Updating workflows/transcriptomics/rnaseq-sr from 1.3 to 1.4 by gxydevbot · Pull Request #1174 · galaxyproject/iwc

gxydevbot · 2026-03-23T07:49:04Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/iuc/fastp/fastp/1.1.0+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.2.0+galaxy0

The workflow release number has been updated from 1.3 to 1.4.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

gxydevbot · 2026-03-30T08:12:17Z

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

gxydevbot · 2026-04-06T08:42:29Z

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

lldelisle · 2026-04-10T14:13:29Z

See #1205

gxydevbot · 2026-04-20T09:08:10Z

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

github-actions · 2026-04-20T09:35:29Z

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ rnaseq-sr.ga_0

Problems:

Output with path /tmp/tmpgqiyxln9/MultiQC Stats table__f7c4eb3c-1b7f-4626-b8d3-acafec92ef67.tabular different than expected
Expected text matching expression 'SRR5085167	0.11[0-9]*	18.3[0-9]*	69.6[0-9]*	0.3[0-9]*	0.3[0-9]*	94.62	0.12[0-9]*	34.43	0.2[0-9]*	36.[0-9]*	46.0	75.0	75	27.27[0-9]*	0.39[0-9]*' in output ('Sample	featurecounts-Assigned	featurecounts-percent_assigned	picard_mark_duplicates-PERCENT_DUPLICATION	star-total_reads	star-mapped	star-mapped_percent	star-uniquely_mapped	star-uniquely_mapped_percent	star-multimapped	fastp-after_filtering_q30_rate	fastp-after_filtering_q30_bases	fastp-filtering_result_passed_filter_reads	fastp-after_filtering_gc_content	fastp-pct_surviving	fastp-pct_adapter	fastp-before_filtering_read1_mean_length	fastqc-percent_duplicates	fastqc-percent_gc	fastqc-avg_sequence_length	fastqc-median_sequence_length	fastqc-percent_fails	fastqc-total_sequences
SRR5085167	0.113508	18.386209532942203	69.63329999999999	0.365218	0.34556899999999996	94.62	0.12573399999999998	34.43	0.219835	90.3007	16.740603	0.365218	43.4478	91.59830155222878	70.41811610741453	75.0	36.3353936353624	46.0	75.0	75	27.27272727272727	0.398717
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Collection of FASTQ files:
- step_state: scheduled
Step 2: Forward adapter:
- step_state: scheduled
Step 3: Generate additional QC reports:
- step_state: scheduled
Step 4: Reference genome:
- step_state: scheduled
Step 5: GTF file of annotation:
- step_state: scheduled
Step 6: Strandedness:
- step_state: scheduled
Step 7: Use featureCounts for generating count tables:
- step_state: scheduled
Step 8: Compute Cufflinks FPKM:
- step_state: scheduled
Step 9: GTF with regions to exclude from FPKM normalization with Cufflinks:
- step_state: scheduled
Step 10: Compute StringTie FPKM:
- step_state: scheduled

Step 11: remove adapters + bad quality bases (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.2+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/fastp:1.3.2--h43da1c4_0

Command Line:

ln -sf '/tmp/tmp1c1xige0/files/c/7/e/dataset_c7ed4581-039c-4d0c-94ff-fab525a2a06f.dat' 'SRR5085167.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'SRR5085167.fastqsanger.gz'  -i 'SRR5085167.fastqsanger.gz'   -o first.fastqsanger.gz     --adapter_sequence 'AGATCGGAAGAG'                  -q 30      -l 15         --dont_eval_duplication                  && mv first.fastqsanger.gz '/tmp/tmp1c1xige0/job_working_directory/000/3/outputs/dataset_4ddf2ad2-ff97-46c7-92e7-6cb7dcfd4ef2.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 398717
total bases: 29903775
Q20 bases: 28246987(94.4596%)
Q30 bases: 25590220(85.5752%)
Q40 bases: 6242708(20.876%)

Read1 after filtering:
total reads: 365218
total bases: 18538728
Q20 bases: 17956039(96.8569%)
Q30 bases: 16740603(90.3007%)
Q40 bases: 4371625(23.581%)

Filtering result:
reads passed filter: 365218
reads failed due to low quality: 25105
reads failed due to too many N: 11
reads failed due to too short: 8202
reads failed due to adapter dimer: 181
reads with adapter trimmed: 280769
bases trimmed due to adapters: 9912013

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title SRR5085167.fastqsanger.gz -i SRR5085167.fastqsanger.gz -o first.fastqsanger.gz --adapter_sequence AGATCGGAAGAG -q 30 -l 15 --dont_eval_duplication 
fastp v1.3.2, time used: 2 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec063c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicated_reads	`{"handling_options": {"__current_case__": 0, "eval_dups": "--dont_eval_duplication"}}`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": "15"}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": "30", "unqualified_percent_limit": null}}`
output_options	`{"report_html": false, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_front_select": {"__current_case__": 1, "cut_front": ""}, "cut_right_select": {"__current_case__": 1, "cut_right": ""}, "cut_tail_select": {"__current_case__": 1, "cut_tail": ""}}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": null, "umi_prefix": null}}
single_paired	`{"__current_case__": 0, "adapter_trimming_options": {"adapter_sequence1": "AGATCGGAAGAG", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_tail1": null}, "in1": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "single"}`

Step 12: no additional QC (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

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__	`"3798ec063c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": true, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 0, "on_unmapped": "input"}`

Step 13: get reference_genome as text parameter (toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec063c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "sacCer3", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 14: Get featureCounts strandedness parameter (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

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__	`"3798ec063c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "stranded - forward", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "1"}, {"__index__": 1, "from": "stranded - reverse", "to": "2"}, {"__index__": 2, "from": "unstranded", "to": "0"}], "type": "text"}`
output_param_type	`"text"`
unmapped	`{"__current_case__": 1, "on_unmapped": "fail"}`

Step 15: Get cufflinks strandedness parameter (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

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__	`"3798ec063c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "stranded - forward", "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 16: Get Stringtie strandedness parameter (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

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__	`"3798ec063c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "stranded - forward", "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 17: STAR: map and count and coverage splitted (toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2f4d4e7150bfb28621e88e8148cc0d0a8d93258c:023cceb1722b5d7c6e872dc9c68e6f27a8d5f28e-0

Command Line:

STAR  --runThreadN ${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir '/cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/sacCer3/sacCer3/dataset_ee6db620-7c48-4da0-8451-017d274c97ca_files' --sjdbOverhang 100 --sjdbGTFfile '/tmp/tmp1c1xige0/files/5/a/3/dataset_5a35a601-f721-469f-bb9e-2d2e5602c1d6.dat' --sjdbGTFfeatureExon 'exon'   --readFilesIn '/tmp/tmp1c1xige0/files/4/d/d/dataset_4ddf2ad2-ff97-46c7-92e7-6cb7dcfd4ef2.dat'   --readFilesCommand zcat   --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/tmp1c1xige0/job_working_directory/000/9/outputs/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.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/sacCer3/sacCer3/dataset_ee6db620-7c48-4da0-8451-017d274c97ca_files --sjdbOverhang 100 --sjdbGTFfile /tmp/tmp1c1xige0/files/5/a/3/dataset_5a35a601-f721-469f-bb9e-2d2e5602c1d6.dat --sjdbGTFfeatureExon exon --readFilesIn /tmp/tmp1c1xige0/files/4/d/d/dataset_4ddf2ad2-ff97-46c7-92e7-6cb7dcfd4ef2.dat --readFilesCommand zcat --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: 2.7.11b   compiled: 2024-11-25T09:14:51+0000 :/opt/conda/conda-bld/star_1732525954305/work/source
Apr 20 09:23:18 ..... started STAR run
Apr 20 09:23:18 ..... loading genome
Apr 20 09:23:45 ..... processing annotations GTF
Apr 20 09:23:45 ..... inserting junctions into the genome indices
Apr 20 09:23:52 ..... started mapping
Apr 20 09:24:08 ..... finished mapping
Apr 20 09:24:08 ..... started sorting BAM
Apr 20 09:24:08 ..... started wiggle output
Apr 20 09:24:09 ..... finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec063c9a11f1898a00224803db6f"`
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/tmp1c1xige0/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", "wasp_conditional": {"__current_case__": 1, "waspOutputMode": ""}}`
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": "sacCer3", "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__": 0, "input1": {"values": [{"id": 2, "src": "dce"}]}, "sPaired": "single"}`
twopass	`{"__current_case__": 0, "sj_precalculated": "", "twopassMode": "None", "twopass_read_subset": ""}`

Step 18: Generate Unstranded Coverage:

step_state: scheduled

Subworkflow Steps

Step 1: STAR log:
- step_state: scheduled
Step 2: STAR BAM:
- step_state: scheduled

Step 3: get scaling factor (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/gawk:5.3.1
```

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp1c1xige0/job_working_directory/000/10/configs/tmpkkf4qvvv' '/tmp/tmp1c1xige0/files/c/5/e/dataset_c5e0def9-f352-47fe-be7b-87a8d17cc15b.dat' > '/tmp/tmp1c1xige0/job_working_directory/000/10/outputs/dataset_7900a757-58cf-4c15-9523-118ec4b4dcfd.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec073c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
code	`"$0~\"Uniquely mapped reads number\"{print 1000000/$NF}"`
dbkey	`"sacCer3"`
variables	`[]`

Step 4: keep uniquely mapped reads (toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:a5d29a3763e96bdce12142816d06b607a8d00eeb-0

Command Line:

cp '/tmp/tmp1c1xige0/job_working_directory/000/11/configs/tmpeywh46i3' '/tmp/tmp1c1xige0/job_working_directory/000/11/outputs/dataset_54b99191-26ff-4f47-b88b-12cc418c5afa.dat' && ln -s '/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat' localbam.bam && ln -s '/tmp/tmp1c1xige0/files/_metadata_files/4/8/3/metadata_483d3f36-2ab2-4b05-a2f8-9d36daea6281.dat' localbam.bam.bai && cat '/tmp/tmp1c1xige0/job_working_directory/000/11/configs/tmpeywh46i3' && bamtools filter -script '/tmp/tmp1c1xige0/job_working_directory/000/11/configs/tmpeywh46i3' -in localbam.bam -out '/tmp/tmp1c1xige0/job_working_directory/000/11/outputs/dataset_d6df06fb-ab6e-4b76-b949-fdfe511cf52c.dat'

Exit Code:

```
0
```

Standard Output:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec073c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
conditions	`[{"__index__": 0, "filters": [{"__index__": 0, "bam_property": {"__current_case__": 21, "bam_property_selector": "tag", "bam_property_value": "NH=1"}}]}]`
dbkey	`"sacCer3"`
rule_configuration	`{"__current_case__": 0, "rules_selector": "false"}`

Step 5: Unlabelled step (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	`"input"`
__workflow_invocation_uuid__	`"3798ec073c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
param_type	`"float"`
remove_newlines	`true`

Step 6: Scaled Coverage both strands combined (toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/bedtools:2.31.1--h13024bc_3

Command Line:

bedtools genomecov  -ibam '/tmp/tmp1c1xige0/files/d/6/d/dataset_d6df06fb-ab6e-4b76-b949-fdfe511cf52c.dat'   -split   -bg  -scale 7.9533     > '/tmp/tmp1c1xige0/job_working_directory/000/32/outputs/dataset_e7f3e7d7-2ab5-4b14-abd5-c4f8d411d3e9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec073c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
d	`false`
dbkey	`"sacCer3"`
dz	`false`
five	`false`
input_type	`{"__current_case__": 1, "input": {"values": [{"id": 14, "src": "dce"}]}, "input_type_select": "bam"}`
report	`{"__current_case__": 0, "report_select": "bg", "scale": "7.9533", "zero_regions": false}`
split	`true`
strand	`""`
three	`false`

Step 7: convert both strands coverage to bigwig (wig_to_bigWig):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/ucsc-wigtobigwig:357--h446ed27_4

Command Line:

grep -v "^track" '/tmp/tmp1c1xige0/files/e/7/f/dataset_e7f3e7d7-2ab5-4b14-abd5-c4f8d411d3e9.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmp1c1xige0/job_working_directory/000/33/outputs/dataset_35d0154c-16ce-454d-92b0-f8ba1ed3fa63.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__	`"3798ec073c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Step 19: Generate Stranded Coverage:

step_state: scheduled

Subworkflow Steps

Step 1: strandedness:
- step_state: scheduled
Step 2: Bedgraph strand 1:
- step_state: scheduled
Step 3: Bedgraph strand 2:
- step_state: scheduled

Step 4: Get replacement for strand2 (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

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__	`"3798ec083c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "stranded - forward", "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 5: Get replacement for strand1 (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

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__	`"3798ec083c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "stranded - forward", "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 6: get identifiers (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp1c1xige0/job_working_directory/000/15/configs/tmp6haw8jqc' '/tmp/tmp1c1xige0/job_working_directory/000/15/outputs/dataset_564873db-08fe-4bd8-9af8-0fc74c8f6f0f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec083c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
input_collection	`{"values": [{"id": 8, "src": "hdca"}]}`

Step 7: New labels strand 2 (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.32
```

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/ab83aa685821/text_processing/find_and_replace' -o '/tmp/tmp1c1xige0/job_working_directory/000/16/outputs/dataset_f8fea8fa-9812-4c24-b9b3-0ae24259ef3d.dat' -g    -r '^(.+)$' '$1_reverse' '/tmp/tmp1c1xige0/files/5/6/4/dataset_564873db-08fe-4bd8-9af8-0fc74c8f6f0f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec083c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
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 8: New labels strand 1 (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.32
```

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/ab83aa685821/text_processing/find_and_replace' -o '/tmp/tmp1c1xige0/job_working_directory/000/17/outputs/dataset_dc49d0ce-aa19-4196-a172-975764bfc572.dat' -g    -r '^(.+)$' '$1_forward' '/tmp/tmp1c1xige0/files/5/6/4/dataset_564873db-08fe-4bd8-9af8-0fc74c8f6f0f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec083c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
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 9: Relabelled strand 2 (__RELABEL_FROM_FILE__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"3798ec083c9a11f1898a00224803db6f"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 25, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 10, "src": "hdca"}]}`

Step 10: Relabelled strand 1 (__RELABEL_FROM_FILE__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"3798ec083c9a11f1898a00224803db6f"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 26, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 8, "src": "hdca"}]}`

Step 11: Unlabelled step (__MERGE_COLLECTION__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"3798ec083c9a11f1898a00224803db6f"`
advanced	`{"conflict": {"__current_case__": 3, "duplicate_options": "keep_first"}}`
inputs	`[{"__index__": 0, "input": {"values": [{"id": 29, "src": "hdca"}]}}, {"__index__": 1, "input": {"values": [{"id": 28, "src": "hdca"}]}}]`

Step 12: convert to bigwig (wig_to_bigWig):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/ucsc-wigtobigwig:357--h446ed27_4

Command Line:

grep -v "^track" '/tmp/tmp1c1xige0/files/1/2/5/dataset_12502985-9b59-4d8c-8509-6d76ede0156a.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmp1c1xige0/job_working_directory/000/30/outputs/dataset_e14572a6-7e9b-477e-9a11-faec49720791.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__	`"3798ec083c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/ucsc-wigtobigwig:357--h446ed27_4

Command Line:

grep -v "^track" '/tmp/tmp1c1xige0/files/c/3/9/dataset_c39e85e2-7bdc-4670-a4da-0b25920731a6.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmp1c1xige0/job_working_directory/000/31/outputs/dataset_3fdacba8-7427-49b5-9ce5-cfca00a752d4.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__	`"3798ec083c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Step 20: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-27fa4b32e71813fff6e1a10b01866abba2fc4c6d:850dc5c6e03b6a7ab9e5a07c7976f62825cdeabb-0

Command Line:

export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&  featureCounts  -a '/tmp/tmp1c1xige0/files/5/a/3/dataset_5a35a601-f721-469f-bb9e-2d2e5602c1d6.dat' -F "GTF"  -o "output" -T ${GALAXY_SLOTS:-2}  -s  1  -Q  0     -t 'exon' -g 'gene_id'            --minOverlap  1 --fracOverlap 0 --fracOverlapFeature 0     '/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat'  && grep -v "^#" "output" | sed -e 's|/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat|SRR5085167|g' > body.txt && cut -f 1,7 body.txt > '/tmp/tmp1c1xige0/job_working_directory/000/18/outputs/dataset_6030dfa4-7679-4be0-b3f9-aeeabcd1328f.dat'    && sed -e 's|/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat|SRR5085167|g' 'output.summary' > '/tmp/tmp1c1xige0/job_working_directory/000/18/outputs/dataset_46cdb5b4-d97e-4d62-bee9-df408334d742.dat'

Exit Code:

```
0
```

Standard Error:

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
	  v2.1.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat ||
||                                                                            ||
||             Output file : output                                           ||
||                 Summary : output.summary                                   ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : dataset_5a35a601-f721-469f-bb9e-2d2e5602c1d6 ... ||
||      Dir for temp files : ./                                               ||
||                                                                            ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file dataset_5a35a601-f721-469f-bb9e-2d2e5602c1d6.dat ...  ||
||    Features : 7507                                                         ||
||    Meta-features : 7127                                                    ||
||    Chromosomes/contigs : 17                                                ||
||                                                                            ||
|| Process BAM file dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat...       ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 617354                                               ||
||    Successfully assigned alignments : 113508 (18.4%)                       ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
|| Summary of counting results can be found in file "output.summary"          ||
||                                                                            ||
\\============================================================================//

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec063c9a11f1898a00224803db6f"`
anno	`{"__current_case__": 2, "anno_select": "history", "gff_feature_attribute": "gene_id", "gff_feature_type": "exon", "reference_gene_sets": {"values": [{"id": 1, "src": "hda"}]}, "summarization_level": false}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
extended_parameters	`{"R": false, "by_read_group": false, "exon_exon_junction_read_counting_enabled": {"__current_case__": 1, "count_exon_exon_junction_reads": ""}, "frac_overlap": "0", "frac_overlap_feature": "0", "largest_overlap": false, "long_reads": false, "min_overlap": "1", "multifeatures": {"__current_case__": 0, "multifeat": ""}, "read_extension_3p": "0", "read_extension_5p": "0", "read_reduction": ""}`
format	`"tabdel_short"`
include_feature_length_file	`false`
pe_parameters	`{"__current_case__": 0, "paired_end_status": "single_end"}`
read_filtering_parameters	`{"ignore_dup": false, "mapping_quality": "0", "primary": false, "splitonly": ""}`
strand_specificity	`"1"`

Step 21: Compute FPKM with StringTie (toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-704aee0c18e3278557ac3bedcbb7986e3913f703:b3c012f26a7d4eba804b5c3f70ec20f899f97bb8-0

Command Line:

mkdir -p ./special_de_output/sample1/ &&   ln -s '/tmp/tmp1c1xige0/files/5/a/3/dataset_5a35a601-f721-469f-bb9e-2d2e5602c1d6.dat' guide.gff &&  stringtie '/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat'  -o '/tmp/tmp1c1xige0/job_working_directory/000/19/outputs/dataset_9117fee1-0955-4c39-8972-65acab6e066e.dat' -p "${GALAXY_SLOTS:-1}"  --fr  -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/tmp1c1xige0/job_working_directory/000/19/outputs/dataset_33663845-aa12-4e93-ab23-5067ed8d5238.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec063c9a11f1898a00224803db6f"`
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/sacCer3.len"`
dbkey	`"sacCer3"`
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": 6, "src": "dce"}]}, "input_mode": "short_reads"}`
rna_strandness	`"--fr"`

Step 22: Compute FPKM with cufflinks (toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-bb748d88d8879d6348f6371e79c99ee26652c849:2f0cd190adf8562df84214d633f0a0cffc191866-2

Command Line:

cufflinks -q --no-update-check '/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat' --num-threads "${GALAXY_SLOTS:-4}" -I 300000 -F 0.1 -j 0.15 --no-effective-length-correction  -G '/tmp/tmp1c1xige0/files/5/a/3/dataset_5a35a601-f721-469f-bb9e-2d2e5602c1d6.dat'   -b '/cvmfs/data.galaxyproject.org/byhand/sacCer3/sam_index/sacCer3.fa'  -u  --library-type fr-secondstrand --frag-len-mean 200 --frag-len-std-dev 80 --max-mle-iterations 5000 --junc-alpha 0.001 --small-anchor-fraction 0.09 --overhang-tolerance 8 --max-bundle-length 10000000 --max-bundle-frags 1000000 --min-intron-length 50 --trim-3-avgcov-thresh 10 --trim-3-dropoff-frac 0.1 2> stderr  && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/6926716bbfb5/cufflinks/mass.py' stderr 'None' "transcripts.gtf"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec063c9a11f1898a00224803db6f"`
advanced_settings	`{"__current_case__": 1, "inner_dist_std_dev": "80", "inner_mean_dist": "200", "junc_alpha": "0.001", "library_type": "fr-secondstrand", "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": "sacCer3", "index_source": "cached"}}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
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 23: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: A dummy featureCounts summary file (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:9.5
```

Command Line:

times=1; yes -- 'Status	Featurecounts_was_not_used' 2>/dev/null | head -n $times >> '/tmp/tmp1c1xige0/job_working_directory/000/21/outputs/dataset_34f0314f-8b9d-4aac-abf2-4d5aba02af3f.dat'; times=1; yes -- 'Assigned	0' 2>/dev/null | head -n $times >> '/tmp/tmp1c1xige0/job_working_directory/000/21/outputs/dataset_34f0314f-8b9d-4aac-abf2-4d5aba02af3f.dat'; times=1; yes -- 'Unassigned_Unmapped	0' 2>/dev/null | head -n $times >> '/tmp/tmp1c1xige0/job_working_directory/000/21/outputs/dataset_34f0314f-8b9d-4aac-abf2-4d5aba02af3f.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec093c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "Status\tFeaturecounts_was_not_used", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "Assigned\t0", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 2, "line": "Unassigned_Unmapped\t0", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 2: featureCounts summaries collection:
- step_state: scheduled
Step 3: Strandness param:
- step_state: scheduled
Step 4: RNA STAR count tables:
- step_state: scheduled
Step 5: featureCounts count table:
- step_state: scheduled

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed --sandbox -r -f '/tmp/tmp1c1xige0/job_working_directory/000/22/configs/tmpwmdxm2h7' '/tmp/tmp1c1xige0/files/3/4/f/dataset_34f0314f-8b9d-4aac-abf2-4d5aba02af3f.dat' > '/tmp/tmp1c1xige0/job_working_directory/000/22/outputs/dataset_9fc33877-a312-45cb-a070-14216ee2c35d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec093c9a11f1898a00224803db6f"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/__tc__/\\t/g"`
dbkey	`"?"`

Step 7: awk command from strand for STAR counts (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

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__	`"3798ec093c9a11f1898a00224803db6f"`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "stranded - forward", "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 8: featureCounts summaries (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

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__	`"3798ec093c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 17, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 37, "src": "hda"}]}}]}}`

Step 9: Extract gene counts (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/gawk:5.3.1
```

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp1c1xige0/job_working_directory/000/25/configs/tmp9nwfmqoa' '/tmp/tmp1c1xige0/files/e/c/f/dataset_ecfd5bb7-a066-4c96-b583-34cad735d44b.dat' > '/tmp/tmp1c1xige0/job_working_directory/000/25/outputs/dataset_2fe6e9c9-4b64-4f5b-a142-63e407bb7471.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec093c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
code	`"NR>4{print $1\"\\t\"$3}"`
dbkey	`"sacCer3"`
variables	`[]`

Step 10: Counts table (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

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__	`"3798ec093c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 16, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 26, "src": "dce"}]}}]}}`

Step 24: Combined MultiQC without additional QC (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec063c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
comment	`""`
dbkey	`"sacCer3"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 8, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 29, "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"}}, {"__index__": 2, "software_cond": {"__current_case__": 10, "input": {"values": [{"id": 25, "src": "hdca"}]}, "software": "featureCounts"}}]
title	`""`

Step 25: Combined MultiQC Quality Report:

step_state: scheduled

Subworkflow Steps

Step 1: FASTQ collection:
- step_state: scheduled
Step 2: fastp Reports:
- step_state: scheduled
Step 3: STAR logs:
- step_state: scheduled
Step 4: STAR counts:
- step_state: scheduled
Step 5: featureCounts summaries:
- step_state: scheduled
Step 6: reference_annotation_gtf:
- step_state: scheduled
Step 7: STAR BAM:
- step_state: scheduled

Step 8: FastQC check read qualities (toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0

Command Line:

ln -s '/tmp/tmp1c1xige0/files/c/7/e/dataset_c7ed4581-039c-4d0c-94ff-fab525a2a06f.dat' 'SRR5085167.gz' && mkdir -p '/tmp/tmp1c1xige0/job_working_directory/000/35/outputs/dataset_f7d6f64c-0693-4c39-b349-ab407773ad5a_files' && fastqc --outdir '/tmp/tmp1c1xige0/job_working_directory/000/35/outputs/dataset_f7d6f64c-0693-4c39-b349-ab407773ad5a_files'   --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract  --kmers 7 -f 'fastq' 'SRR5085167.gz'  && cp '/tmp/tmp1c1xige0/job_working_directory/000/35/outputs/dataset_f7d6f64c-0693-4c39-b349-ab407773ad5a_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmp1c1xige0/job_working_directory/000/35/outputs/dataset_f7d6f64c-0693-4c39-b349-ab407773ad5a_files'/*\.html output.html

Exit Code:

```
0
```

Standard Output:

```
application/gzip
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec0a3c9a11f1898a00224803db6f"`
adapters	`None`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 9: convert gtf to bed12 (toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-6ab052c2a495e1ceaab8525e0897839fed1d9f74:dd7404a5c5f1a50099356d334fde1c5657327e50-2

Command Line:

gtfToGenePred '/tmp/tmp1c1xige0/files/5/a/3/dataset_5a35a601-f721-469f-bb9e-2d2e5602c1d6.dat' 'temp.genePred' && genePredToBed 'temp.genePred' '/tmp/tmp1c1xige0/job_working_directory/000/36/outputs/dataset_9448fec8-58cb-48a6-add4-3978620e5bb9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gtf"`
__workflow_invocation_uuid__	`"3798ec0a3c9a11f1898a00224803db6f"`
advanced_options	`{"__current_case__": 0, "advanced_options_selector": "default"}`
chromInfo	`"/tmp/tmp1c1xige0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 10: Subsample 200k reads (toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:8f53bfe77285b2fc8b6545efd875a0b3d1d12061-0

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat' infile && ln -s '/tmp/tmp1c1xige0/files/_metadata_files/4/8/3/metadata_483d3f36-2ab2-4b05-a2f8-9d36daea6281.dat' infile.bai &&               sample_fragment=`samtools view -c  -f 0 -F 0 -G 0 infile  | awk '{s=$1} END {fac=s/200000; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` &&  samtools view -@ $addthreads -b  -f 0 -F 0 -G 0 --subsample-seed 1 --subsample ${sample_fragment}   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec0a3c9a11f1898a00224803db6f"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": null, "library": "", "qname_file": null, "quality": null, "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 1, "seed": "1", "select_subsample": "target", "target": "200000"}}}

Step 11: Get reads number per chromosome (toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.8):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/samtools:1.22--h96c455f_0

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat' infile && ln -s '/tmp/tmp1c1xige0/files/_metadata_files/4/8/3/metadata_483d3f36-2ab2-4b05-a2f8-9d36daea6281.dat' infile.bai &&  samtools idxstats -@ $addthreads infile  > '/tmp/tmp1c1xige0/job_working_directory/000/38/outputs/dataset_7ce81f00-fce4-49be-955a-cfbe7c54abc7.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec0a3c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`

Step 12: Remove duplicates (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/picard:3.1.1--hdfd78af_0

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat' 'SRR5085167' &&  picard MarkDuplicates  --INPUT 'SRR5085167' --OUTPUT '/tmp/tmp1c1xige0/job_working_directory/000/39/outputs/dataset_aacbb356-37fd-4cb8-addc-a6e5165898c1.dat'  --METRICS_FILE '/tmp/tmp1c1xige0/job_working_directory/000/39/outputs/dataset_b783214d-1222-4055-861f-0b21738af880.dat'  --REMOVE_DUPLICATES 'false' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmp1c1xige0/job_working_directory/000/39/tmp
Apr 20, 2026 9:32:38 AM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec0a3c9a11f1898a00224803db6f"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
comments	`[]`
dbkey	`"sacCer3"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`false`
validation_stringency	`"LENIENT"`

Step 13: Read distribution over genomic features (toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/rseqc:5.0.3--py312hf67a6ed_3

Command Line:

ln -s -f '/tmp/tmp1c1xige0/files/9/0/e/dataset_90e42a17-e263-4aa6-91e3-787a409e6e2b.dat' 'input.bam' && ln -s -f '/tmp/tmp1c1xige0/files/_metadata_files/4/8/3/metadata_483d3f36-2ab2-4b05-a2f8-9d36daea6281.dat' 'input.bam.bai' &&  read_distribution.py -i 'input.bam' -r '/tmp/tmp1c1xige0/files/9/4/4/dataset_9448fec8-58cb-48a6-add4-3978620e5bb9.dat' > '/tmp/tmp1c1xige0/job_working_directory/000/40/outputs/dataset_44168540-42a5-41d4-bdcb-d6b899b1f66e.dat'

Exit Code:

```
0
```

Standard Error:

processing /tmp/tmp1c1xige0/files/9/4/4/dataset_9448fec8-58cb-48a6-add4-3978620e5bb9.dat ... Done
processing input.bam ... Finished

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec0a3c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`

Step 14: Get gene body coverage (toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/rseqc:5.0.3--py312hf67a6ed_3

Command Line:

ln -sf '/tmp/tmp1c1xige0/files/f/0/b/dataset_f0b5bdf2-b0fe-4274-bd71-c97585877bb2.dat' 'SRR5085167.bam' && ln -sf '/tmp/tmp1c1xige0/files/_metadata_files/b/5/8/metadata_b585abe2-4253-4301-94f4-92cfb4ab3cdc.dat' 'SRR5085167.bam.bai' && geneBody_coverage.py -i 'SRR5085167.bam' -r '/tmp/tmp1c1xige0/files/9/4/4/dataset_9448fec8-58cb-48a6-add4-3978620e5bb9.dat' --minimum_length 100 -o output

Exit Code:

```
0
```

Standard Error:

@ 2026-04-20 09:33:16: Read BED file (reference gene model) ...
@ 2026-04-20 09:33:17: Total 7127 transcripts loaded
@ 2026-04-20 09:33:17: Get BAM file(s) ...
	SRR5085167.bam
@ 2026-04-20 09:33:17: Processing SRR5085167.bam ...
	100 transcripts finished
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	Sample	Skewness
	SRR5085167	4.413411450952844
@ 2026-04-20 09:33:23: Running R script ...

Standard Output:

```
null device 
          1 
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec0a3c9a11f1898a00224803db6f"`
batch_mode	`{"__current_case__": 0, "batch_mode_selector": "batch", "input": {"values": [{"id": 38, "src": "dce"}]}}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
minimum_length	`"100"`
rscript_output	`false`

Step 15: Combined Quality Report (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/multiqc:1.33--pyhdfd78af_0

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&      mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' &&   ln -s '/tmp/tmp1c1xige0/files/e/b/8/dataset_eb8e83c0-3494-42c1-9565-5c7a7f9b1c5f.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt'  &&    mkdir multiqc_WDir/fastp_1 &&         grep -Pq '"before_filtering": {' /tmp/tmp1c1xige0/files/8/a/6/dataset_8a663d64-33ad-4e54-9d22-98264776fb51.dat || die "Module 'fastp: '"before_filtering": {' not found in the file 'SRR5085167'" && ln -s '/tmp/tmp1c1xige0/files/8/a/6/dataset_8a663d64-33ad-4e54-9d22-98264776fb51.dat' 'multiqc_WDir/fastp_1/SRR5085167.json'  &&    mkdir multiqc_WDir/star_2 &&    mkdir 'multiqc_WDir/star_2/log_0' &&      ln -s '/tmp/tmp1c1xige0/files/c/5/e/dataset_c5e0def9-f352-47fe-be7b-87a8d17cc15b.dat' 'multiqc_WDir/star_2/log_0/SRR5085167_Log.final.out'  &&     mkdir 'multiqc_WDir/star_2/genecounts_1' &&      ln -s '/tmp/tmp1c1xige0/files/e/c/f/dataset_ecfd5bb7-a066-4c96-b583-34cad735d44b.dat' 'multiqc_WDir/star_2/genecounts_1/SRR5085167_ReadsPerGene.out.tab'  &&    mkdir multiqc_WDir/featureCounts_3 &&     if grep -qw Status '/tmp/tmp1c1xige0/files/4/6/c/dataset_46cdb5b4-d97e-4d62-bee9-df408334d742.dat'; then ln -s '/tmp/tmp1c1xige0/files/4/6/c/dataset_46cdb5b4-d97e-4d62-bee9-df408334d742.dat' 'multiqc_WDir/featureCounts_3/SRR5085167.summary'; else echo -e 'Status\tSRR5085167' > 'multiqc_WDir/featureCounts_3/SRR5085167.summary'; cat '/tmp/tmp1c1xige0/files/4/6/c/dataset_46cdb5b4-d97e-4d62-bee9-df408334d742.dat' >> 'multiqc_WDir/featureCounts_3/SRR5085167.summary'; fi &&  mkdir multiqc_WDir/rseqc_4 &&    mkdir 'multiqc_WDir/rseqc_4/read_distribution_0' &&      grep -Pq 'Group               Total_bases         Tag_count           Tags/Kb' /tmp/tmp1c1xige0/files/4/4/1/dataset_44168540-42a5-41d4-bdcb-d6b899b1f66e.dat || die "Module 'rseqc: 'Group               Total_bases         Tag_count           Tags/Kb' not found in the file 'SRR5085167'" && ln -s '/tmp/tmp1c1xige0/files/4/4/1/dataset_44168540-42a5-41d4-bdcb-d6b899b1f66e.dat' 'multiqc_WDir/rseqc_4/read_distribution_0/SRR5085167'  &&     mkdir 'multiqc_WDir/rseqc_4/gene_body_coverage_1' &&      ln -s '/tmp/tmp1c1xige0/files/9/b/1/dataset_9b17bdd4-fbfe-4c71-b6cf-37c0b294f31d.dat' 'multiqc_WDir/rseqc_4/gene_body_coverage_1/SRR5085167.geneBodyCoverage.txt'  &&    mkdir multiqc_WDir/samtools_5 &&    mkdir 'multiqc_WDir/samtools_5/idxstats_0' &&      ln -s '/tmp/tmp1c1xige0/files/7/c/e/dataset_7ce81f00-fce4-49be-955a-cfbe7c54abc7.dat' 'multiqc_WDir/samtools_5/idxstats_0/SRR5085167_idxstat'  &&    mkdir multiqc_WDir/picard_6 &&      mkdir 'multiqc_WDir/picard_6/markdups_0' &&    grep -Pq 'MarkDuplicates' /tmp/tmp1c1xige0/files/b/7/8/dataset_b783214d-1222-4055-861f-0b21738af880.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR5085167'" && ln -s '/tmp/tmp1c1xige0/files/b/7/8/dataset_b783214d-1222-4055-861f-0b21738af880.dat' 'multiqc_WDir/picard_6/markdups_0/SRR5085167'  &&        multiqc multiqc_WDir --filename 'report'  --title 'Combined Quality Report '      && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.33

     update_config | Report title: Combined Quality Report 
       file_search | Search path: /tmp/tmp1c1xige0/job_working_directory/000/42/working/multiqc_WDir

             rseqc | Found 1 read_distribution reports
             rseqc | Found 1 gene_body_coverage reports
     featurecounts | Found 1 reports
            picard | Found 1 MarkDuplicates reports
          samtools | Found 1 idxstats reports
              star | Found 1 reports and 1 gene count files
             fastp | Found 1 reports
            fastqc | Found 1 reports

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

Standard Output:

total 3484
-rw-r--r-- 1 1001 1001    1434 Apr 20 09:34 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1435 Apr 20 09:34 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1194 Apr 20 09:34 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1292 Apr 20 09:34 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1267 Apr 20 09:34 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1263 Apr 20 09:34 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001     126 Apr 20 09:34 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 1001     317 Apr 20 09:34 fastqc-status-check-heatmap.txt
-rw-r--r-- 1 1001 1001    3444 Apr 20 09:34 fastqc_adapter_content_plot.txt
-rw-r--r-- 1 1001 1001     127 Apr 20 09:34 fastqc_overrepresented_sequences_plot.txt
-rw-r--r-- 1 1001 1001    1613 Apr 20 09:34 fastqc_per_base_n_content_plot.txt
-rw-r--r-- 1 1001 1001    2043 Apr 20 09:34 fastqc_per_base_sequence_quality_plot.txt
-rw-r--r-- 1 1001 1001    1680 Apr 20 09:34 fastqc_per_sequence_gc_content_plot_Counts.txt
-rw-r--r-- 1 1001 1001    2619 Apr 20 09:34 fastqc_per_sequence_gc_content_plot_Percentages.txt
-rw-r--r-- 1 1001 1001     686 Apr 20 09:34 fastqc_per_sequence_quality_scores_plot.txt
-rw-r--r-- 1 1001 1001      65 Apr 20 09:34 fastqc_sequence_counts_plot.txt
-rw-r--r-- 1 1001 1001     451 Apr 20 09:34 fastqc_sequence_duplication_levels_plot.txt
-rw-r--r-- 1 1001 1001    1503 Apr 20 09:34 fastqc_top_overrepresented_sequences_table.txt
-rw-r--r-- 1 1001 1001     131 Apr 20 09:34 featureCounts_assignment_plot.txt
-rw-r--r-- 1 1001 1001   44962 Apr 20 09:34 llms-full.txt
-rw-r--r-- 1 1001 1001   33921 Apr 20 09:34 multiqc.log
-rw-r--r-- 1 1001 1001 2313341 Apr 20 09:34 multiqc.parquet
-rw-r--r-- 1 1001 1001     367 Apr 20 09:34 multiqc_citations.txt
-rw-r--r-- 1 1001 1001  945330 Apr 20 09:34 multiqc_data.json
-rw-r--r-- 1 1001 1001   51235 Apr 20 09:34 multiqc_fastp.txt
-rw-r--r-- 1 1001 1001     638 Apr 20 09:34 multiqc_fastqc.txt
-rw-r--r-- 1 1001 1001     412 Apr 20 09:34 multiqc_featurecounts.txt
-rw-r--r-- 1 1001 1001     843 Apr 20 09:34 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001     303 Apr 20 09:34 multiqc_picard_dups.txt
-rw-r--r-- 1 1001 1001    1344 Apr 20 09:34 multiqc_rseqc_read_distribution.txt
-rw-r--r-- 1 1001 1001     410 Apr 20 09:34 multiqc_samtools_idxstats.txt
-rw-r--r-- 1 1001 1001      48 Apr 20 09:34 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001    1297 Apr 20 09:34 multiqc_sources.txt
-rw-r--r-- 1 1001 1001     692 Apr 20 09:34 multiqc_star.txt
-rw-r--r-- 1 1001 1001       0 Apr 20 09:34 picard_MarkIlluminaAdapters_histogram.txt
-rw-r--r-- 1 1001 1001       0 Apr 20 09:34 picard_MeanQualityByCycle_histogram.txt
-rw-r--r-- 1 1001 1001       0 Apr 20 09:34 picard_MeanQualityByCycle_histogram_1.txt
-rw-r--r-- 1 1001 1001       0 Apr 20 09:34 picard_QualityScoreDistribution_histogram.txt
-rw-r--r-- 1 1001 1001      71 Apr 20 09:34 picard_deduplication.txt
-rw-r--r-- 1 1001 1001    1057 Apr 20 09:34 rseqc_gene_body_cov.txt
-rw-r--r-- 1 1001 1001    1647 Apr 20 09:34 rseqc_gene_body_coverage_plot_Counts.txt
-rw-r--r-- 1 1001 1001    2717 Apr 20 09:34 rseqc_gene_body_coverage_plot_Percentages.txt
-rw-r--r-- 1 1001 1001     133 Apr 20 09:34 rseqc_read_distribution_plot.txt
-rw-r--r-- 1 1001 1001     575 Apr 20 09:34 samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt
-rw-r--r-- 1 1001 1001     556 Apr 20 09:34 samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt
-rw-r--r-- 1 1001 1001     337 Apr 20 09:34 samtools-idxstats-mapped-reads-plot_Raw_Counts.txt
-rw-r--r-- 1 1001 1001     157 Apr 20 09:34 star_alignment_plot.txt
-rw-r--r-- 1 1001 1001     125 Apr 20 09:34 star_gene_counts_Reverse_Stranded.txt
-rw-r--r-- 1 1001 1001     128 Apr 20 09:34 star_gene_counts_Same_Stranded.txt
-rw-r--r-- 1 1001 1001     129 Apr 20 09:34 star_gene_counts_Unstranded.txt
-rw-r--r-- 1 1001 1001     365 Apr 20 09:34 star_summary_table.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3798ec0a3c9a11f1898a00224803db6f"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
comment	`""`
dbkey	`"sacCer3"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 9, "output": [{"__index__": 0, "input": {"values": [{"id": 35, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}, {"__index__": 1, "software_cond": {"__current_case__": 8, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 2, "software_cond": {"__current_case__": 29, "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"}}, {"__index__": 3, "software_cond": {"__current_case__": 10, "input": {"values": [{"id": 25, "src": "hdca"}]}, "software": "featureCounts"}}, {"__index__": 4, "software_cond": {"__current_case__": 23, "output": [{"__index__": 0, "type": {"__current_case__": 6, "input": {"values": [{"id": 40, "src": "hdca"}]}, "type": "read_distribution"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 42, "src": "hdca"}]}, "type": "gene_body_coverage"}}], "software": "rseqc"}}, {"__index__": 5, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 2, "input": {"values": [{"id": 37, "src": "hdca"}]}, "type": "idxstats"}}], "software": "samtools"}}, {"__index__": 6, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 38, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
title	`"Combined Quality Report "`

Other invocation details
- history_id
  - 4f26a002111b3027
- history_state
  - skipped
- invocation_id
  - 4f26a002111b3027
- invocation_state
  - scheduled
- workflow_id
  - 867ae168a99e11b8

gxydevbot changed the title ~~Updating workflows/transcriptomics/rnaseq-sr from 1.3 to 1.4~~ Updating workflows/transcriptomics/rnaseq-sr from 1.3 to 1.4 Mar 30, 2026

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gxydevbot force-pushed the workflows/transcriptomics/rnaseq-sr branch from 12c156e to a863e46 Compare April 6, 2026 08:42

Updating workflows/transcriptomics/rnaseq-sr from 1.3 to 1.4

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gxydevbot force-pushed the workflows/transcriptomics/rnaseq-sr branch from a863e46 to ab5763d Compare April 20, 2026 09:08

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Updating workflows/transcriptomics/rnaseq-sr from 1.3 to 1.4 #1174

Updating workflows/transcriptomics/rnaseq-sr from 1.3 to 1.4 #1174
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