../; python _evaluate_expression_.py

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "10f88df3db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/tmp/tmpiqoz1m1_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                  dbkey "?"
                  input_param_type {"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_reverse"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_forward"}, {"__index__": 2, "from": "unstranded", "to": "$1_reverse"}], "type": "text"}
                  output_param_type "text"
                  unmapped {"__current_case__": 1, "on_unmapped": "fail"}

          • Step 6: get identifiers:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • mv '/tmp/tmpiqoz1m1_/job_working_directory/000/16/configs/tmpyocthjot' '/tmp/tmpiqoz1m1_/job_working_directory/000/16/outputs/dataset_4bbfc207-307b-4f8e-ade2-f3d73191633a.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "bedgraph"
                  __workflow_invocation_uuid__ "10f88df3db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  input_collection {"values": [{"id": 8, "src": "hdca"}]}

          • Step 7: New labels strand 1:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/12615d397df7/text_processing/find_and_replace' -o '/tmp/tmpiqoz1m1_/job_working_directory/000/18/outputs/dataset_c5415cb9-435b-47c9-93c5-a5e8c26a766a.dat' -g    -r '^(.+)$' '$1_forward' '/tmp/tmpiqoz1m1_/files/4/b/b/dataset_4bbfc207-307b-4f8e-ade2-f3d73191633a.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "10f88df3db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  find_and_replace [{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_forward", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

          • Step 8: New labels strand 2:

            • step_state: scheduled

            • Jobs

              • Job 1:

                • Job state is ok

                Command Line:

                • perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/12615d397df7/text_processing/find_and_replace' -o '/tmp/tmpiqoz1m1_/job_working_directory/000/19/outputs/dataset_02f0224c-7fc8-4c08-88e2-0cae74ddd8aa.dat' -g    -r '^(.+)$' '$1_reverse' '/tmp/tmpiqoz1m1_/files/4/b/b/dataset_4bbfc207-307b-4f8e-ade2-f3d73191633a.dat'

                Exit Code:

                • 0

                Job Parameters:

                • Job parameter Parameter value
                  __input_ext "input"
                  __workflow_invocation_uuid__ "10f88df3db2f11ee94fbe3bd9700bdd3"
                  chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
                  dbkey "dm6"
                  find_and_replace [{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_reverse", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

          • Step 9: Relabelled strand 1:

            • step_state: new

          • Step 10: Relabelled strand 2:

            • step_state: new

      • Step 19: Compute FPKM with cufflinks:

        • step_state: new

      • Step 20: Extract gene counts:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpiqoz1m1_/job_working_directory/000/17/configs/tmpcp7jp_q5' '/tmp/tmpiqoz1m1_/files/b/a/7/dataset_ba7cd7e8-c901-4bae-aa55-e849d7ac89d1.dat' > '/tmp/tmpiqoz1m1_/job_working_directory/000/17/outputs/dataset_282cc057-be2c-43e7-9f19-8d9c2a887d55.dat'

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "10f88df1db2f11ee94fbe3bd9700bdd3"
              chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"
              code "NR>4{print $1\"\\t\"$2}"
              dbkey "dm6"

      • Step 3: reverse_adapter:

        • step_state: scheduled

      • Step 21: Compute FPKM with StringTie:

        • step_state: new

      • Step 4: reference_genome:

        • step_state: scheduled

      • Step 5: gtf:

        • step_state: scheduled

      • Step 6: strandedness:

        • step_state: scheduled

      • Step 7: cufflinks_FPKM:

        • step_state: scheduled

      • Step 8: gtf with regions to exclude from FPKM normalization with Cufflinks:

        • step_state: scheduled

      • Step 9: stringtie_FPKM:

        • step_state: scheduled

      • Step 10: Cutadapt (remove adapter + bad quality bases):

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • ln -f -s '/tmp/tmpiqoz1m1_/files/a/9/2/dataset_a9208117-c30e-469e-93d4-15b1c137f4a3.dat' 'GSM461177_1.fq' &&  ln -f -s '/tmp/tmpiqoz1m1_/files/f/d/5/dataset_fd53ba9a-2a8e-4b00-97a2-bd2d4c7625b7.dat' 'GSM461177_2.fq' &&    cutadapt  -j=${GALAXY_SLOTS:-4}       -a 'Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'             -A 'Dummy-Adapter (do not use me)'='TGTAGGCC'       --output='out1.fq' --paired-output='out2.fq'  --error-rate=0.1 --times=1 --overlap=3    --action=trim      --minimum-length=15 --pair-filter=any    --quality-cutoff=30      'GSM461177_1.fq' 'GSM461177_2.fq'  > report.txt

            Exit Code:

            • 0

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __job_resource {"__current_case__": 0, "__job_resource__select": "no"}
              __workflow_invocation_uuid__ "10f88df1db2f11ee94fbe3bd9700bdd3"
              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/tmpiqoz1m1_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              filter_options {"discard_cassava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": "15", "pair_filter": "any"}
              library {"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_name": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source": {"__current_case__": 1, "adapter": "TGTAGGCC", "adapter_source_list": "builtin"}, "single_noindels": false}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "maximum_length2": null, "minimum_length2": null, "quality_cutoff2": null}, "type": "paired_collection"}
              output_selector ["report"]
              read_mod_options {"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "30", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}
    • Other invocation details

      • error_message

        • Final state of invocation 518bb681ddc45917 is [failed]

      • history_id

        • c489183ea05816bf

      • history_state

        • ok

      • invocation_id

        • c489183ea05816bf

      • invocation_state

        • failed

      • messages

        • [{'details': None, 'reason': 'expression_evaluation_failed', 'workflow_step_id': 18}]

      • workflow_id

        • 518bb681ddc45917

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Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 1
Failure 0
Skipped 0
Errored Tests
  • ❌ rnaseq-pe.ga_0

    Execution Problem:

    • Final state of invocation 78fa7c6adfe12b78 is [failed]

    Workflow invocation details

    • Invocation Messages

      • Invocation scheduling failed because step 19 contains an expression that could not be evaluated.
    • Steps

      • Step 1: PE fastq input:

        • step_state: scheduled

      • Step 2: forward_adapter:

        • step_state: scheduled

      • Step 11: get reference_genome as text parameter:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Traceback:

            • 

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"1be3b2d8e15d11ee8e386d668327c804"

              

              
chromInfo
"/tmp/tmpj0d0eqdo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
components
[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "dm6", "select_param_type": "text"}}]

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 12: awk command from strand:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"1be3b2d8e15d11ee8e386d668327c804"

              

              
chromInfo
"/tmp/tmpj0d0eqdo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "NR>4{print $1\"\\t\"$3}"}, {"__index__": 1, "from": "stranded - reverse", "to": "NR>4{print $1\"\\t\"$4}"}, {"__index__": 2, "from": "unstranded", "to": "NR>4{print $1\"\\t\"$2}"}], "type": "text"}

              

              
output_param_type
"text"

              

              
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 13: Get cufflinks strandess parameter:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"1be3b2d8e15d11ee8e386d668327c804"

              

              
chromInfo
"/tmp/tmpj0d0eqdo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "fr-secondstrand"}, {"__index__": 1, "from": "stranded - reverse", "to": "fr-firststrand"}, {"__index__": 2, "from": "unstranded", "to": "fr-unstranded"}], "type": "text"}

              

              
output_param_type
"text"

              

              
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 14: Get Stringtie strandedness parameter:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"1be3b2d8e15d11ee8e386d668327c804"

              

              
chromInfo
"/tmp/tmpj0d0eqdo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "--fr"}, {"__index__": 1, "from": "stranded - reverse", "to": "--rf"}, {"__index__": 2, "from": "unstranded", "to": ""}], "type": "text"}

              

              
output_param_type
"text"

              

              
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 15: STAR: map and count and coverage splitted:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              STAR  --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir '/cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files' --sjdbOverhang 100 --sjdbGTFfile '/tmp/tmpj0d0eqdo/files/a/2/1/dataset_a21354d2-02ce-4cf1-90a5-560135f93fa0.dat' --sjdbGTFfeatureExon 'exon'   --readFilesIn '/tmp/tmpj0d0eqdo/files/5/a/9/dataset_5a909302-b0b0-4001-b3ea-1fc42576573c.dat' '/tmp/tmpj0d0eqdo/files/3/5/c/dataset_35c44b25-8023-431c-923c-4398b3dea429.dat'   --outSAMtype BAM SortedByCoordinate  --twopassMode None ''  --quantMode GeneCounts   --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM  --outSAMprimaryFlag OneBestScore  --outSAMmapqUnique 255     --outSAMunmapped None  --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1   --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10  --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01   --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000   --outBAMsortingThreadN ${GALAXY_SLOTS:-4} --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM $((${GALAXY_MEMORY_MB:-0}*1000000))    --outWigType 'bedGraph' '' --outWigStrand 'Stranded' --outWigReferencesPrefix '-' --outWigNorm 'RPM'  && samtools view -b -o '/tmp/tmpj0d0eqdo/job_working_directory/000/9/outputs/dataset_53ab11aa-6b42-420b-b21c-39a68d47754b.dat' Aligned.sortedByCoord.out.bam  && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              	/usr/local/bin/STAR-avx2 --runThreadN 1 --genomeLoad NoSharedMemory --genomeDir /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files --sjdbOverhang 100 --sjdbGTFfile /tmp/tmpj0d0eqdo/files/a/2/1/dataset_a21354d2-02ce-4cf1-90a5-560135f93fa0.dat --sjdbGTFfeatureExon exon --readFilesIn /tmp/tmpj0d0eqdo/files/5/a/9/dataset_5a909302-b0b0-4001-b3ea-1fc42576573c.dat /tmp/tmpj0d0eqdo/files/3/5/c/dataset_35c44b25-8023-431c-923c-4398b3dea429.dat --outSAMtype BAM SortedByCoordinate --twopassMode None  --quantMode GeneCounts --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 255 --outSAMunmapped None --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1 --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000 --outBAMsortingThreadN 1 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 0 --outWigType bedGraph  --outWigStrand Stranded --outWigReferencesPrefix - --outWigNorm RPM
	STAR version: 2.7.11a   compiled: 2023-09-15T02:58:53+0000 :/opt/conda/conda-bld/star_1694746407721/work/source
Mar 13 17:14:57 ..... started STAR run
Mar 13 17:14:58 ..... loading genome
Mar 13 17:23:45 ..... processing annotations GTF
Mar 13 17:23:46 ..... inserting junctions into the genome indices
Mar 13 17:25:01 ..... started mapping
Mar 13 17:26:47 ..... finished mapping
Mar 13 17:26:47 ..... started sorting BAM
Mar 13 17:26:50 ..... started wiggle output
Mar 13 17:26:56 ..... finished successfully

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"1be3b2d8e15d11ee8e386d668327c804"

              

              
algo
{"params": {"__current_case__": 3, "align": {"alignEndsType": "Local", "alignIntronMax": "1000000", "alignIntronMin": "20", "alignMatesGapMax": "1000000", "alignSJDBoverhangMin": "1", "alignSJoverhangMin": "8", "alignSJstitchMismatchNmax": {"alignSJstitchMismatchNmax1": "0", "alignSJstitchMismatchNmax2": "-1", "alignSJstitchMismatchNmax3": "0", "alignSJstitchMismatchNmax4": "0"}, "alignSplicedMateMapLmin": "0", "alignSplicedMateMapLminOverLmate": "0.66", "alignTranscriptsPerReadNmax": "10000", "alignTranscriptsPerWindowNmax": "100", "alignWindowsPerReadNmax": "10000", "peOverlapMMp": "0.01", "peOverlapNbasesMin": "0"}, "chim_settings": {"chimFilter": true, "chimJunctionOverhangMin": "20", "chimMainSegmentMultNmax": "10", "chimMultimapNmax": "1", "chimMultimapScoreRange": "1", "chimScoreDropMax": "20", "chimScoreJunctionNonGTAG": "-1", "chimScoreMin": "0", "chimScoreSeparation": "10", "chimSegmentMin": "12", "chimSegmentReadGapMax": "0"}, "junction_limits": {"limitOutSJcollapsed": "1000000", "limitOutSJoneRead": "1000", "limitSjdbInsertNsj": "1000000"}, "seed": {"seedMultimapNmax": "10000", "seedNoneLociPerWindow": "10", "seedPerReadNmax": "1000", "seedPerWindowNmax": "50", "seedSearchLmax": "0", "seedSearchStartLmax": "50", "seedSearchStartLmaxOverLread": "1.0"}, "settingsType": "full"}}

              

              
chimOutType
""

              

              
chromInfo
"/tmp/tmpj0d0eqdo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
filter
{"basic_filters": ["exclude_unmapped"], "output_params2": {"__current_case__": 0, "outFilterMatchNmin": "0", "outFilterMatchNminOverLread": "0.66", "outFilterMismatchNmax": "999", "outFilterMismatchNoverLmax": "0.3", "outFilterMismatchNoverReadLmax": "0.04", "outFilterMultimapNmax": "20", "outFilterMultimapScoreRange": "1", "outFilterScoreMin": "0", "outFilterScoreMinOverLread": "0.66", "outFilterType": true, "outSAMmultNmax": "-1", "outSAMtlen": "1", "output_select2": "yes"}}

              

              
oformat
{"HI_offset": "1", "outSAMattributes": ["NH", "HI", "AS", "nM"], "outSAMmapqUnique": "255", "outSAMprimaryFlag": "OneBestScore"}

              

              
outWig
{"__current_case__": 1, "outWigNorm": true, "outWigReferencesPrefix": "-", "outWigStrand": true, "outWigType": "bedGraph", "outWigTypeSecondWord": ""}

              

              
perf
{"outBAMsortingBinsN": "50", "winAnchorMultimapNmax": "50"}

              

              
refGenomeSource
{"GTFconditional": {"GTFselect": "without-gtf-with-gtf", "__current_case__": 1, "genomeDir": "dm6", "quantmode_output": {"__current_case__": 1, "quantMode": "GeneCounts"}, "sjdbGTFfeatureExon": "exon", "sjdbGTFfile": {"values": [{"id": 1, "src": "hda"}]}, "sjdbOverhang": "100"}, "__current_case__": 0, "geneSource": "indexed"}

              

              
singlePaired
{"__current_case__": 2, "input": {"values": [{"id": 4, "src": "dce"}]}, "sPaired": "paired_collection"}

              

              
twopass
{"__current_case__": 0, "sj_precalculated": "", "twopassMode": "None", "twopass_read_subset": ""}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 16: MultiQC:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/cutadapt_0 &&    ln -s '/tmp/tmpj0d0eqdo/files/b/9/e/dataset_b9e91072-1284-46b2-be9f-68198bac97fa.dat' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/GSM461177.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && mkdir multiqc_WDir/star_1 &&    mkdir 'multiqc_WDir/star_1/log_0' &&     ln -s '/tmp/tmpj0d0eqdo/files/c/2/2/dataset_c22c2610-4448-4637-9427-93b49d0a74af.dat' 'multiqc_WDir/star_1/log_0/GSM461177_Log.final.out' &&   mkdir 'multiqc_WDir/star_1/genecounts_1' &&     ln -s '/tmp/tmpj0d0eqdo/files/a/8/6/dataset_a8624a1c-c056-468c-80d6-6cfd60d33813.dat' 'multiqc_WDir/star_1/genecounts_1/GSM461177_ReadsPerGene.out.tab' &&   multiqc multiqc_WDir --filename 'report'    --export
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

                /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmpj0d0eqdo/job_working_directory/000/10/working/multiqc_WDir
|              star | Found 1 reports and 1 gene count files
|          cutadapt | Found 1 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | Plots       : report_plots
|           multiqc | MultiQC complete

              

              • 

            

            Standard Output:
            

              

            • 

              |         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4  
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"1be3b2d8e15d11ee8e386d668327c804"

              

              
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

              

              
comment
""

              

              
dbkey
"dm6"

              

              
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__": 28, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 4, "src": "hdca"}]}, "type": "log"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "genecounts"}}], "software": "star"}}]

              

              
saveLog
false

              

              
title
""

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 17: Unlabelled step:
        

          

        • 

          step_state: new
          

          • 

        • 

          Subworkflow Steps

            

          • 

            Step 1: STAR BAM:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 2: STAR log:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 3: keep uniquely mapped reads:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  cp '/tmp/tmpj0d0eqdo/job_working_directory/000/11/configs/tmpb17jgpkg' '/tmp/tmpj0d0eqdo/job_working_directory/000/11/outputs/dataset_88430fc4-a0e5-42d7-a529-8d458bf49e1e.dat' && ln -s '/tmp/tmpj0d0eqdo/files/5/3/a/dataset_53ab11aa-6b42-420b-b21c-39a68d47754b.dat' localbam.bam && ln -s '/tmp/tmpj0d0eqdo/files/_metadata_files/c/c/a/metadata_cca77b75-e337-41ad-872b-1adbd838fad1.dat' localbam.bam.bai && cat '/tmp/tmpj0d0eqdo/job_working_directory/000/11/configs/tmpb17jgpkg' && bamtools filter -script '/tmp/tmpj0d0eqdo/job_working_directory/000/11/configs/tmpb17jgpkg' -in localbam.bam -out '/tmp/tmpj0d0eqdo/job_working_directory/000/11/outputs/dataset_8cb0e827-f0a0-4a13-9f06-e54495ef78f6.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Standard Output:
                

                  

                • 

                          
{
    "filters": [
        {
            "id": "1",
            "tag": "NH=1"
        }
    ]
}

        
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"bam"

                  

                  
__workflow_invocation_uuid__
"1be3b2d9e15d11ee8e386d668327c804"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
conditions
[{"__index__": 0, "filters": [{"__index__": 0, "bam_property": {"__current_case__": 21, "bam_property_selector": "tag", "bam_property_value": "NH=1"}}]}]

                  

                  
dbkey
"dm6"

                  

                  
rule_configuration
{"__current_case__": 0, "rules_selector": false}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 4: get scaling factor:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpj0d0eqdo/job_working_directory/000/12/configs/tmp3_xi259m' '/tmp/tmpj0d0eqdo/files/c/2/2/dataset_c22c2610-4448-4637-9427-93b49d0a74af.dat' > '/tmp/tmpj0d0eqdo/job_working_directory/000/12/outputs/dataset_3f5c7317-b73c-45d6-b864-c222c9fe0748.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"1be3b2d9e15d11ee8e386d668327c804"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
code
"$0~\"Uniquely mapped reads number\"{print 1000000/$NF}"

                  

                  
dbkey
"dm6"

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 5: param_value_from_file:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  cd ../; python _evaluate_expression_.py
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"txt"

                  

                  
__workflow_invocation_uuid__
"1be3b2d9e15d11ee8e386d668327c804"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
param_type
"float"

                  

                  
remove_newlines
true

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 6: Scaled Coverage both strands combined:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  bedtools genomecov  -ibam '/tmp/tmpj0d0eqdo/files/8/c/b/dataset_8cb0e827-f0a0-4a13-9f06-e54495ef78f6.dat'   -split   -bg  -scale 1.17005     > '/tmp/tmpj0d0eqdo/job_working_directory/000/20/outputs/dataset_9d11827c-20a6-4674-8b92-4530ba2f82fc.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"1be3b2d9e15d11ee8e386d668327c804"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
d
false

                  

                  
dbkey
"dm6"

                  

                  
dz
false

                  

                  
five
false

                  

                  
input_type
{"__current_case__": 1, "input": {"values": [{"id": 17, "src": "dce"}]}, "input_type_select": "bam"}

                  

                  
report
{"__current_case__": 0, "report_select": "bg", "scale": "1.17005", "zero_regions": false}

                  

                  
split
true

                  

                  
strand
""

                  

                  
three
false

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 7: convert both strands coverage to bigwig:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  grep -v "^track" '/tmp/tmpj0d0eqdo/files/9/d/1/dataset_9d11827c-20a6-4674-8b92-4530ba2f82fc.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len' '/tmp/tmpj0d0eqdo/job_working_directory/000/21/outputs/dataset_69733c4f-9a3b-4ae9-a9a6-098e2c56ae88.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"bedgraph"

                  

                  
__workflow_invocation_uuid__
"1be3b2d9e15d11ee8e386d668327c804"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
settings
{"__current_case__": 0, "settingsType": "preset"}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          

          • 

        

        • 

      • 

        Step 18: Unlabelled step:
        

          

        • 

          step_state: new
          

          • 

        • 

          Subworkflow Steps

            

          • 

            Step 1: strandedness:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 2: Bedgraph strand 1:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 11: Unlabelled step:
            

              

            • step_state: new
              • 

            

            • 

          • 

            Step 12: convert to bigwig:
            

              

            • step_state: new
              • 

            

            • 

          • 

            Step 3: Bedgraph strand 2:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 4: Get replacement for strand1:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  cd ../; python _evaluate_expression_.py
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"1be3b2dae15d11ee8e386d668327c804"

                  

                  
chromInfo
"/tmp/tmpj0d0eqdo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

                  

                  
dbkey
"?"

                  

                  
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_forward"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_reverse"}, {"__index__": 2, "from": "unstranded", "to": "$1_forward"}], "type": "text"}

                  

                  
output_param_type
"text"

                  

                  
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 5: Get replacement for strand2:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  cd ../; python _evaluate_expression_.py
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"1be3b2dae15d11ee8e386d668327c804"

                  

                  
chromInfo
"/tmp/tmpj0d0eqdo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

                  

                  
dbkey
"?"

                  

                  
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_reverse"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_forward"}, {"__index__": 2, "from": "unstranded", "to": "$1_reverse"}], "type": "text"}

                  

                  
output_param_type
"text"

                  

                  
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 6: get identifiers:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  mv '/tmp/tmpj0d0eqdo/job_working_directory/000/16/configs/tmpx14s7iud' '/tmp/tmpj0d0eqdo/job_working_directory/000/16/outputs/dataset_5f555939-259c-419c-adc9-dbfd67a0f703.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"bedgraph"

                  

                  
__workflow_invocation_uuid__
"1be3b2dae15d11ee8e386d668327c804"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
input_collection
{"values": [{"id": 8, "src": "hdca"}]}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 7: New labels strand 1:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/12615d397df7/text_processing/find_and_replace' -o '/tmp/tmpj0d0eqdo/job_working_directory/000/18/outputs/dataset_557fc397-bb86-4091-8664-c162a015cddc.dat' -g    -r '^(.+)$' '$1_forward' '/tmp/tmpj0d0eqdo/files/5/f/5/dataset_5f555939-259c-419c-adc9-dbfd67a0f703.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"1be3b2dae15d11ee8e386d668327c804"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
find_and_replace
[{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_forward", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 8: New labels strand 2:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/12615d397df7/text_processing/find_and_replace' -o '/tmp/tmpj0d0eqdo/job_working_directory/000/19/outputs/dataset_51166afa-ef16-4fd3-bedc-0f8e2f3af978.dat' -g    -r '^(.+)$' '$1_reverse' '/tmp/tmpj0d0eqdo/files/5/f/5/dataset_5f555939-259c-419c-adc9-dbfd67a0f703.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"1be3b2dae15d11ee8e386d668327c804"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
find_and_replace
[{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_reverse", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 9: Relabelled strand 1:
            

              

            • step_state: new
              • 

            

            • 

          • 

            Step 10: Relabelled strand 2:
            

              

            • step_state: new
              • 

            

            • 

          

          • 

        

        • 

      • 

        Step 19: Compute FPKM with cufflinks:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 20: Extract gene counts:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpj0d0eqdo/job_working_directory/000/17/configs/tmpbo0pcdx3' '/tmp/tmpj0d0eqdo/files/a/8/6/dataset_a8624a1c-c056-468c-80d6-6cfd60d33813.dat' > '/tmp/tmpj0d0eqdo/job_working_directory/000/17/outputs/dataset_81960860-4917-4b4a-a5e8-2561841f4bd4.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"1be3b2d8e15d11ee8e386d668327c804"

              

              
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

              

              
code
"NR>4{print $1\"\\t\"$2}"

              

              
dbkey
"dm6"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 3: reverse_adapter:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 21: Compute FPKM with StringTie:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 4: reference_genome:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 5: gtf:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 6: strandedness:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 7: cufflinks_FPKM:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 8: gtf with regions to exclude from FPKM normalization with Cufflinks:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 9: stringtie_FPKM:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 10: Cutadapt (remove adapter + bad quality bases):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -f -s '/tmp/tmpj0d0eqdo/files/e/8/f/dataset_e8fbf42a-98e6-4062-abbb-5d93d97dc4eb.dat' 'GSM461177_1.fq' &&  ln -f -s '/tmp/tmpj0d0eqdo/files/4/7/d/dataset_47db29c8-a744-4174-9932-1ca8ba7b4eb0.dat' 'GSM461177_2.fq' &&    cutadapt  -j=${GALAXY_SLOTS:-4}       -a 'Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'             -A 'Dummy-Adapter (do not use me)'='TGTAGGCC'       --output='out1.fq' --paired-output='out2.fq'  --error-rate=0.1 --times=1 --overlap=3    --action=trim      --minimum-length=15 --pair-filter=any    --quality-cutoff=30      'GSM461177_1.fq' 'GSM461177_2.fq'  > report.txt
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

              

              
__workflow_invocation_uuid__
"1be3b2d8e15d11ee8e386d668327c804"

              

              
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/tmpj0d0eqdo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
filter_options
{"discard_cassava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": "15", "pair_filter": "any"}

              

              
library
{"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_name": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source": {"__current_case__": 1, "adapter": "TGTAGGCC", "adapter_source_list": "builtin"}, "single_noindels": false}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "maximum_length2": null, "minimum_length2": null, "quality_cutoff2": null}, "type": "paired_collection"}

              

              
output_selector
["report"]

              

              
read_mod_options
{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "30", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      

      • 

    • 

      Other invocation details

        

      • 

        error_message
        

          

        • Final state of invocation 78fa7c6adfe12b78 is [failed]
          • 

        

        • 

      • 

        history_id
        

          

        • ff93b2b7acc78c54
          • 

        

        • 

      • 

        history_state
        

          

        • ok
          • 

        

        • 

      • 

        invocation_id
        

          

        • ff93b2b7acc78c54
          • 

        

        • 

      • 

        invocation_state
        

          

        • failed
          • 

        

        • 

      • 

        messages
        

          

        • [{'details': None, 'reason': 'expression_evaluation_failed', 'workflow_step_id': 18}]
          • 

        

        • 

      • 

        workflow_id
        

          

        • 78fa7c6adfe12b78
          • 

        
  
      

      • 

    

    • 







      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
        





      

  
      



  

  @github-actions

    
      GitHub Actions
    




  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      



      

  


  

    

  





      


        


  
    

      
          
Test Results (powered by Planemo)


Test Summary



  

  

  

  

  

  








Test State
Count






Total
1




Passed
0




Error
0




Failure
1




Skipped
0






Failed Tests

    

  • 

    ❌ rnaseq-pe.ga_0
    

    Problems:
    

      

    • 

      Output with path /tmp/tmpd5dk4hbd/cutadapt__1c1fd3e4-0c1c-4206-be28-959ca091ffd9 different than expected
Expected text 'GSM461177_2	4.4	1057657	25033	25779	25250	1032407	78266618	3650637	73538382	6.041191149974054' in output ('Sample	cutadapt_version	pairs_processed	r1_with_adapters	r2_with_adapters	pairs_too_short	pairs_written	bp_processed	quality_trimmed	bp_written	percent_trimmed
GSM461177_2	4.6	1057657	25033	25779	25250	1032407	78266618	3650637	73538382	6.041191149974054
')

      

      • 

    

    Workflow invocation details
    

      

    • 

      Invocation Messages
      

      • 

    • 

      Steps

        

      • 

        Step 1: PE fastq input:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 2: forward_adapter:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 11: get reference_genome as text parameter:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
chromInfo
"/tmp/tmphtne8z30/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
components
[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "dm6", "select_param_type": "text"}}]

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 12: awk command from strand:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
chromInfo
"/tmp/tmphtne8z30/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "NR>4{print $1\"\\t\"$3}"}, {"__index__": 1, "from": "stranded - reverse", "to": "NR>4{print $1\"\\t\"$4}"}, {"__index__": 2, "from": "unstranded", "to": "NR>4{print $1\"\\t\"$2}"}], "type": "text"}

              

              
output_param_type
"text"

              

              
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 13: Get cufflinks strandess parameter:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
chromInfo
"/tmp/tmphtne8z30/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "fr-secondstrand"}, {"__index__": 1, "from": "stranded - reverse", "to": "fr-firststrand"}, {"__index__": 2, "from": "unstranded", "to": "fr-unstranded"}], "type": "text"}

              

              
output_param_type
"text"

              

              
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 14: Get Stringtie strandedness parameter:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
chromInfo
"/tmp/tmphtne8z30/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "--fr"}, {"__index__": 1, "from": "stranded - reverse", "to": "--rf"}, {"__index__": 2, "from": "unstranded", "to": ""}], "type": "text"}

              

              
output_param_type
"text"

              

              
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 15: STAR: map and count and coverage splitted:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              STAR  --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir '/cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files' --sjdbOverhang 100 --sjdbGTFfile '/tmp/tmphtne8z30/files/f/0/6/dataset_f066bd02-6e70-4d99-bd03-ea172d9e0d33.dat' --sjdbGTFfeatureExon 'exon'   --readFilesIn '/tmp/tmphtne8z30/files/5/f/3/dataset_5f3059dc-8ba2-4988-af7c-b2887b4a2bff.dat' '/tmp/tmphtne8z30/files/4/2/0/dataset_420e1137-0a7a-4b69-b785-2b65e7087393.dat'   --outSAMtype BAM SortedByCoordinate  --twopassMode None ''  --quantMode GeneCounts   --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM  --outSAMprimaryFlag OneBestScore  --outSAMmapqUnique 255     --outSAMunmapped None  --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1   --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10  --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01   --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000   --outBAMsortingThreadN ${GALAXY_SLOTS:-4} --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM $((${GALAXY_MEMORY_MB:-0}*1000000))    --outWigType 'bedGraph' '' --outWigStrand 'Stranded' --outWigReferencesPrefix '-' --outWigNorm 'RPM'  && samtools view -b -o '/tmp/tmphtne8z30/job_working_directory/000/9/outputs/dataset_39790d75-397a-475a-a31e-671a92614bda.dat' Aligned.sortedByCoord.out.bam  && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              	/usr/local/bin/STAR-avx2 --runThreadN 1 --genomeLoad NoSharedMemory --genomeDir /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files --sjdbOverhang 100 --sjdbGTFfile /tmp/tmphtne8z30/files/f/0/6/dataset_f066bd02-6e70-4d99-bd03-ea172d9e0d33.dat --sjdbGTFfeatureExon exon --readFilesIn /tmp/tmphtne8z30/files/5/f/3/dataset_5f3059dc-8ba2-4988-af7c-b2887b4a2bff.dat /tmp/tmphtne8z30/files/4/2/0/dataset_420e1137-0a7a-4b69-b785-2b65e7087393.dat --outSAMtype BAM SortedByCoordinate --twopassMode None  --quantMode GeneCounts --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 255 --outSAMunmapped None --outFilterType BySJout --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1 --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 1.0 --seedSearchLmax 0 --seedMultimapNmax 10000 --seedPerReadNmax 1000 --seedPerWindowNmax 50 --seedNoneLociPerWindow 10 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 0 -1 0 0 --alignSJDBoverhangMin 1 --alignSplicedMateMapLmin 0 --alignSplicedMateMapLminOverLmate 0.66 --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100 --alignTranscriptsPerReadNmax 10000 --alignEndsType Local --peOverlapNbasesMin 0 --peOverlapMMp 0.01 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000 --outBAMsortingThreadN 1 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 0 --outWigType bedGraph  --outWigStrand Stranded --outWigReferencesPrefix - --outWigNorm RPM
	STAR version: 2.7.11a   compiled: 2023-09-15T02:58:53+0000 :/opt/conda/conda-bld/star_1694746407721/work/source
Mar 14 11:39:13 ..... started STAR run
Mar 14 11:39:14 ..... loading genome
Mar 14 11:45:06 ..... processing annotations GTF
Mar 14 11:45:08 ..... inserting junctions into the genome indices
Mar 14 11:46:24 ..... started mapping
Mar 14 11:48:11 ..... finished mapping
Mar 14 11:48:11 ..... started sorting BAM
Mar 14 11:48:14 ..... started wiggle output
Mar 14 11:48:19 ..... finished successfully

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
algo
{"params": {"__current_case__": 3, "align": {"alignEndsType": "Local", "alignIntronMax": "1000000", "alignIntronMin": "20", "alignMatesGapMax": "1000000", "alignSJDBoverhangMin": "1", "alignSJoverhangMin": "8", "alignSJstitchMismatchNmax": {"alignSJstitchMismatchNmax1": "0", "alignSJstitchMismatchNmax2": "-1", "alignSJstitchMismatchNmax3": "0", "alignSJstitchMismatchNmax4": "0"}, "alignSplicedMateMapLmin": "0", "alignSplicedMateMapLminOverLmate": "0.66", "alignTranscriptsPerReadNmax": "10000", "alignTranscriptsPerWindowNmax": "100", "alignWindowsPerReadNmax": "10000", "peOverlapMMp": "0.01", "peOverlapNbasesMin": "0"}, "chim_settings": {"chimFilter": true, "chimJunctionOverhangMin": "20", "chimMainSegmentMultNmax": "10", "chimMultimapNmax": "1", "chimMultimapScoreRange": "1", "chimScoreDropMax": "20", "chimScoreJunctionNonGTAG": "-1", "chimScoreMin": "0", "chimScoreSeparation": "10", "chimSegmentMin": "12", "chimSegmentReadGapMax": "0"}, "junction_limits": {"limitOutSJcollapsed": "1000000", "limitOutSJoneRead": "1000", "limitSjdbInsertNsj": "1000000"}, "seed": {"seedMultimapNmax": "10000", "seedNoneLociPerWindow": "10", "seedPerReadNmax": "1000", "seedPerWindowNmax": "50", "seedSearchLmax": "0", "seedSearchStartLmax": "50", "seedSearchStartLmaxOverLread": "1.0"}, "settingsType": "full"}}

              

              
chimOutType
""

              

              
chromInfo
"/tmp/tmphtne8z30/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
filter
{"basic_filters": ["exclude_unmapped"], "output_params2": {"__current_case__": 0, "outFilterMatchNmin": "0", "outFilterMatchNminOverLread": "0.66", "outFilterMismatchNmax": "999", "outFilterMismatchNoverLmax": "0.3", "outFilterMismatchNoverReadLmax": "0.04", "outFilterMultimapNmax": "20", "outFilterMultimapScoreRange": "1", "outFilterScoreMin": "0", "outFilterScoreMinOverLread": "0.66", "outFilterType": true, "outSAMmultNmax": "-1", "outSAMtlen": "1", "output_select2": "yes"}}

              

              
oformat
{"HI_offset": "1", "outSAMattributes": ["NH", "HI", "AS", "nM"], "outSAMmapqUnique": "255", "outSAMprimaryFlag": "OneBestScore"}

              

              
outWig
{"__current_case__": 1, "outWigNorm": true, "outWigReferencesPrefix": "-", "outWigStrand": true, "outWigType": "bedGraph", "outWigTypeSecondWord": ""}

              

              
perf
{"outBAMsortingBinsN": "50", "winAnchorMultimapNmax": "50"}

              

              
refGenomeSource
{"GTFconditional": {"GTFselect": "without-gtf-with-gtf", "__current_case__": 1, "genomeDir": "dm6", "quantmode_output": {"__current_case__": 1, "quantMode": "GeneCounts"}, "sjdbGTFfeatureExon": "exon", "sjdbGTFfile": {"values": [{"id": 1, "src": "hda"}]}, "sjdbOverhang": "100"}, "__current_case__": 0, "geneSource": "indexed"}

              

              
singlePaired
{"__current_case__": 2, "input": {"values": [{"id": 4, "src": "dce"}]}, "sPaired": "paired_collection"}

              

              
twopass
{"__current_case__": 0, "sj_precalculated": "", "twopassMode": "None", "twopass_read_subset": ""}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 16: MultiQC:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/cutadapt_0 &&    ln -s '/tmp/tmphtne8z30/files/0/0/e/dataset_00e59aa5-2f3b-4b55-8897-4b73bf91b9a1.dat' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/GSM461177.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/GSM461177.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && mkdir multiqc_WDir/star_1 &&    mkdir 'multiqc_WDir/star_1/log_0' &&     ln -s '/tmp/tmphtne8z30/files/6/1/6/dataset_6168ca82-00d1-4206-83ff-2288df8fde16.dat' 'multiqc_WDir/star_1/log_0/GSM461177_Log.final.out' &&   mkdir 'multiqc_WDir/star_1/genecounts_1' &&     ln -s '/tmp/tmphtne8z30/files/3/0/3/dataset_303bd9fc-ac6f-4e2d-b62b-aeabda7961ce.dat' 'multiqc_WDir/star_1/genecounts_1/GSM461177_ReadsPerGene.out.tab' &&   multiqc multiqc_WDir --filename 'report'    --export
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

                /// MultiQC 🔍 | v1.11

|           multiqc | MultiQC Version v1.21 now available!
|           multiqc | Search path : /tmp/tmphtne8z30/job_working_directory/000/10/working/multiqc_WDir
|              star | Found 1 reports and 1 gene count files
|          cutadapt | Found 1 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : report.html
|           multiqc | Data        : report_data
|           multiqc | Plots       : report_plots
|           multiqc | MultiQC complete

              

              • 

            

            Standard Output:
            

              

            • 

              |         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4  
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

              

              
comment
""

              

              
dbkey
"dm6"

              

              
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__": 28, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 4, "src": "hdca"}]}, "type": "log"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "genecounts"}}], "software": "star"}}]

              

              
saveLog
false

              

              
title
""

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 17: Unlabelled step:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Subworkflow Steps

            

          • 

            Step 1: STAR BAM:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 2: STAR log:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 3: keep uniquely mapped reads:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  cp '/tmp/tmphtne8z30/job_working_directory/000/11/configs/tmplw105ry2' '/tmp/tmphtne8z30/job_working_directory/000/11/outputs/dataset_4e4c8467-ea4a-4e9c-8317-386a4eaba9f6.dat' && ln -s '/tmp/tmphtne8z30/files/3/9/7/dataset_39790d75-397a-475a-a31e-671a92614bda.dat' localbam.bam && ln -s '/tmp/tmphtne8z30/files/_metadata_files/2/d/3/metadata_2d33c247-3b4a-4a51-9052-1c553e94658a.dat' localbam.bam.bai && cat '/tmp/tmphtne8z30/job_working_directory/000/11/configs/tmplw105ry2' && bamtools filter -script '/tmp/tmphtne8z30/job_working_directory/000/11/configs/tmplw105ry2' -in localbam.bam -out '/tmp/tmphtne8z30/job_working_directory/000/11/outputs/dataset_9b3ffb27-0780-4c94-99d2-c13387a342ad.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Standard Output:
                

                  

                • 

                          
{
    "filters": [
        {
            "id": "1",
            "tag": "NH=1"
        }
    ]
}

        
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"bam"

                  

                  
__workflow_invocation_uuid__
"602a73c5e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
conditions
[{"__index__": 0, "filters": [{"__index__": 0, "bam_property": {"__current_case__": 21, "bam_property_selector": "tag", "bam_property_value": "NH=1"}}]}]

                  

                  
dbkey
"dm6"

                  

                  
rule_configuration
{"__current_case__": 0, "rules_selector": false}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 4: get scaling factor:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmphtne8z30/job_working_directory/000/12/configs/tmpb9gpxd3g' '/tmp/tmphtne8z30/files/6/1/6/dataset_6168ca82-00d1-4206-83ff-2288df8fde16.dat' > '/tmp/tmphtne8z30/job_working_directory/000/12/outputs/dataset_2b004d78-2c01-40d1-9727-790c3afbb6bc.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"602a73c5e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
code
"$0~\"Uniquely mapped reads number\"{print 1000000/$NF}"

                  

                  
dbkey
"dm6"

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 5: param_value_from_file:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  cd ../; python _evaluate_expression_.py
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"txt"

                  

                  
__workflow_invocation_uuid__
"602a73c5e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
param_type
"float"

                  

                  
remove_newlines
true

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 6: Scaled Coverage both strands combined:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  bedtools genomecov  -ibam '/tmp/tmphtne8z30/files/9/b/3/dataset_9b3ffb27-0780-4c94-99d2-c13387a342ad.dat'   -split   -bg  -scale 1.16985     > '/tmp/tmphtne8z30/job_working_directory/000/27/outputs/dataset_f185ede0-72df-4c20-8e29-bc2b9bb7f961.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"602a73c5e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
d
false

                  

                  
dbkey
"dm6"

                  

                  
dz
false

                  

                  
five
false

                  

                  
input_type
{"__current_case__": 1, "input": {"values": [{"id": 17, "src": "dce"}]}, "input_type_select": "bam"}

                  

                  
report
{"__current_case__": 0, "report_select": "bg", "scale": "1.16985", "zero_regions": false}

                  

                  
split
true

                  

                  
strand
""

                  

                  
three
false

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 7: convert both strands coverage to bigwig:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  grep -v "^track" '/tmp/tmphtne8z30/files/f/1/8/dataset_f185ede0-72df-4c20-8e29-bc2b9bb7f961.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len' '/tmp/tmphtne8z30/job_working_directory/000/28/outputs/dataset_c8887398-7b03-4f60-b80b-d582392aa6ba.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"bedgraph"

                  

                  
__workflow_invocation_uuid__
"602a73c5e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
settings
{"__current_case__": 0, "settingsType": "preset"}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          

          • 

        

        • 

      • 

        Step 18: Unlabelled step:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Subworkflow Steps

            

          • 

            Step 1: strandedness:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 2: Bedgraph strand 1:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 11: __MERGE_COLLECTION__:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
advanced
{"conflict": {"__current_case__": 3, "duplicate_options": "keep_first"}}

                  

                  
inputs
[{"__index__": 0, "input": {"values": [{"id": 26, "src": "hdca"}]}}, {"__index__": 1, "input": {"values": [{"id": 27, "src": "hdca"}]}}]

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 12: convert to bigwig:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  grep -v "^track" '/tmp/tmphtne8z30/files/4/d/7/dataset_4d7c5d80-88d5-4836-8ed2-a395c00b520f.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len' '/tmp/tmphtne8z30/job_working_directory/000/25/outputs/dataset_c5ca0d0c-bf1d-40d2-9bcb-53db1f28d6c8.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"bedgraph"

                  

                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
settings
{"__current_case__": 0, "settingsType": "preset"}

                  
                  

                  

                  • 

                

                • 

              • 

                Job 2:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  grep -v "^track" '/tmp/tmphtne8z30/files/f/1/4/dataset_f141ab1a-2301-4850-9e59-337979a77d35.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len' '/tmp/tmphtne8z30/job_working_directory/000/26/outputs/dataset_ddea283a-1b24-4576-9ad6-1b0ef4024e35.dat' -clip 2>&1 || echo "Error running wigToBigWig." >&2
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"bedgraph"

                  

                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
settings
{"__current_case__": 0, "settingsType": "preset"}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 3: Bedgraph strand 2:
            

              

            • step_state: scheduled
              • 

            

            • 

          • 

            Step 4: Get replacement for strand1:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  cd ../; python _evaluate_expression_.py
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/tmp/tmphtne8z30/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

                  

                  
dbkey
"?"

                  

                  
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_forward"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_reverse"}, {"__index__": 2, "from": "unstranded", "to": "$1_forward"}], "type": "text"}

                  

                  
output_param_type
"text"

                  

                  
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 5: Get replacement for strand2:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  cd ../; python _evaluate_expression_.py
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/tmp/tmphtne8z30/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

                  

                  
dbkey
"?"

                  

                  
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "$1_reverse"}, {"__index__": 1, "from": "stranded - reverse", "to": "$1_forward"}, {"__index__": 2, "from": "unstranded", "to": "$1_reverse"}], "type": "text"}

                  

                  
output_param_type
"text"

                  

                  
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 6: get identifiers:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  mv '/tmp/tmphtne8z30/job_working_directory/000/16/configs/tmp08wgn_n2' '/tmp/tmphtne8z30/job_working_directory/000/16/outputs/dataset_5858fc65-03c8-451e-a365-02c8ac94c497.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"bedgraph"

                  

                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
input_collection
{"values": [{"id": 8, "src": "hdca"}]}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 7: New labels strand 1:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/12615d397df7/text_processing/find_and_replace' -o '/tmp/tmphtne8z30/job_working_directory/000/18/outputs/dataset_847a4e58-c9ed-4477-ae16-51d1e359bc9c.dat' -g    -r '^(.+)$' '$1_forward' '/tmp/tmphtne8z30/files/5/8/5/dataset_5858fc65-03c8-451e-a365-02c8ac94c497.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
find_and_replace
[{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_forward", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 8: New labels strand 2:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Command Line:
                

                  

                • 

                  perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/12615d397df7/text_processing/find_and_replace' -o '/tmp/tmphtne8z30/job_working_directory/000/19/outputs/dataset_7c3c3f87-9d18-40b5-984e-cf2fffc587d9.dat' -g    -r '^(.+)$' '$1_reverse' '/tmp/tmphtne8z30/files/5/8/5/dataset_5858fc65-03c8-451e-a365-02c8ac94c497.dat'
                  

                  • 

                

                Exit Code:
                

                  

                • 

                  0
                  

                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__input_ext
"input"

                  

                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

                  

                  
dbkey
"dm6"

                  

                  
find_and_replace
[{"__index__": 0, "caseinsensitive": false, "find_pattern": "^(.+)$", "global": true, "is_regex": true, "replace_pattern": "$1_reverse", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 9: Relabelled strand 1:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
how
{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 28, "src": "hda"}]}, "strict": false}

                  

                  
input
{"values": [{"id": 8, "src": "hdca"}]}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          • 

            Step 10: Relabelled strand 2:
            

              

            • 

              step_state: scheduled
              

              • 

            • 

              Jobs

                

              • 

                Job 1:
                

                  

                • Job state is ok
                  • 

                

                Traceback:
                

                  

                • 

                  

                  • 

                

                Job Parameters:
                

                  

                • 

                  


                  
Job parameter
Parameter value

                  
                  


                  
__workflow_invocation_uuid__
"602a73c6e1f711ee98ffa3fba4dff42a"

                  

                  
how
{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 29, "src": "hda"}]}, "strict": false}

                  

                  
input
{"values": [{"id": 10, "src": "hdca"}]}

                  
                  

                  

                  • 

                

                • 

              

              

              • 

            

            • 

          

          • 

        

        • 

      • 

        Step 19: Compute FPKM with cufflinks:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is skipped
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"bam"

              

              
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
advanced_settings
{"__current_case__": 1, "inner_dist_std_dev": "80", "inner_mean_dist": "200", "junc_alpha": "0.001", "library_type": "fr-unstranded", "mask_file": null, "max_bundle_frags": "1000000", "max_bundle_length": "10000000", "max_mle_iterations": "5000", "min_intron_length": "50", "overhang_tolerance": "8", "small_anchor_fraction": "0.09", "trim_three_avgcov_thresh": "10", "trim_three_dropoff_frac": "0.1", "use_advanced_settings": "Yes"}

              

              
bias_correction
{"__current_case__": 0, "do_bias_correction": "Yes", "seq_source": {"__current_case__": 0, "index": "dm6", "index_source": "cached"}}

              

              
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

              

              
dbkey
"dm6"

              

              
global_model
None

              

              
length_correction
"--no-effective-length-correction"

              

              
max_intron_len
"300000"

              

              
min_isoform_fraction
"0.1"

              

              
multiread_correct
true

              

              
pre_mrna_fraction
"0.15"

              

              
reference_annotation
{"__current_case__": 1, "compatible_hits_norm": "", "reference_annotation_file": {"values": [{"id": 1, "src": "hda"}]}, "use_ref": "Use reference annotation"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 20: Extract gene counts:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmphtne8z30/job_working_directory/000/17/configs/tmpdo375swg' '/tmp/tmphtne8z30/files/3/0/3/dataset_303bd9fc-ac6f-4e2d-b62b-aeabda7961ce.dat' > '/tmp/tmphtne8z30/job_working_directory/000/17/outputs/dataset_b7bfeef6-c25d-4478-813c-d6c1ad01d808.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

              

              
code
"NR>4{print $1\"\\t\"$2}"

              

              
dbkey
"dm6"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 3: reverse_adapter:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 21: Compute FPKM with StringTie:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              mkdir -p ./special_de_output/sample1/ &&   ln -s '/tmp/tmphtne8z30/files/f/0/6/dataset_f066bd02-6e70-4d99-bd03-ea172d9e0d33.dat' guide.gff &&  stringtie '/tmp/tmphtne8z30/files/3/9/7/dataset_39790d75-397a-475a-a31e-671a92614bda.dat'  -o '/tmp/tmphtne8z30/job_working_directory/000/21/outputs/dataset_2d6598b7-7887-4353-9839-c21daae2f1f2.dat' -p "${GALAXY_SLOTS:-1}"    -G guide.gff -e -b ./special_de_output/sample1/  -f '0.01' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0'   -A '/tmp/tmphtne8z30/job_working_directory/000/21/outputs/dataset_299cddfd-379b-4535-afe4-7a74186d541f.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
adv
{"abundance_estimation": true, "bdist": "50", "bundle_fraction": "1.0", "disable_trimming": false, "fraction": "0.01", "min_anchor_cov": "1", "min_anchor_len": "10", "min_bundle_cov": "1", "min_tlen": "200", "multi_mapping": false, "name_prefix": null, "omit_sequences": "", "point_features": null}

              

              
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/dm6.len"

              

              
dbkey
"dm6"

              

              
guide
{"__current_case__": 1, "coverage_file": false, "guide_source": {"__current_case__": 1, "guide_gff_select": "history", "ref_hist": {"values": [{"id": 1, "src": "hda"}]}}, "input_estimation": true, "special_outputs": {"__current_case__": 2, "special_outputs_select": "no"}, "use_guide": "yes"}

              

              
input_options
{"__current_case__": 0, "input_bam": {"values": [{"id": 10, "src": "dce"}]}, "input_mode": "short_reads"}

              

              
rna_strandness
""

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 4: reference_genome:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 5: gtf:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 6: strandedness:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 7: cufflinks_FPKM:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 8: gtf with regions to exclude from FPKM normalization with Cufflinks:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 9: stringtie_FPKM:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 10: Cutadapt (remove adapter + bad quality bases):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -f -s '/tmp/tmphtne8z30/files/3/9/5/dataset_3950a4ac-321c-42ce-8657-e739ef0e3df7.dat' 'GSM461177_1.fq' &&  ln -f -s '/tmp/tmphtne8z30/files/b/d/4/dataset_bd4d258e-87c8-40ca-80fe-3a196df455f7.dat' 'GSM461177_2.fq' &&    cutadapt  -j=${GALAXY_SLOTS:-4}       -a 'Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'             -A 'Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'='GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'       --output='out1.fq' --paired-output='out2.fq'  --error-rate=0.1 --times=1 --overlap=3    --action=trim      --minimum-length=15 --pair-filter=any    --quality-cutoff=30      'GSM461177_1.fq' 'GSM461177_2.fq'  > report.txt
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"602a73c4e1f711ee98ffa3fba4dff42a"

              

              
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/tmphtne8z30/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
filter_options
{"discard_cassava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": "15", "pair_filter": "any"}

              

              
library
{"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_name": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", "adapter_name": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", "adapter_source_list": "user"}, "single_noindels": false}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "maximum_length2": null, "minimum_length2": null, "quality_cutoff2": null}, "type": "paired_collection"}

              

              
output_selector
["report"]

              

              
read_mod_options
{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "30", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      

      • 

    • 

      Other invocation details

        

      • 

        history_id
        

          

        • 78300b55ee9c3c83
          • 

        

        • 

      • 

        history_state
        

          

        • ok
          • 

        

        • 

      • 

        invocation_id
        

          

        • 78300b55ee9c3c83
          • 

        

        • 

      • 

        invocation_state
        

          

        • scheduled
          • 

        

        • 

      • 

        workflow_id
        

          

        • f3f282c05de6a708
          • 

        
  
      

      • 

    

    • 







      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
        





      

  
        





      

  
          

  

    
  

  


        
        @lldelisle
  lldelisle



        merged commit 3169543
      into

      
  
    galaxyproject:main
  


    Mar 14, 2024

      

        6 checks passed
      


      

        
          
  
    
    

        
      

  







  

  
  

  
      @gxydevbot
  gxydevbot


    
    deleted the
    
      
        workflows/transcriptomics/rnaseq-pe
    
    branch

    March 18, 2024 04:32    
    













  
  

    

      

  




    


    

      

              

  
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      4 participants
    

    

        
          @gxydevbot 
        
          @mvdbeek 
        
          @bgruening 
        
          @lldelisle