Update both rnaseq workflows by lldelisle · Pull Request #1205 · galaxyproject/iwc

lldelisle · 2026-04-07T20:16:51Z

FOR CONTRIBUTOR:

I have read the Adding workflows guidelines
License permits unrestricted use (educational + commercial)
Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

.dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
Changelog contains appropriate entries
Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

…aseq-sr' into update_both_RNAseq

…aseq-pe' into update_both_RNAseq

lldelisle · 2026-04-07T20:18:25Z

I have an issue when you don't do additional QCs multiQC is failing. I need to think if I need to do 2 multiQC or if I can improve the wrapper.

github-actions · 2026-04-08T08:41:30Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	0
Error	2
Failure	0
Skipped	0

Errored Tests

❌ rnaseq-pe.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy2 (version 1.33+galaxy2)","err_code":0}

❌ rnaseq-sr.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0 (version 5.0.3+galaxy0), toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0 (version 5.0.3+galaxy0), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 (version 0.2.0), toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy2 (version 1.33+galaxy2)","err_code":0}

lldelisle · 2026-04-08T08:44:56Z

The error is Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy2 (version 1.33+galaxy2)","err_code":0} but this tool is installed on usegalaxy.org...

wm75 · 2026-04-08T20:10:24Z

The full error was

.. ERROR: The ToolShed returned an error when searching for the most recent version of toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy2: GET: error 429: b'<html>\r\n<head><title>429 Too Many Requests</title></head>\r\n<body>\r\n<center><h1>429 Too Many Requests</h1></center>\r\n<hr><center>nginx/1.22.1</center>\r\n</body>\r\n</html>\r\n', 0 attempts left: <html>

I triggered a rerun of the CI and hopefully that's all that's needed.

wm75 · 2026-04-08T20:21:33Z

Well, it wasn't enough:

.. ERROR: The ToolShed returned an error when searching for the most recent version of toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3: GET: error 429: b'<html>\r\n<head><title>429 Too Many Requests</title></head>\r\n<body>\r\n<center><h1>429 Too Many Requests</h1></center>\r\n<hr><center>nginx/1.22.1</center>\r\n</body>\r\n</html>\r\n', 0 attempts left: <html>
<head><title>429 Too Many Requests</title></head>
<body>
<center><h1>429 Too Many Requests</h1></center>
<hr><center>nginx/1.22.1</center>
</body>
</html>

.. ERROR: The ToolShed returned an error when searching for the most recent version of toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3: GET: error 429: b'<html>\r\n<head><title>429 Too Many Requests</title></head>\r\n<body>\r\n<center><h1>429 Too Many Requests</h1></center>\r\n<hr><center>nginx/1.22.1</center>\r\n</body>\r\n</html>\r\n', 0 attempts left: <html>
<head><title>429 Too Many Requests</title></head>
<body>
<center><h1>429 Too Many Requests</h1></center>
<hr><center>nginx/1.22.1</center>
</body>
</html>

.. ERROR: The ToolShed returned an error when searching for the most recent version of toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy0: GET: error 429: b'<html>\r\n<head><title>429 Too Many Requests</title></head>\r\n<body>\r\n<center><h1>429 Too Many Requests</h1></center>\r\n<hr><center>nginx/1.22.1</center>\r\n</body>\r\n</html>\r\n', 0 attempts left: <html>
<head><title>429 Too Many Requests</title></head>
<body>
<center><h1>429 Too Many Requests</h1></center>
<hr><center>nginx/1.22.1</center>
</body>
</html>

.. ERROR: The ToolShed returned an error when searching for the most recent version of toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0: GET: error 429: b'<html>\r\n<head><title>429 Too Many Requests</title></head>\r\n<body>\r\n<center><h1>429 Too Many Requests</h1></center>\r\n<hr><center>nginx/1.22.1</center>\r\n</body>\r\n</html>\r\n', 0 attempts left: <html>
<head><title>429 Too Many Requests</title></head>
<body>
<center><h1>429 Too Many Requests</h1></center>
<hr><center>nginx/1.22.1</center>
</body>
</html>

don't know what's wrong here.

github-actions · 2026-04-08T20:39:00Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	1
Error	0
Failure	1
Skipped	0

Failed Tests

❌ rnaseq-pe.ga_0

Problems:

Output with path /tmp/tmpuyg1j17l/MultiQC on dataset 12, 25, and others and collection 9, 17, and others Stats__40c5d63a-496c-4248-a78f-4df431db4432.tabular different than expected
Expected text matching expression 'SRR5085167_forward	*27.27[0-9]*	46.0	75.0	75	36.33[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	fastp-before_filtering_read2_mean_length	fastqc-percent_duplicates	fastqc-percent_gc	fastqc-avg_sequence_length	fastqc-median_sequence_length	fastqc-percent_fails	fastqc-total_sequences
SRR5085167	0.10037599999999999	16.456322935827945	43.3806	0.32331099999999996	0.30311699999999997	93.75	0.110873	34.29	0.192244														
SRR5085167_forward																		27.096500000000006	46.0	75.0	75	36.36363636363637	0.398717
SRR5085167_reverse																		27.343199999999996	46.0	75.0	75	45.45454545454545	0.398717
fastp report for SRR5085167										91.8082	30.049028	0.6466219999999999	43.5788	81.08783924437634	72.63234324094533	75.0	75.0						
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Collection paired FASTQ files:
- step_state: scheduled
Step 2: Forward adapter:
- step_state: scheduled
Step 3: Reverse adapter:
- step_state: scheduled
Step 4: Generate additional QC reports:
- step_state: scheduled
Step 5: Reference genome:
- step_state: scheduled
Step 6: GTF file of annotation:
- step_state: scheduled
Step 7: Strandedness:
- step_state: scheduled
Step 8: Use featureCounts for generating count tables:
- step_state: scheduled
Step 9: Compute Cufflinks FPKM:
- step_state: scheduled
Step 10: GTF with regions to exclude from FPKM normalization with Cufflinks:
- step_state: scheduled
Step 11: Compute StringTie FPKM:
- step_state: scheduled
Step 12: Unlabelled step (__FLATTEN__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "7d8e545a338811f19acb6045bd022039"
      
      input {"values": [{"id": 1, "src": "hdca"}]}
      
      join_identifier "_"

Step 13: remove adapters + bad quality bases (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.2.0+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/fastp:1.2.0--h43da1c4_0

Command Line:

ln -sf '/tmp/tmpvuf2v_a9/files/f/0/d/dataset_f0d2cfe5-9c49-44ca-a614-195752c58754.dat' 'SRR5085167.fastqsanger.gz' && ln -sf '/tmp/tmpvuf2v_a9/files/7/4/c/dataset_74c6f62d-7527-421e-83a3-265bb1a4b9a1.dat' 'SRR5085167_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR5085167.fastqsanger.gz'  -i 'SRR5085167.fastqsanger.gz'   -I 'SRR5085167_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz     --adapter_sequence 'AGATCGGAAGAG'  --adapter_sequence_r2 'GATCGTCGGACT'                  -q 30      -l 15         --dont_eval_duplication                  && mv first.fastqsanger.gz '/tmp/tmpvuf2v_a9/job_working_directory/000/5/outputs/dataset_dfb4106d-23a6-46da-be5e-196e9a13ee4d.dat' && mv second.fastqsanger.gz '/tmp/tmpvuf2v_a9/job_working_directory/000/5/outputs/dataset_aa440969-9d4b-4fdb-9e90-42f2c5ce70fb.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%)

Read2 before filtering:
total reads: 398717
total bases: 29903775
Q20 bases: 26550112(88.7852%)
Q30 bases: 23530708(78.6881%)
Q40 bases: 5657118(18.9177%)

Read1 after filtering:
total reads: 323311
total bases: 16352713
Q20 bases: 15945937(97.5125%)
Q30 bases: 15035996(91.948%)
Q40 bases: 4201548(25.6933%)

Read2 after filtering:
total reads: 323311
total bases: 16377517
Q20 bases: 15991110(97.6406%)
Q30 bases: 15013032(91.6685%)
Q40 bases: 4198080(25.6332%)

Filtering result:
reads passed filter: 646622
reads failed due to low quality: 136440
reads failed due to too many N: 38
reads failed due to too short: 14074
reads failed due to adapter dimer: 260
reads with adapter trimmed: 579195
bases trimmed due to adapters: 19681642

Insert size peak (evaluated by paired-end reads): 31

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

fastp --thread 1 --report_title fastp report for SRR5085167.fastqsanger.gz -i SRR5085167.fastqsanger.gz -I SRR5085167_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz --adapter_sequence AGATCGGAAGAG --adapter_sequence_r2 GATCGTCGGACT -q 30 -l 15 --dont_eval_duplication 
fastp v1.2.0, time used: 5 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545a338811f19acb6045bd022039"`
chromInfo	`"/tmp/tmpvuf2v_a9/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__": 1, "adapter_trimming_options": {"adapter_sequence1": "AGATCGGAAGAG", "adapter_sequence2": "GATCGTCGGACT", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 14: 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__	`"7d8e545a338811f19acb6045bd022039"`
chromInfo	`"/tmp/tmpvuf2v_a9/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 15: 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__	`"7d8e545a338811f19acb6045bd022039"`
chromInfo	`"/tmp/tmpvuf2v_a9/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 16: 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__	`"7d8e545a338811f19acb6045bd022039"`
chromInfo	`"/tmp/tmpvuf2v_a9/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 17: 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__	`"7d8e545a338811f19acb6045bd022039"`
chromInfo	`"/tmp/tmpvuf2v_a9/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 18: STAR: map and count and coverage splitted (toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy0):

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/tmpvuf2v_a9/files/2/2/d/dataset_22d2ce1e-6682-445f-abc7-bcd810d06d01.dat' --sjdbGTFfeatureExon 'exon'   --readFilesIn '/tmp/tmpvuf2v_a9/files/d/f/b/dataset_dfb4106d-23a6-46da-be5e-196e9a13ee4d.dat' '/tmp/tmpvuf2v_a9/files/a/a/4/dataset_aa440969-9d4b-4fdb-9e90-42f2c5ce70fb.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/tmpvuf2v_a9/job_working_directory/000/10/outputs/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.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/tmpvuf2v_a9/files/2/2/d/dataset_22d2ce1e-6682-445f-abc7-bcd810d06d01.dat --sjdbGTFfeatureExon exon --readFilesIn /tmp/tmpvuf2v_a9/files/d/f/b/dataset_dfb4106d-23a6-46da-be5e-196e9a13ee4d.dat /tmp/tmpvuf2v_a9/files/a/a/4/dataset_aa440969-9d4b-4fdb-9e90-42f2c5ce70fb.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 08 20:23:38 ..... started STAR run
Apr 08 20:23:38 ..... loading genome
Apr 08 20:24:05 ..... processing annotations GTF
Apr 08 20:24:05 ..... inserting junctions into the genome indices
Apr 08 20:24:12 ..... started mapping
Apr 08 20:24:36 ..... finished mapping
Apr 08 20:24:36 ..... started sorting BAM
Apr 08 20:24:37 ..... started wiggle output
Apr 08 20:24:38 ..... finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545a338811f19acb6045bd022039"`
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/tmpvuf2v_a9/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__": 2, "input": {"values": [{"id": 6, "src": "dce"}]}, "sPaired": "paired_collection"}`
twopass	`{"__current_case__": 0, "sj_precalculated": "", "twopassMode": "None", "twopass_read_subset": ""}`

Step 19: 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/tmpvuf2v_a9/job_working_directory/000/11/configs/tmpxbdf33m9' '/tmp/tmpvuf2v_a9/files/8/e/a/dataset_8eaadab2-a695-4448-a8ff-a1ef1782de96.dat' > '/tmp/tmpvuf2v_a9/job_working_directory/000/11/outputs/dataset_d5f5a045-619d-479f-9dd5-6eb14e5a816b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545b338811f19acb6045bd022039"`
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/tmpvuf2v_a9/job_working_directory/000/12/configs/tmpm6m62dmf' '/tmp/tmpvuf2v_a9/job_working_directory/000/12/outputs/dataset_aa2897ab-c1c6-4721-a6cc-3e92157249a5.dat' && ln -s '/tmp/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat' localbam.bam && ln -s '/tmp/tmpvuf2v_a9/files/_metadata_files/3/e/f/metadata_3ef915a9-ddfd-474a-9520-104817ed3ab6.dat' localbam.bam.bai && cat '/tmp/tmpvuf2v_a9/job_working_directory/000/12/configs/tmpm6m62dmf' && bamtools filter -script '/tmp/tmpvuf2v_a9/job_working_directory/000/12/configs/tmpm6m62dmf' -in localbam.bam -out '/tmp/tmpvuf2v_a9/job_working_directory/000/12/outputs/dataset_96183166-69f9-4319-be0d-0632c48b190e.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__	`"7d8e545b338811f19acb6045bd022039"`
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__	`"7d8e545b338811f19acb6045bd022039"`
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/tmpvuf2v_a9/files/9/6/1/dataset_96183166-69f9-4319-be0d-0632c48b190e.dat'   -split   -bg  -scale 9.01933     > '/tmp/tmpvuf2v_a9/job_working_directory/000/34/outputs/dataset_d5d24baa-182e-4b14-86d3-e4556a0e548d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545b338811f19acb6045bd022039"`
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": 20, "src": "dce"}]}, "input_type_select": "bam"}`
report	`{"__current_case__": 0, "report_select": "bg", "scale": "9.01933", "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/tmpvuf2v_a9/files/d/5/d/dataset_d5d24baa-182e-4b14-86d3-e4556a0e548d.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmpvuf2v_a9/job_working_directory/000/35/outputs/dataset_f7399e3d-1ab0-45bb-b0ab-6006a96e923f.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__	`"7d8e545b338811f19acb6045bd022039"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Step 20: 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__	`"7d8e545c338811f19acb6045bd022039"`
chromInfo	`"/tmp/tmpvuf2v_a9/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__	`"7d8e545c338811f19acb6045bd022039"`
chromInfo	`"/tmp/tmpvuf2v_a9/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/tmpvuf2v_a9/job_working_directory/000/16/configs/tmp7zr08clx' '/tmp/tmpvuf2v_a9/job_working_directory/000/16/outputs/dataset_f8e32846-0f3b-489f-a52c-b4f503d2805c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545c338811f19acb6045bd022039"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
input_collection	`{"values": [{"id": 9, "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/tmpvuf2v_a9/job_working_directory/000/17/outputs/dataset_6f0cc075-1210-409a-8913-fccb47cb4d54.dat' -g    -r '^(.+)$' '$1_reverse' '/tmp/tmpvuf2v_a9/files/f/8/e/dataset_f8e32846-0f3b-489f-a52c-b4f503d2805c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545c338811f19acb6045bd022039"`
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/tmpvuf2v_a9/job_working_directory/000/18/outputs/dataset_379f116b-963a-482f-b633-45ec7ee52861.dat' -g    -r '^(.+)$' '$1_forward' '/tmp/tmpvuf2v_a9/files/f/8/e/dataset_f8e32846-0f3b-489f-a52c-b4f503d2805c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545c338811f19acb6045bd022039"`
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__	`"7d8e545c338811f19acb6045bd022039"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 28, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 11, "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__	`"7d8e545c338811f19acb6045bd022039"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 29, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 9, "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__	`"7d8e545c338811f19acb6045bd022039"`
advanced	`{"conflict": {"__current_case__": 3, "duplicate_options": "keep_first"}}`
inputs	`[{"__index__": 0, "input": {"values": [{"id": 40, "src": "hdca"}]}}, {"__index__": 1, "input": {"values": [{"id": 39, "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/tmpvuf2v_a9/files/6/8/3/dataset_6837a956-3d64-460f-832e-a7fa0e4964d3.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmpvuf2v_a9/job_working_directory/000/39/outputs/dataset_4a56c904-9c56-4f42-ac86-670915d32a14.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__	`"7d8e545c338811f19acb6045bd022039"`
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/tmpvuf2v_a9/files/0/8/e/dataset_08ef192c-2eed-408f-bbdf-50c37f704f76.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmpvuf2v_a9/job_working_directory/000/40/outputs/dataset_0087bd53-0556-423c-914d-642c1f7d5b31.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__	`"7d8e545c338811f19acb6045bd022039"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Step 21: 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/tmpvuf2v_a9/files/2/2/d/dataset_22d2ce1e-6682-445f-abc7-bcd810d06d01.dat' -F "GTF"  -o "output" -T ${GALAXY_SLOTS:-2}  -s  1  -Q  0     -t 'exon' -g 'gene_id'            --minOverlap  1 --fracOverlap 0 --fracOverlapFeature 0    -p  -C --countReadPairs  '/tmp/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat'  && grep -v "^#" "output" | sed -e 's|/tmp/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat|SRR5085167|g' > body.txt && cut -f 1,7 body.txt > '/tmp/tmpvuf2v_a9/job_working_directory/000/19/outputs/dataset_17c77723-600b-4422-b77e-e415ce185240.dat'    && sed -e 's|/tmp/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat|SRR5085167|g' 'output.summary' > '/tmp/tmpvuf2v_a9/job_working_directory/000/19/outputs/dataset_a5526da1-6bd5-4096-bb6a-deb84d02f980.dat'

Exit Code:

```
0
```

Standard Error:

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat ||
||                                                                            ||
||             Output file : output                                           ||
||                 Summary : output.summary                                   ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : dataset_22d2ce1e-6682-445f-abc7-bcd810d06d01 ... ||
||      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_22d2ce1e-6682-445f-abc7-bcd810d06d01.dat ...  ||
||    Features : 7507                                                         ||
||    Meta-features : 7127                                                    ||
||    Chromosomes/contigs : 17                                                ||
||                                                                            ||
|| Process BAM file dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat...       ||
||    Strand specific : stranded                                              ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 609954                                               ||
||    Successfully assigned alignments : 100376 (16.5%)                       ||
||    Running time : 0.03 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__	`"7d8e545a338811f19acb6045bd022039"`
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__": 2, "check_distance_enabled": {"__current_case__": 1, "checkFragLength": "false"}, "exclude_chimerics": true, "only_both_ends": false, "paired_end_status": "PE_fragments"}`
read_filtering_parameters	`{"ignore_dup": false, "mapping_quality": "0", "primary": false, "splitonly": ""}`
strand_specificity	`"1"`

Step 22: 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/tmpvuf2v_a9/files/2/2/d/dataset_22d2ce1e-6682-445f-abc7-bcd810d06d01.dat' guide.gff &&  stringtie '/tmp/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat'  -o '/tmp/tmpvuf2v_a9/job_working_directory/000/20/outputs/dataset_c35821fc-4ccd-435e-baf7-3d516870b9d1.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/tmpvuf2v_a9/job_working_directory/000/20/outputs/dataset_ac929de0-0db4-4138-95e6-ca541a5988fc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545a338811f19acb6045bd022039"`
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": 12, "src": "dce"}]}, "input_mode": "short_reads"}`
rna_strandness	`"--fr"`

Step 23: 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/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat' --num-threads "${GALAXY_SLOTS:-4}" -I 300000 -F 0.1 -j 0.15 --no-effective-length-correction  -G '/tmp/tmpvuf2v_a9/files/2/2/d/dataset_22d2ce1e-6682-445f-abc7-bcd810d06d01.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__	`"7d8e545a338811f19acb6045bd022039"`
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 24: More QC:

step_state: scheduled

Subworkflow Steps

Step 1: FASTQ collection:
- step_state: scheduled
Step 2: reference_annotation_gtf:
- step_state: scheduled
Step 3: STAR BAM:
- step_state: scheduled

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/falco:1.2.4--h077b44d_1

Command Line:

ln -s '/tmp/tmpvuf2v_a9/files/f/0/d/dataset_f0d2cfe5-9c49-44ca-a614-195752c58754.dat' 'SRR5085167_forward' && falco   --threads ${GALAXY_SLOTS:-2} --quiet  -f 'fastq.gz' 'SRR5085167_forward'   -skip-summary

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545d338811f19acb6045bd022039"`
adapters	`None`
bisulfite	`false`
chromInfo	`"/tmp/tmpvuf2v_a9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
generate_summary	`false`
limits	`None`
nogroup	`false`
reverse_complement	`false`
subsample	`"1"`

Job 2:

Job state is ok

Container:

quay.io/biocontainers/falco:1.2.4--h077b44d_1

Command Line:

ln -s '/tmp/tmpvuf2v_a9/files/7/4/c/dataset_74c6f62d-7527-421e-83a3-265bb1a4b9a1.dat' 'SRR5085167_reverse' && falco   --threads ${GALAXY_SLOTS:-2} --quiet  -f 'fastq.gz' 'SRR5085167_reverse'   -skip-summary

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545d338811f19acb6045bd022039"`
adapters	`None`
bisulfite	`false`
chromInfo	`"/tmp/tmpvuf2v_a9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
generate_summary	`false`
limits	`None`
nogroup	`false`
reverse_complement	`false`
subsample	`"1"`

Step 5: 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/tmpvuf2v_a9/files/2/2/d/dataset_22d2ce1e-6682-445f-abc7-bcd810d06d01.dat' 'temp.genePred' && genePredToBed 'temp.genePred' '/tmp/tmpvuf2v_a9/job_working_directory/000/24/outputs/dataset_7b03a5aa-dcb0-487e-8984-4cbaaad49d93.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gtf"`
__workflow_invocation_uuid__	`"7d8e545d338811f19acb6045bd022039"`
advanced_options	`{"__current_case__": 0, "advanced_options_selector": "default"}`
chromInfo	`"/tmp/tmpvuf2v_a9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 6: 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/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat' infile && ln -s '/tmp/tmpvuf2v_a9/files/_metadata_files/3/e/f/metadata_3ef915a9-ddfd-474a-9520-104817ed3ab6.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__	`"7d8e545d338811f19acb6045bd022039"`
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 7: 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/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat' infile && ln -s '/tmp/tmpvuf2v_a9/files/_metadata_files/3/e/f/metadata_3ef915a9-ddfd-474a-9520-104817ed3ab6.dat' infile.bai &&  samtools idxstats -@ $addthreads infile  > '/tmp/tmpvuf2v_a9/job_working_directory/000/26/outputs/dataset_fd2bab27-9c48-4669-8a87-262d3e581c04.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545d338811f19acb6045bd022039"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`

Step 8: 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/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat' 'SRR5085167' &&  picard MarkDuplicates  --INPUT 'SRR5085167' --OUTPUT '/tmp/tmpvuf2v_a9/job_working_directory/000/27/outputs/dataset_7cb3508f-cbe6-4c26-9e6f-05b63f5c5f22.dat'  --METRICS_FILE '/tmp/tmpvuf2v_a9/job_working_directory/000/27/outputs/dataset_8f0edb92-a484-4174-8122-b7a5fae3958a.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/tmpvuf2v_a9/job_working_directory/000/27/tmp
Apr 08, 2026 8:31:15 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545d338811f19acb6045bd022039"`
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 9: 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/tmpvuf2v_a9/files/0/4/9/dataset_04931deb-462b-4d23-8fad-8b1e97d2b204.dat' 'input.bam' && ln -s -f '/tmp/tmpvuf2v_a9/files/_metadata_files/3/e/f/metadata_3ef915a9-ddfd-474a-9520-104817ed3ab6.dat' 'input.bam.bai' &&  read_distribution.py -i 'input.bam' -r '/tmp/tmpvuf2v_a9/files/7/b/0/dataset_7b03a5aa-dcb0-487e-8984-4cbaaad49d93.dat' > '/tmp/tmpvuf2v_a9/job_working_directory/000/28/outputs/dataset_e353540d-fb30-4993-966a-0f0e520c657e.dat'

Exit Code:

```
0
```

Standard Error:

processing /tmp/tmpvuf2v_a9/files/7/b/0/dataset_7b03a5aa-dcb0-487e-8984-4cbaaad49d93.dat ... Done
processing input.bam ... Finished

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545d338811f19acb6045bd022039"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`

Step 10: 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/tmpvuf2v_a9/files/9/3/f/dataset_93febf47-bc9e-4bc7-b9c3-0ddad4818574.dat' 'SRR5085167.bam' && ln -sf '/tmp/tmpvuf2v_a9/files/_metadata_files/7/7/3/metadata_7735809d-bede-421b-8b6a-fb583245607f.dat' 'SRR5085167.bam.bai' && geneBody_coverage.py -i 'SRR5085167.bam' -r '/tmp/tmpvuf2v_a9/files/7/b/0/dataset_7b03a5aa-dcb0-487e-8984-4cbaaad49d93.dat' --minimum_length 100 -o output

Exit Code:

```
0
```

Standard Error:

@ 2026-04-08 20:33:07: Read BED file (reference gene model) ...
@ 2026-04-08 20:33:07: Total 7127 transcripts loaded
@ 2026-04-08 20:33:07: Get BAM file(s) ...
	SRR5085167.bam
@ 2026-04-08 20:33:07: Processing SRR5085167.bam ...
	100 transcripts finished
 	200 transcripts finished
 	300 transcripts finished
 	400 transcripts finished
 	500 transcripts finished
 	600 transcripts finished
 	700 transcripts finished
 	800 transcripts finished
 	900 transcripts finished
 	1000 transcripts finished
 	1100 transcripts finished
 	1200 transcripts finished
 	1300 transcripts finished
 	1400 transcripts finished
 	1500 transcripts finished
 	1600 transcripts finished
 	1700 transcripts finished
 	1800 transcripts finished
 	1900 transcripts finished
 	2000 transcripts finished
 	2100 transcripts finished
 	2200 transcripts finished
 	2300 transcripts finished
 	2400 transcripts finished
 	2500 transcripts finished
 	2600 transcripts finished
 	2700 transcripts finished
 	2800 transcripts finished
 	2900 transcripts finished
 	3000 transcripts finished
 	3100 transcripts finished
 	3200 transcripts finished
 	3300 transcripts finished
 	3400 transcripts finished
 	3500 transcripts finished
 	3600 transcripts finished
 	3700 transcripts finished
 	3800 transcripts finished
 	3900 transcripts finished
 	4000 transcripts finished
 	4100 transcripts finished
 	4200 transcripts finished
 	4300 transcripts finished
 	4400 transcripts finished
 	4500 transcripts finished
 	4600 transcripts finished
 	4700 transcripts finished
 	4800 transcripts finished
 	4900 transcripts finished
 	5000 transcripts finished
 	5100 transcripts finished
 	5200 transcripts finished
 	5300 transcripts finished
 	5400 transcripts finished
 	5500 transcripts finished
 	5600 transcripts finished
 	5700 transcripts finished
 	5800 transcripts finished
 	5900 transcripts finished
 	6000 transcripts finished
 	6100 transcripts finished
 	6200 transcripts finished
 	6300 transcripts finished
 	6400 transcripts finished
 	6500 transcripts finished
 	6600 transcripts finished
 	6700 transcripts finished
 


	Sample	Skewness
	SRR5085167	5.900198198625909
@ 2026-04-08 20:33:13: Running R script ...

Standard Output:

```
null device 
          1 
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545d338811f19acb6045bd022039"`
batch_mode	`{"__current_case__": 0, "batch_mode_selector": "batch", "input": {"values": [{"id": 35, "src": "dce"}]}}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
minimum_length	`"100"`
rscript_output	`false`

Step 25: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Strandness param:
- step_state: scheduled
Step 2: RNA STAR count tables:
- step_state: scheduled
Step 3: featureCounts count table:
- step_state: scheduled

Step 4: 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__	`"7d8e545e338811f19acb6045bd022039"`
chromInfo	`"/tmp/tmpvuf2v_a9/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 5: 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/tmpvuf2v_a9/job_working_directory/000/32/configs/tmp7g39g_uo' '/tmp/tmpvuf2v_a9/files/f/2/f/dataset_f2f9b22f-c653-4ade-bc98-a9742f736fdd.dat' > '/tmp/tmpvuf2v_a9/job_working_directory/000/32/outputs/dataset_4a47ba4e-f87b-415f-a980-5ffe1d8d462d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545e338811f19acb6045bd022039"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
code	`"NR>4{print $1\"\\t\"$3}"`
dbkey	`"sacCer3"`
variables	`[]`

Step 6: 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__	`"7d8e545e338811f19acb6045bd022039"`
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": 22, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 42, "src": "dce"}]}}]}}`

Step 26: MultiQC (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy2):

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/fastp_0 &&     ln -s '/tmp/tmpvuf2v_a9/files/e/0/4/dataset_e04c247c-418a-4b76-8659-9c84ef16ae68.dat' 'multiqc_WDir/fastp_0/SRR5085167fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/SRR5085167fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/star_1 &&    mkdir 'multiqc_WDir/star_1/log_0' &&     ln -s '/tmp/tmpvuf2v_a9/files/8/e/a/dataset_8eaadab2-a695-4448-a8ff-a1ef1782de96.dat' 'multiqc_WDir/star_1/log_0/SRR5085167_Log.final.out' &&   mkdir 'multiqc_WDir/star_1/genecounts_1' &&     ln -s '/tmp/tmpvuf2v_a9/files/f/2/f/dataset_f2f9b22f-c653-4ade-bc98-a9742f736fdd.dat' 'multiqc_WDir/star_1/genecounts_1/SRR5085167_ReadsPerGene.out.tab' &&  mkdir multiqc_WDir/featureCounts_2 &&     if grep -qw Status '/tmp/tmpvuf2v_a9/files/a/5/5/dataset_a5526da1-6bd5-4096-bb6a-deb84d02f980.dat'; then ln -s '/tmp/tmpvuf2v_a9/files/a/5/5/dataset_a5526da1-6bd5-4096-bb6a-deb84d02f980.dat' 'multiqc_WDir/featureCounts_2/SRR5085167.summary'; else echo -e 'Status\tSRR5085167' > 'multiqc_WDir/featureCounts_2/SRR5085167.summary'; cat '/tmp/tmpvuf2v_a9/files/a/5/5/dataset_a5526da1-6bd5-4096-bb6a-deb84d02f980.dat' >> 'multiqc_WDir/featureCounts_2/SRR5085167.summary'; fi &&  mkdir multiqc_WDir/fastqc_3 &&    mkdir 'multiqc_WDir/fastqc_3/data_0' &&  mkdir 'multiqc_WDir/fastqc_3/data_0/file_0' && ln -s '/tmp/tmpvuf2v_a9/files/d/6/5/dataset_d65b0c52-c8b4-4908-8b59-afc7f359f19d.dat' 'multiqc_WDir/fastqc_3/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_3/data_0/file_1' && ln -s '/tmp/tmpvuf2v_a9/files/0/a/0/dataset_0a0b5034-0328-485b-a352-7303116ae048.dat' 'multiqc_WDir/fastqc_3/data_0/file_1/fastqc_data.txt' &&  mkdir multiqc_WDir/samtools_4 &&    mkdir 'multiqc_WDir/samtools_4/idxstats_0' &&     ln -s '/tmp/tmpvuf2v_a9/files/f/d/2/dataset_fd2bab27-9c48-4669-8a87-262d3e581c04.dat' 'multiqc_WDir/samtools_4/idxstats_0/SRR5085167_idxstat' &&  mkdir multiqc_WDir/picard_5 &&      mkdir 'multiqc_WDir/picard_5/markdups_0' &&    grep -Pq 'MarkDuplicates' /tmp/tmpvuf2v_a9/files/8/f/0/dataset_8f0edb92-a484-4174-8122-b7a5fae3958a.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR5085167'" && ln -s '/tmp/tmpvuf2v_a9/files/8/f/0/dataset_8f0edb92-a484-4174-8122-b7a5fae3958a.dat' 'multiqc_WDir/picard_5/markdups_0/SRR5085167'  &&    mkdir multiqc_WDir/rseqc_6 &&    mkdir 'multiqc_WDir/rseqc_6/read_distribution_0' &&      grep -Pq 'Group               Total_bases         Tag_count           Tags/Kb' /tmp/tmpvuf2v_a9/files/e/3/5/dataset_e353540d-fb30-4993-966a-0f0e520c657e.dat || die "Module 'rseqc: 'Group               Total_bases         Tag_count           Tags/Kb' not found in the file 'SRR5085167'" && ln -s '/tmp/tmpvuf2v_a9/files/e/3/5/dataset_e353540d-fb30-4993-966a-0f0e520c657e.dat' 'multiqc_WDir/rseqc_6/read_distribution_0/SRR5085167'  &&     mkdir 'multiqc_WDir/rseqc_6/gene_body_coverage_1' &&  ln -s '/tmp/tmpvuf2v_a9/files/1/2/6/dataset_1264f5bd-f86d-45a6-aed7-97d8ca33f37a.dat' 'multiqc_WDir/rseqc_6/gene_body_coverage_1/file_0.geneBodyCoverage.txt' &&      multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.33

       file_search | Search path: /tmp/tmpvuf2v_a9/job_working_directory/000/31/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 2 reports

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

Standard Output:

total 4100
-rw-r--r-- 1 1001 1001    2950 Apr  8 20:34 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 1001    1461 Apr  8 20:34 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1452 Apr  8 20:34 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1461 Apr  8 20:34 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    1444 Apr  8 20:34 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1151 Apr  8 20:34 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1309 Apr  8 20:34 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1159 Apr  8 20:34 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    1537 Apr  8 20:34 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1283 Apr  8 20:34 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1280 Apr  8 20:34 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1280 Apr  8 20:34 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    1285 Apr  8 20:34 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001     145 Apr  8 20:34 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 1001     378 Apr  8 20:34 fastqc-status-check-heatmap.txt
-rw-r--r-- 1 1001 1001    4784 Apr  8 20:34 fastqc_adapter_content_plot.txt
-rw-r--r-- 1 1001 1001     172 Apr  8 20:34 fastqc_overrepresented_sequences_plot.txt
-rw-r--r-- 1 1001 1001    2336 Apr  8 20:34 fastqc_per_base_n_content_plot.txt
-rw-r--r-- 1 1001 1001    2325 Apr  8 20:34 fastqc_per_base_sequence_quality_plot.txt
-rw-r--r-- 1 1001 1001    3095 Apr  8 20:34 fastqc_per_sequence_gc_content_plot_Counts.txt
-rw-r--r-- 1 1001 1001    5075 Apr  8 20:34 fastqc_per_sequence_gc_content_plot_Percentages.txt
-rw-r--r-- 1 1001 1001    1296 Apr  8 20:34 fastqc_per_sequence_quality_scores_plot.txt
-rw-r--r-- 1 1001 1001     110 Apr  8 20:34 fastqc_sequence_counts_plot.txt
-rw-r--r-- 1 1001 1001     585 Apr  8 20:34 fastqc_sequence_duplication_levels_plot.txt
-rw-r--r-- 1 1001 1001    2087 Apr  8 20:34 fastqc_top_overrepresented_sequences_table.txt
-rw-r--r-- 1 1001 1001     131 Apr  8 20:34 featureCounts_assignment_plot.txt
-rw-r--r-- 1 1001 1001   61247 Apr  8 20:34 llms-full.txt
-rw-r--r-- 1 1001 1001   33619 Apr  8 20:34 multiqc.log
-rw-r--r-- 1 1001 1001 2444213 Apr  8 20:34 multiqc.parquet
-rw-r--r-- 1 1001 1001     367 Apr  8 20:34 multiqc_citations.txt
-rw-r--r-- 1 1001 1001 1338106 Apr  8 20:34 multiqc_data.json
-rw-r--r-- 1 1001 1001  103529 Apr  8 20:34 multiqc_fastp.txt
-rw-r--r-- 1 1001 1001     799 Apr  8 20:34 multiqc_fastqc.txt
-rw-r--r-- 1 1001 1001     412 Apr  8 20:34 multiqc_featurecounts.txt
-rw-r--r-- 1 1001 1001    1090 Apr  8 20:34 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001     312 Apr  8 20:34 multiqc_picard_dups.txt
-rw-r--r-- 1 1001 1001    1344 Apr  8 20:34 multiqc_rseqc_read_distribution.txt
-rw-r--r-- 1 1001 1001     412 Apr  8 20:34 multiqc_samtools_idxstats.txt
-rw-r--r-- 1 1001 1001      25 Apr  8 20:34 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001    1468 Apr  8 20:34 multiqc_sources.txt
-rw-r--r-- 1 1001 1001     693 Apr  8 20:34 multiqc_star.txt
-rw-r--r-- 1 1001 1001       0 Apr  8 20:34 picard_MarkIlluminaAdapters_histogram.txt
-rw-r--r-- 1 1001 1001       0 Apr  8 20:34 picard_MeanQualityByCycle_histogram.txt
-rw-r--r-- 1 1001 1001       0 Apr  8 20:34 picard_MeanQualityByCycle_histogram_1.txt
-rw-r--r-- 1 1001 1001       0 Apr  8 20:34 picard_QualityScoreDistribution_histogram.txt
-rw-r--r-- 1 1001 1001     105 Apr  8 20:34 picard_deduplication.txt
-rw-r--r-- 1 1001 1001    1010 Apr  8 20:34 rseqc_gene_body_cov.txt
-rw-r--r-- 1 1001 1001    1600 Apr  8 20:34 rseqc_gene_body_coverage_plot_Counts.txt
-rw-r--r-- 1 1001 1001    2719 Apr  8 20:34 rseqc_gene_body_coverage_plot_Percentages.txt
-rw-r--r-- 1 1001 1001     134 Apr  8 20:34 rseqc_read_distribution_plot.txt
-rw-r--r-- 1 1001 1001     575 Apr  8 20:34 samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt
-rw-r--r-- 1 1001 1001     556 Apr  8 20:34 samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt
-rw-r--r-- 1 1001 1001     339 Apr  8 20:34 samtools-idxstats-mapped-reads-plot_Raw_Counts.txt
-rw-r--r-- 1 1001 1001     156 Apr  8 20:34 star_alignment_plot.txt
-rw-r--r-- 1 1001 1001     125 Apr  8 20:34 star_gene_counts_Reverse_Stranded.txt
-rw-r--r-- 1 1001 1001     128 Apr  8 20:34 star_gene_counts_Same_Stranded.txt
-rw-r--r-- 1 1001 1001     127 Apr  8 20:34 star_gene_counts_Unstranded.txt
-rw-r--r-- 1 1001 1001     396 Apr  8 20:34 star_summary_table.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"7d8e545a338811f19acb6045bd022039"`
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": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 29, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 5, "src": "hdca"}]}, "type": "log"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 8, "src": "hdca"}]}, "type": "genecounts"}}], "software": "star"}}, {"__index__": 2, "software_cond": {"__current_case__": 10, "input": {"values": [{"id": 18, "src": "hdca"}]}, "software": "featureCounts"}}, {"__index__": 3, "software_cond": {"__current_case__": 9, "output": [{"__index__": 0, "input": {"values": [{"id": 27, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}, {"__index__": 4, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 2, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "idxstats"}}], "software": "samtools"}}, {"__index__": 5, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 30, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}, {"__index__": 6, "software_cond": {"__current_case__": 23, "output": [{"__index__": 0, "type": {"__current_case__": 6, "input": {"values": [{"id": 32, "src": "hdca"}]}, "type": "read_distribution"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 34, "src": "hdca"}]}, "type": "gene_body_coverage"}}], "software": "rseqc"}}]
title	`""`

Other invocation details
- history_id
  - 62d07e355d50541c
- history_state
  - ok
- invocation_id
  - 62d07e355d50541c
- invocation_state
  - scheduled
- workflow_id
  - c19d1054b6b866c2

Passed Tests

✅ rnaseq-sr.ga_0

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/1.2.0+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/fastp:1.2.0--h43da1c4_0

Command Line:

ln -sf '/tmp/tmpd2k2zeu7/files/5/b/0/dataset_5b0a86e0-ee3d-4d00-afa2-833ee66581af.dat' 'SRR5085167.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for 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/tmpd2k2zeu7/job_working_directory/000/3/outputs/dataset_bb780dac-35a3-49f9-b424-06820aa20a77.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 fastp report for SRR5085167.fastqsanger.gz -i SRR5085167.fastqsanger.gz -o first.fastqsanger.gz --adapter_sequence AGATCGGAAGAG -q 30 -l 15 --dont_eval_duplication 
fastp v1.2.0, time used: 2 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f882338911f1b6276045bd03ad8e"`
chromInfo	`"/tmp/tmpd2k2zeu7/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: 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__	`"0fa2f882338911f1b6276045bd03ad8e"`
chromInfo	`"/tmp/tmpd2k2zeu7/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 13: 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__	`"0fa2f882338911f1b6276045bd03ad8e"`
chromInfo	`"/tmp/tmpd2k2zeu7/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 14: 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__	`"0fa2f882338911f1b6276045bd03ad8e"`
chromInfo	`"/tmp/tmpd2k2zeu7/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 15: 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__	`"0fa2f882338911f1b6276045bd03ad8e"`
chromInfo	`"/tmp/tmpd2k2zeu7/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 16: STAR: map and count and coverage splitted (toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy0):

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/tmpd2k2zeu7/files/1/c/2/dataset_1c219fba-36af-46b6-83a6-4af66867483e.dat' --sjdbGTFfeatureExon 'exon'   --readFilesIn '/tmp/tmpd2k2zeu7/files/b/b/7/dataset_bb780dac-35a3-49f9-b424-06820aa20a77.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/tmpd2k2zeu7/job_working_directory/000/8/outputs/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.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/tmpd2k2zeu7/files/1/c/2/dataset_1c219fba-36af-46b6-83a6-4af66867483e.dat --sjdbGTFfeatureExon exon --readFilesIn /tmp/tmpd2k2zeu7/files/b/b/7/dataset_bb780dac-35a3-49f9-b424-06820aa20a77.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 08 20:27:39 ..... started STAR run
Apr 08 20:27:40 ..... loading genome
Apr 08 20:28:00 ..... processing annotations GTF
Apr 08 20:28:00 ..... inserting junctions into the genome indices
Apr 08 20:28:07 ..... started mapping
Apr 08 20:28:23 ..... finished mapping
Apr 08 20:28:23 ..... started sorting BAM
Apr 08 20:28:24 ..... started wiggle output
Apr 08 20:28:25 ..... finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f882338911f1b6276045bd03ad8e"`
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/tmpd2k2zeu7/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 17: 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/tmpd2k2zeu7/job_working_directory/000/9/configs/tmpxmv2svv7' '/tmp/tmpd2k2zeu7/files/1/4/2/dataset_142a8845-afbc-480f-8a62-0bb5a8202e38.dat' > '/tmp/tmpd2k2zeu7/job_working_directory/000/9/outputs/dataset_1f46150f-4026-45d4-8021-3cbc7fc5c569.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f883338911f1b6276045bd03ad8e"`
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/tmpd2k2zeu7/job_working_directory/000/10/configs/tmp0n2qn4ou' '/tmp/tmpd2k2zeu7/job_working_directory/000/10/outputs/dataset_97f23d39-7640-4b37-a017-cb2693badc49.dat' && ln -s '/tmp/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat' localbam.bam && ln -s '/tmp/tmpd2k2zeu7/files/_metadata_files/e/b/7/metadata_eb727426-38bc-43f2-ae67-8fcffcc4e1d9.dat' localbam.bam.bai && cat '/tmp/tmpd2k2zeu7/job_working_directory/000/10/configs/tmp0n2qn4ou' && bamtools filter -script '/tmp/tmpd2k2zeu7/job_working_directory/000/10/configs/tmp0n2qn4ou' -in localbam.bam -out '/tmp/tmpd2k2zeu7/job_working_directory/000/10/outputs/dataset_be0d8c8e-cc05-4fa7-a30f-c25c94c80495.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__	`"0fa2f883338911f1b6276045bd03ad8e"`
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__	`"0fa2f883338911f1b6276045bd03ad8e"`
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/tmpd2k2zeu7/files/b/e/0/dataset_be0d8c8e-cc05-4fa7-a30f-c25c94c80495.dat'   -split   -bg  -scale 7.9533     > '/tmp/tmpd2k2zeu7/job_working_directory/000/36/outputs/dataset_4428d5f0-5539-46b1-a62e-f4cafb5b35fc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f883338911f1b6276045bd03ad8e"`
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/tmpd2k2zeu7/files/4/4/2/dataset_4428d5f0-5539-46b1-a62e-f4cafb5b35fc.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmpd2k2zeu7/job_working_directory/000/37/outputs/dataset_1267998a-05f0-46e7-89d5-00672c6888d0.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__	`"0fa2f883338911f1b6276045bd03ad8e"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Step 18: 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__	`"0fa2f884338911f1b6276045bd03ad8e"`
chromInfo	`"/tmp/tmpd2k2zeu7/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__	`"0fa2f884338911f1b6276045bd03ad8e"`
chromInfo	`"/tmp/tmpd2k2zeu7/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/tmpd2k2zeu7/job_working_directory/000/14/configs/tmp7p0jkols' '/tmp/tmpd2k2zeu7/job_working_directory/000/14/outputs/dataset_3bfb9c62-bd8a-43e0-ae9a-46e73c2381c0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f884338911f1b6276045bd03ad8e"`
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/tmpd2k2zeu7/job_working_directory/000/15/outputs/dataset_f040eb00-0745-4d29-8517-10960ac52c70.dat' -g    -r '^(.+)$' '$1_reverse' '/tmp/tmpd2k2zeu7/files/3/b/f/dataset_3bfb9c62-bd8a-43e0-ae9a-46e73c2381c0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f884338911f1b6276045bd03ad8e"`
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/tmpd2k2zeu7/job_working_directory/000/16/outputs/dataset_9b3ffd5d-43b1-459c-8e5f-e967f20cf7a0.dat' -g    -r '^(.+)$' '$1_forward' '/tmp/tmpd2k2zeu7/files/3/b/f/dataset_3bfb9c62-bd8a-43e0-ae9a-46e73c2381c0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f884338911f1b6276045bd03ad8e"`
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__	`"0fa2f884338911f1b6276045bd03ad8e"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 24, "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__	`"0fa2f884338911f1b6276045bd03ad8e"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 25, "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__	`"0fa2f884338911f1b6276045bd03ad8e"`
advanced	`{"conflict": {"__current_case__": 3, "duplicate_options": "keep_first"}}`
inputs	`[{"__index__": 0, "input": {"values": [{"id": 37, "src": "hdca"}]}}, {"__index__": 1, "input": {"values": [{"id": 36, "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/tmpd2k2zeu7/files/7/1/f/dataset_71fd7e83-ff66-4317-b15c-3da69d058f8f.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmpd2k2zeu7/job_working_directory/000/34/outputs/dataset_d40afccd-2965-4418-af80-d7f52a741412.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__	`"0fa2f884338911f1b6276045bd03ad8e"`
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/tmpd2k2zeu7/files/d/d/d/dataset_ddd1bc25-4b96-414e-a53d-e8f7eb4cc514.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len' '/tmp/tmpd2k2zeu7/job_working_directory/000/35/outputs/dataset_f26f8d85-ada6-49d6-afa5-7f4e1970b5af.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__	`"0fa2f884338911f1b6276045bd03ad8e"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Step 19: 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/tmpd2k2zeu7/files/1/c/2/dataset_1c219fba-36af-46b6-83a6-4af66867483e.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/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat'  && grep -v "^#" "output" | sed -e 's|/tmp/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat|SRR5085167|g' > body.txt && cut -f 1,7 body.txt > '/tmp/tmpd2k2zeu7/job_working_directory/000/17/outputs/dataset_8a8d8e5b-086a-422b-83de-dd088b266752.dat'    && sed -e 's|/tmp/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat|SRR5085167|g' 'output.summary' > '/tmp/tmpd2k2zeu7/job_working_directory/000/17/outputs/dataset_a6d713ad-dc22-4e3d-b310-67bab3a64f0d.dat'

Exit Code:

```
0
```

Standard Error:

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

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat ||
||                                                                            ||
||             Output file : output                                           ||
||                 Summary : output.summary                                   ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : dataset_1c219fba-36af-46b6-83a6-4af66867483e ... ||
||      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_1c219fba-36af-46b6-83a6-4af66867483e.dat ...  ||
||    Features : 7507                                                         ||
||    Meta-features : 7127                                                    ||
||    Chromosomes/contigs : 17                                                ||
||                                                                            ||
|| Process BAM file dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.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__	`"0fa2f882338911f1b6276045bd03ad8e"`
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 20: 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/tmpd2k2zeu7/files/1/c/2/dataset_1c219fba-36af-46b6-83a6-4af66867483e.dat' guide.gff &&  stringtie '/tmp/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat'  -o '/tmp/tmpd2k2zeu7/job_working_directory/000/18/outputs/dataset_13a2661e-98d6-4f80-834c-a9e10a6121ff.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/tmpd2k2zeu7/job_working_directory/000/18/outputs/dataset_2d82930f-4fca-4a64-af67-f4f8bf9478f5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f882338911f1b6276045bd03ad8e"`
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 21: 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/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat' --num-threads "${GALAXY_SLOTS:-4}" -I 300000 -F 0.1 -j 0.15 --no-effective-length-correction  -G '/tmp/tmpd2k2zeu7/files/1/c/2/dataset_1c219fba-36af-46b6-83a6-4af66867483e.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__	`"0fa2f882338911f1b6276045bd03ad8e"`
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 22: More QC:

step_state: scheduled

Subworkflow Steps

Step 1: FASTQ collection:
- step_state: scheduled
Step 2: reference_annotation_gtf:
- step_state: scheduled
Step 3: STAR BAM:
- step_state: scheduled

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/falco:1.2.4--h077b44d_1

Command Line:

ln -s '/tmp/tmpd2k2zeu7/files/5/b/0/dataset_5b0a86e0-ee3d-4d00-afa2-833ee66581af.dat' 'SRR5085167' && falco   --threads ${GALAXY_SLOTS:-2} --quiet  -f 'fastq.gz' 'SRR5085167'   -skip-summary

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f885338911f1b6276045bd03ad8e"`
adapters	`None`
bisulfite	`false`
chromInfo	`"/tmp/tmpd2k2zeu7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
generate_summary	`false`
limits	`None`
nogroup	`false`
reverse_complement	`false`
subsample	`"1"`

Step 5: 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/tmpd2k2zeu7/files/1/c/2/dataset_1c219fba-36af-46b6-83a6-4af66867483e.dat' 'temp.genePred' && genePredToBed 'temp.genePred' '/tmp/tmpd2k2zeu7/job_working_directory/000/21/outputs/dataset_69253b51-81f9-4cf5-ab9d-f5eb439a40e5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"gtf"`
__workflow_invocation_uuid__	`"0fa2f885338911f1b6276045bd03ad8e"`
advanced_options	`{"__current_case__": 0, "advanced_options_selector": "default"}`
chromInfo	`"/tmp/tmpd2k2zeu7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 6: 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/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat' infile && ln -s '/tmp/tmpd2k2zeu7/files/_metadata_files/e/b/7/metadata_eb727426-38bc-43f2-ae67-8fcffcc4e1d9.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__	`"0fa2f885338911f1b6276045bd03ad8e"`
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 7: 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/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat' infile && ln -s '/tmp/tmpd2k2zeu7/files/_metadata_files/e/b/7/metadata_eb727426-38bc-43f2-ae67-8fcffcc4e1d9.dat' infile.bai &&  samtools idxstats -@ $addthreads infile  > '/tmp/tmpd2k2zeu7/job_working_directory/000/23/outputs/dataset_19eeaeea-0bbd-4687-800f-ef5426f959a7.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f885338911f1b6276045bd03ad8e"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`

Step 8: 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/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat' 'SRR5085167' &&  picard MarkDuplicates  --INPUT 'SRR5085167' --OUTPUT '/tmp/tmpd2k2zeu7/job_working_directory/000/24/outputs/dataset_5ac16a43-e73e-4aae-8bd1-6c552ab8c153.dat'  --METRICS_FILE '/tmp/tmpd2k2zeu7/job_working_directory/000/24/outputs/dataset_81289554-b0da-480d-ae8f-d20ed7402314.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/tmpd2k2zeu7/job_working_directory/000/24/tmp
Apr 08, 2026 8:34:46 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f885338911f1b6276045bd03ad8e"`
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 9: 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/tmpd2k2zeu7/files/e/f/1/dataset_ef1b92ef-b0c6-426a-bc3f-f274b4a44489.dat' 'input.bam' && ln -s -f '/tmp/tmpd2k2zeu7/files/_metadata_files/e/b/7/metadata_eb727426-38bc-43f2-ae67-8fcffcc4e1d9.dat' 'input.bam.bai' &&  read_distribution.py -i 'input.bam' -r '/tmp/tmpd2k2zeu7/files/6/9/2/dataset_69253b51-81f9-4cf5-ab9d-f5eb439a40e5.dat' > '/tmp/tmpd2k2zeu7/job_working_directory/000/25/outputs/dataset_9f8cda90-3ed8-42ba-b4f1-d2713ae5517e.dat'

Exit Code:

```
0
```

Standard Error:

processing /tmp/tmpd2k2zeu7/files/6/9/2/dataset_69253b51-81f9-4cf5-ab9d-f5eb439a40e5.dat ... Done
processing input.bam ... Finished

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f885338911f1b6276045bd03ad8e"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`

Step 10: 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/tmpd2k2zeu7/files/2/e/c/dataset_2eccf46d-2fe9-4bc1-9d20-0c5aadf3d5fe.dat' 'SRR5085167.bam' && ln -sf '/tmp/tmpd2k2zeu7/files/_metadata_files/f/a/3/metadata_fa379d47-916e-4940-8fe4-408d54b5cb07.dat' 'SRR5085167.bam.bai' && geneBody_coverage.py -i 'SRR5085167.bam' -r '/tmp/tmpd2k2zeu7/files/6/9/2/dataset_69253b51-81f9-4cf5-ab9d-f5eb439a40e5.dat' --minimum_length 100 -o output

Exit Code:

```
0
```

Standard Error:

@ 2026-04-08 20:36:05: Read BED file (reference gene model) ...
@ 2026-04-08 20:36:06: Total 7127 transcripts loaded
@ 2026-04-08 20:36:06: Get BAM file(s) ...
	SRR5085167.bam
@ 2026-04-08 20:36:06: Processing SRR5085167.bam ...
	100 transcripts finished
 	200 transcripts finished
 	300 transcripts finished
 	400 transcripts finished
 	500 transcripts finished
 	600 transcripts finished
 	700 transcripts finished
 	800 transcripts finished
 	900 transcripts finished
 	1000 transcripts finished
 	1100 transcripts finished
 	1200 transcripts finished
 	1300 transcripts finished
 	1400 transcripts finished
 	1500 transcripts finished
 	1600 transcripts finished
 	1700 transcripts finished
 	1800 transcripts finished
 	1900 transcripts finished
 	2000 transcripts finished
 	2100 transcripts finished
 	2200 transcripts finished
 	2300 transcripts finished
 	2400 transcripts finished
 	2500 transcripts finished
 	2600 transcripts finished
 	2700 transcripts finished
 	2800 transcripts finished
 	2900 transcripts finished
 	3000 transcripts finished
 	3100 transcripts finished
 	3200 transcripts finished
 	3300 transcripts finished
 	3400 transcripts finished
 	3500 transcripts finished
 	3600 transcripts finished
 	3700 transcripts finished
 	3800 transcripts finished
 	3900 transcripts finished
 	4000 transcripts finished
 	4100 transcripts finished
 	4200 transcripts finished
 	4300 transcripts finished
 	4400 transcripts finished
 	4500 transcripts finished
 	4600 transcripts finished
 	4700 transcripts finished
 	4800 transcripts finished
 	4900 transcripts finished
 	5000 transcripts finished
 	5100 transcripts finished
 	5200 transcripts finished
 	5300 transcripts finished
 	5400 transcripts finished
 	5500 transcripts finished
 	5600 transcripts finished
 	5700 transcripts finished
 	5800 transcripts finished
 	5900 transcripts finished
 	6000 transcripts finished
 	6100 transcripts finished
 	6200 transcripts finished
 	6300 transcripts finished
 	6400 transcripts finished
 	6500 transcripts finished
 	6600 transcripts finished
 	6700 transcripts finished
 


	Sample	Skewness
	SRR5085167	4.413411450952844
@ 2026-04-08 20:36:12: Running R script ...

Standard Output:

```
null device 
          1 
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f885338911f1b6276045bd03ad8e"`
batch_mode	`{"__current_case__": 0, "batch_mode_selector": "batch", "input": {"values": [{"id": 27, "src": "dce"}]}}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
dbkey	`"sacCer3"`
minimum_length	`"100"`
rscript_output	`false`

Step 23: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Strandness param:
- step_state: scheduled
Step 2: RNA STAR count tables:
- step_state: scheduled
Step 3: featureCounts count table:
- step_state: scheduled

Step 4: 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__	`"0fa2f886338911f1b6276045bd03ad8e"`
chromInfo	`"/tmp/tmpd2k2zeu7/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 5: 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/tmpd2k2zeu7/job_working_directory/000/29/configs/tmp3f7c40ye' '/tmp/tmpd2k2zeu7/files/9/5/c/dataset_95c0597d-78f7-417a-a85b-b884eb37f6a8.dat' > '/tmp/tmpd2k2zeu7/job_working_directory/000/29/outputs/dataset_1ed17214-8c84-4343-9bdf-0d9270b0a4b1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f886338911f1b6276045bd03ad8e"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/sacCer3.len"`
code	`"NR>4{print $1\"\\t\"$3}"`
dbkey	`"sacCer3"`
variables	`[]`

Step 6: 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__	`"0fa2f886338911f1b6276045bd03ad8e"`
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": 34, "src": "dce"}]}}]}}`

Step 24: MultiQC (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy2):

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/fastp_0 &&     ln -s '/tmp/tmpd2k2zeu7/files/5/3/b/dataset_53b585d3-7a78-4207-80fe-e7cef5c75446.dat' 'multiqc_WDir/fastp_0/SRR5085167fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/SRR5085167fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/star_1 &&    mkdir 'multiqc_WDir/star_1/log_0' &&     ln -s '/tmp/tmpd2k2zeu7/files/1/4/2/dataset_142a8845-afbc-480f-8a62-0bb5a8202e38.dat' 'multiqc_WDir/star_1/log_0/SRR5085167_Log.final.out' &&   mkdir 'multiqc_WDir/star_1/genecounts_1' &&     ln -s '/tmp/tmpd2k2zeu7/files/9/5/c/dataset_95c0597d-78f7-417a-a85b-b884eb37f6a8.dat' 'multiqc_WDir/star_1/genecounts_1/SRR5085167_ReadsPerGene.out.tab' &&  mkdir multiqc_WDir/featureCounts_2 &&     if grep -qw Status '/tmp/tmpd2k2zeu7/files/a/6/d/dataset_a6d713ad-dc22-4e3d-b310-67bab3a64f0d.dat'; then ln -s '/tmp/tmpd2k2zeu7/files/a/6/d/dataset_a6d713ad-dc22-4e3d-b310-67bab3a64f0d.dat' 'multiqc_WDir/featureCounts_2/SRR5085167.summary'; else echo -e 'Status\tSRR5085167' > 'multiqc_WDir/featureCounts_2/SRR5085167.summary'; cat '/tmp/tmpd2k2zeu7/files/a/6/d/dataset_a6d713ad-dc22-4e3d-b310-67bab3a64f0d.dat' >> 'multiqc_WDir/featureCounts_2/SRR5085167.summary'; fi &&  mkdir multiqc_WDir/fastqc_3 &&    mkdir 'multiqc_WDir/fastqc_3/data_0' &&  mkdir 'multiqc_WDir/fastqc_3/data_0/file_0' && ln -s '/tmp/tmpd2k2zeu7/files/3/2/e/dataset_32e93adf-48a2-41ff-ac7c-647080f4df6f.dat' 'multiqc_WDir/fastqc_3/data_0/file_0/fastqc_data.txt' &&  mkdir multiqc_WDir/samtools_4 &&    mkdir 'multiqc_WDir/samtools_4/idxstats_0' &&     ln -s '/tmp/tmpd2k2zeu7/files/1/9/e/dataset_19eeaeea-0bbd-4687-800f-ef5426f959a7.dat' 'multiqc_WDir/samtools_4/idxstats_0/SRR5085167_idxstat' &&  mkdir multiqc_WDir/picard_5 &&      mkdir 'multiqc_WDir/picard_5/markdups_0' &&    grep -Pq 'MarkDuplicates' /tmp/tmpd2k2zeu7/files/8/1/2/dataset_81289554-b0da-480d-ae8f-d20ed7402314.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR5085167'" && ln -s '/tmp/tmpd2k2zeu7/files/8/1/2/dataset_81289554-b0da-480d-ae8f-d20ed7402314.dat' 'multiqc_WDir/picard_5/markdups_0/SRR5085167'  &&    mkdir multiqc_WDir/rseqc_6 &&    mkdir 'multiqc_WDir/rseqc_6/read_distribution_0' &&      grep -Pq 'Group               Total_bases         Tag_count           Tags/Kb' /tmp/tmpd2k2zeu7/files/9/f/8/dataset_9f8cda90-3ed8-42ba-b4f1-d2713ae5517e.dat || die "Module 'rseqc: 'Group               Total_bases         Tag_count           Tags/Kb' not found in the file 'SRR5085167'" && ln -s '/tmp/tmpd2k2zeu7/files/9/f/8/dataset_9f8cda90-3ed8-42ba-b4f1-d2713ae5517e.dat' 'multiqc_WDir/rseqc_6/read_distribution_0/SRR5085167'  &&     mkdir 'multiqc_WDir/rseqc_6/gene_body_coverage_1' &&  ln -s '/tmp/tmpd2k2zeu7/files/c/6/f/dataset_c6fbf96d-4951-4645-a340-19e605a94f3d.dat' 'multiqc_WDir/rseqc_6/gene_body_coverage_1/file_0.geneBodyCoverage.txt' &&      multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.33

       file_search | Search path: /tmp/tmpd2k2zeu7/job_working_directory/000/28/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 3468
-rw-r--r-- 1 1001 1001    1451 Apr  8 20:37 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1452 Apr  8 20:37 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1211 Apr  8 20:37 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1309 Apr  8 20:37 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    1284 Apr  8 20:37 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    1280 Apr  8 20:37 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001     143 Apr  8 20:37 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 1001     314 Apr  8 20:37 fastqc-status-check-heatmap.txt
-rw-r--r-- 1 1001 1001    2471 Apr  8 20:37 fastqc_adapter_content_plot.txt
-rw-r--r-- 1 1001 1001     118 Apr  8 20:37 fastqc_overrepresented_sequences_plot.txt
-rw-r--r-- 1 1001 1001    1229 Apr  8 20:37 fastqc_per_base_n_content_plot.txt
-rw-r--r-- 1 1001 1001    1263 Apr  8 20:37 fastqc_per_base_sequence_quality_plot.txt
-rw-r--r-- 1 1001 1001    1680 Apr  8 20:37 fastqc_per_sequence_gc_content_plot_Counts.txt
-rw-r--r-- 1 1001 1001    2619 Apr  8 20:37 fastqc_per_sequence_gc_content_plot_Percentages.txt
-rw-r--r-- 1 1001 1001     686 Apr  8 20:37 fastqc_per_sequence_quality_scores_plot.txt
-rw-r--r-- 1 1001 1001      65 Apr  8 20:37 fastqc_sequence_counts_plot.txt
-rw-r--r-- 1 1001 1001     308 Apr  8 20:37 fastqc_sequence_duplication_levels_plot.txt
-rw-r--r-- 1 1001 1001    1674 Apr  8 20:37 fastqc_top_overrepresented_sequences_table.txt
-rw-r--r-- 1 1001 1001     131 Apr  8 20:37 featureCounts_assignment_plot.txt
-rw-r--r-- 1 1001 1001   45538 Apr  8 20:37 llms-full.txt
-rw-r--r-- 1 1001 1001   33965 Apr  8 20:37 multiqc.log
-rw-r--r-- 1 1001 1001 2292127 Apr  8 20:37 multiqc.parquet
-rw-r--r-- 1 1001 1001     367 Apr  8 20:37 multiqc_citations.txt
-rw-r--r-- 1 1001 1001  943738 Apr  8 20:37 multiqc_data.json
-rw-r--r-- 1 1001 1001   51269 Apr  8 20:37 multiqc_fastp.txt
-rw-r--r-- 1 1001 1001     605 Apr  8 20:37 multiqc_fastqc.txt
-rw-r--r-- 1 1001 1001     412 Apr  8 20:37 multiqc_featurecounts.txt
-rw-r--r-- 1 1001 1001     895 Apr  8 20:37 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001     303 Apr  8 20:37 multiqc_picard_dups.txt
-rw-r--r-- 1 1001 1001    1344 Apr  8 20:37 multiqc_rseqc_read_distribution.txt
-rw-r--r-- 1 1001 1001     410 Apr  8 20:37 multiqc_samtools_idxstats.txt
-rw-r--r-- 1 1001 1001      25 Apr  8 20:37 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001    1315 Apr  8 20:37 multiqc_sources.txt
-rw-r--r-- 1 1001 1001     692 Apr  8 20:37 multiqc_star.txt
-rw-r--r-- 1 1001 1001       0 Apr  8 20:37 picard_MarkIlluminaAdapters_histogram.txt
-rw-r--r-- 1 1001 1001       0 Apr  8 20:37 picard_MeanQualityByCycle_histogram.txt
-rw-r--r-- 1 1001 1001       0 Apr  8 20:37 picard_MeanQualityByCycle_histogram_1.txt
-rw-r--r-- 1 1001 1001       0 Apr  8 20:37 picard_QualityScoreDistribution_histogram.txt
-rw-r--r-- 1 1001 1001      71 Apr  8 20:37 picard_deduplication.txt
-rw-r--r-- 1 1001 1001    1057 Apr  8 20:37 rseqc_gene_body_cov.txt
-rw-r--r-- 1 1001 1001    1647 Apr  8 20:37 rseqc_gene_body_coverage_plot_Counts.txt
-rw-r--r-- 1 1001 1001    2717 Apr  8 20:37 rseqc_gene_body_coverage_plot_Percentages.txt
-rw-r--r-- 1 1001 1001     133 Apr  8 20:37 rseqc_read_distribution_plot.txt
-rw-r--r-- 1 1001 1001     575 Apr  8 20:37 samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt
-rw-r--r-- 1 1001 1001     556 Apr  8 20:37 samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt
-rw-r--r-- 1 1001 1001     337 Apr  8 20:37 samtools-idxstats-mapped-reads-plot_Raw_Counts.txt
-rw-r--r-- 1 1001 1001     157 Apr  8 20:37 star_alignment_plot.txt
-rw-r--r-- 1 1001 1001     125 Apr  8 20:37 star_gene_counts_Reverse_Stranded.txt
-rw-r--r-- 1 1001 1001     128 Apr  8 20:37 star_gene_counts_Same_Stranded.txt
-rw-r--r-- 1 1001 1001     129 Apr  8 20:37 star_gene_counts_Unstranded.txt
-rw-r--r-- 1 1001 1001     365 Apr  8 20:37 star_summary_table.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0fa2f882338911f1b6276045bd03ad8e"`
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": 17, "src": "hdca"}]}, "software": "featureCounts"}}, {"__index__": 3, "software_cond": {"__current_case__": 9, "output": [{"__index__": 0, "input": {"values": [{"id": 26, "src": "hdca"}]}, "type": "data"}], "software": "fastqc"}}, {"__index__": 4, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 2, "input": {"values": [{"id": 28, "src": "hdca"}]}, "type": "idxstats"}}], "software": "samtools"}}, {"__index__": 5, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 29, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}, {"__index__": 6, "software_cond": {"__current_case__": 23, "output": [{"__index__": 0, "type": {"__current_case__": 6, "input": {"values": [{"id": 31, "src": "hdca"}]}, "type": "read_distribution"}}, {"__index__": 1, "type": {"__current_case__": 1, "input": {"values": [{"id": 33, "src": "hdca"}]}, "type": "gene_body_coverage"}}], "software": "rseqc"}}]
title	`""`

Other invocation details
- history_id
  - 042edd3d3d0c7345
- history_state
  - ok
- invocation_id
  - 042edd3d3d0c7345
- invocation_state
  - scheduled
- workflow_id
  - b00c14ffa335c584

lldelisle · 2026-04-08T21:18:44Z

There is an issue with the toolshed. We probably need to wait for a fix.

lldelisle · 2026-04-09T16:00:53Z

I finally decided to have 2 MultiQC as before (one when extra QC, one without).

This new version fixes the MultiQC error when FeatureCount was not used.

wm75 · 2026-04-15T08:39:16Z

@lldelisle we discussed somewhere a Pick param step selecting the MultiQC job that was actually run and making that the unconditional combined QC report workflow output. Do you still want to implement this here?

lldelisle · 2026-04-15T12:05:35Z

Ah instead of doing 2 workflow output, just have one workflow output. I don't remember that we talked about it. Let's add it. I will try to do it tonight.

lldelisle · 2026-04-17T07:36:09Z

@wm75 I have done the change.

planemo-autoupdate and others added 7 commits April 6, 2026 08:39

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

2c51ad6

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

a863e46

Merge remote-tracking branch 'autoupdate/workflows/transcriptomics/rn…

443ee11

…aseq-sr' into update_both_RNAseq

Merge remote-tracking branch 'autoupdate/workflows/transcriptomics/rn…

dabf5bb

…aseq-pe' into update_both_RNAseq

update workflows

1ff63a2

change test due to change in multiqc order

8042a0f

change due to change fastqc -> falco

1267809

put back 2 MultiQC and change fastp version

5703d8b

put in CHANGELOG the fix for no featureCounts

48b942c

This was referenced Apr 10, 2026

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

Open

Updating workflows/transcriptomics/rnaseq-pe from 1.3 to 1.4 #1173

Open

add a pick param step to have a single workflow output

e6aa80c

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update both rnaseq workflows#1205

Update both rnaseq workflows#1205
lldelisle wants to merge 10 commits intogalaxyproject:mainfrom
lldelisle:update_both_RNAseq

lldelisle commented Apr 7, 2026

Uh oh!

lldelisle commented Apr 7, 2026

Uh oh!

github-actions bot commented Apr 8, 2026

Uh oh!

lldelisle commented Apr 8, 2026

Uh oh!

wm75 commented Apr 8, 2026

Uh oh!

wm75 commented Apr 8, 2026

Uh oh!

github-actions bot commented Apr 8, 2026

Workflow invocation details

Workflow invocation details

Uh oh!

lldelisle commented Apr 8, 2026

Uh oh!

lldelisle commented Apr 9, 2026

Uh oh!

wm75 commented Apr 15, 2026

Uh oh!

lldelisle commented Apr 15, 2026

Uh oh!

lldelisle commented Apr 17, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

lldelisle commented Apr 7, 2026

Uh oh!

lldelisle commented Apr 7, 2026

Uh oh!

github-actions bot commented Apr 8, 2026

Test Results (powered by Planemo)

Test Summary

Uh oh!

lldelisle commented Apr 8, 2026

Uh oh!

wm75 commented Apr 8, 2026

Uh oh!

wm75 commented Apr 8, 2026

Uh oh!

github-actions bot commented Apr 8, 2026

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Workflow invocation details

Uh oh!

lldelisle commented Apr 8, 2026

Uh oh!

lldelisle commented Apr 9, 2026

Uh oh!

wm75 commented Apr 15, 2026

Uh oh!

lldelisle commented Apr 15, 2026

Uh oh!

lldelisle commented Apr 17, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants