Update ChIP PE #963

lldelisle · 2025-10-03T12:32:21Z

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

lldelisle · 2025-10-03T12:33:09Z

The annotation of my workflow is:
Complete ChIP-seq analysis for paired-end sequencing data. It goes from fastqs to peaks and coverage.
Is it OK?

github-actions · 2025-10-03T12:56:06Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ chipseq-pe.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: PE fastq input:
- step_state: scheduled
Step 2: Percentage of bad quality bases per read:
- step_state: scheduled

Step 11: Bigwig from MACS2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -v "^track" '/tmp/tmpusn_gcn_/files/1/5/1/dataset_1517c302-dec5-472c-bc4c-5bb15bbd45d3.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len' '/tmp/tmpusn_gcn_/job_working_directory/000/8/outputs/dataset_310a7b4d-4926-4618-864d-34f2146ce884.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__	`"6376fc76a05711f099ef6045bd007b6d"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
dbkey	`"mm10"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Step 12: MultiQC:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpusn_gcn_/files/e/b/b/dataset_ebbd20ab-e78b-48bc-8822-d2f9a65aa8ff.dat' 'multiqc_WDir/fastp_0/wt_H3K4me3fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/wt_H3K4me3fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/bowtie2_1 &&         grep -Pq '% overall alignment rate' /tmp/tmpusn_gcn_/files/5/d/6/dataset_5d6b55aa-91b0-4f71-aa74-9e71925679b3.dat || die "Module 'bowtie2: '% overall alignment rate' not found in the file 'wt_H3K4me3'" && ln -s '/tmp/tmpusn_gcn_/files/5/d/6/dataset_5d6b55aa-91b0-4f71-aa74-9e71925679b3.dat' 'multiqc_WDir/bowtie2_1/wt_H3K4me3'  &&    mkdir multiqc_WDir/macs2_2 &&    grep -q "# This file is generated by MACS" /tmp/tmpusn_gcn_/files/9/a/0/dataset_9a0b34be-2fba-48d8-bef9-2d6fa95294af.dat || die "'# This file is generated by MACS' not found in the file" && ln -s '/tmp/tmpusn_gcn_/files/9/a/0/dataset_9a0b34be-2fba-48d8-bef9-2d6fa95294af.dat' 'multiqc_WDir/macs2_2/wt_H3K4me3_peaks.xls' &&   multiqc multiqc_WDir --filename 'report'    --export   && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.27

     version_check | MultiQC Version v1.31 now available!
       file_search | Search path: /tmp/tmpusn_gcn_/job_working_directory/000/9/working/multiqc_WDir

             macs2 | Found 1 logs
           bowtie2 | Found 1 reports
             fastp | Found 1 reports
     write_results | Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag

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

Standard Output:

total 704
-rw-r--r-- 1 1001 1001    199 Oct  3 12:54 bowtie2_pe_plot.txt
-rw-r--r-- 1 1001 1001   1530 Oct  3 12:54 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 1001   1089 Oct  3 12:54 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001   1048 Oct  3 12:54 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001   1100 Oct  3 12:54 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001   1048 Oct  3 12:54 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    679 Oct  3 12:54 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    703 Oct  3 12:54 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    786 Oct  3 12:54 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    835 Oct  3 12:54 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    858 Oct  3 12:54 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    863 Oct  3 12:54 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    856 Oct  3 12:54 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    863 Oct  3 12:54 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    102 Oct  3 12:54 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 1001    894 Oct  3 12:54 multiqc.log
-rw-r--r-- 1 1001 1001    393 Oct  3 12:54 multiqc_bowtie2.txt
-rw-r--r-- 1 1001 1001    422 Oct  3 12:54 multiqc_citations.txt
-rw-r--r-- 1 1001 1001 537217 Oct  3 12:54 multiqc_data.json
-rw-r--r-- 1 1001 1001  88291 Oct  3 12:54 multiqc_fastp.txt
-rw-r--r-- 1 1001 1001    393 Oct  3 12:54 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001    196 Oct  3 12:54 multiqc_macs.txt
-rw-r--r-- 1 1001 1001     47 Oct  3 12:54 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001    413 Oct  3 12:54 multiqc_sources.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6376fc76a05711f099ef6045bd007b6d"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
comment	`""`
dbkey	`"mm10"`
export	`true`
flat	`false`
image_content_input	`None`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 3, "input": {"values": [{"id": 6, "src": "hdca"}]}, "software": "bowtie2"}}, {"__index__": 2, "software_cond": {"__current_case__": 16, "input": {"values": [{"id": 8, "src": "hdca"}]}, "software": "macs2"}}]`
title	`""`

Step 3: Reference genome:
- step_state: scheduled
Step 4: Effective genome size:
- step_state: scheduled
Step 5: Normalize profile:
- step_state: scheduled

Step 6: Fastp (remove adapter and bad quality reads):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmpusn_gcn_/files/8/8/b/dataset_88b94ddb-5d8b-4c84-ba51-2b0fead5f389.dat' 'wt_H3K4me3.fastqsanger.gz' && ln -sf '/tmp/tmpusn_gcn_/files/1/2/9/dataset_1298947a-5207-4c5f-aaf7-30e889eb9d7f.dat' 'wt_H3K4me3_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for wt_H3K4me3.fastqsanger.gz'  -i 'wt_H3K4me3.fastqsanger.gz'   -I 'wt_H3K4me3_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                       -q 30 -u 70                            && mv first.fastqsanger.gz '/tmp/tmpusn_gcn_/job_working_directory/000/3/outputs/dataset_a466cccb-b7c5-48ce-ac67-380a8c38ef02.dat' && mv second.fastqsanger.gz '/tmp/tmpusn_gcn_/job_working_directory/000/3/outputs/dataset_fe933b2f-7a8d-47f9-ba5a-cb74993ed90a.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 50000
total bases: 2550000
Q20 bases: 2486726(97.5187%)
Q30 bases: 2377575(93.2382%)
Q40 bases: 936574(36.7284%)

Read2 before filtering:
total reads: 50000
total bases: 2550000
Q20 bases: 2388223(93.6558%)
Q30 bases: 2254599(88.4156%)
Q40 bases: 860843(33.7585%)

Read1 after filtering:
total reads: 47581
total bases: 2425445
Q20 bases: 2380779(98.1584%)
Q30 bases: 2290757(94.4469%)
Q40 bases: 924416(38.1133%)

Read2 after filtering:
total reads: 47581
total bases: 2425445
Q20 bases: 2354909(97.0918%)
Q30 bases: 2237103(92.2347%)
Q40 bases: 859699(35.445%)

Filtering result:
reads passed filter: 95162
reads failed due to low quality: 4810
reads failed due to too many N: 28
reads failed due to too short: 0
reads with adapter trimmed: 198
bases trimmed due to adapters: 2404

Duplication rate: 0.002%

Insert size peak (evaluated by paired-end reads): 36

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

fastp --thread 1 --report_title fastp report for wt_H3K4me3.fastqsanger.gz -i wt_H3K4me3.fastqsanger.gz -I wt_H3K4me3_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz -q 30 -u 70 
fastp v1.0.1, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6376fc76a05711f099ef6045bd007b6d"`
chromInfo	`"/tmp/tmpusn_gcn_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "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": "70"}}`
output_options	`{"report_html": true, "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": null, "adapter_sequence2": null, "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 7: Bowtie2 map on reference:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;   ln -f -s '/tmp/tmpusn_gcn_/files/a/4/6/dataset_a466cccb-b7c5-48ce-ac67-380a8c38ef02.dat' input_f.fastq.gz &&  ln -f -s '/tmp/tmpusn_gcn_/files/f/e/9/dataset_fe933b2f-7a8d-47f9-ba5a-cb74993ed90a.dat' input_r.fastq.gz &&   THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x '/cvmfs/data.galaxyproject.org/byhand/mm10/bowtie2_index/mm10'   -1 'input_f.fastq.gz' -2 'input_r.fastq.gz'                2> >(tee '/tmp/tmpusn_gcn_/job_working_directory/000/4/outputs/dataset_5d6b55aa-91b0-4f71-aa74-9e71925679b3.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpusn_gcn_/job_working_directory/000/4/outputs/dataset_eed38044-70a8-4485-85df-16a07bf21b43.dat'

Exit Code:

```
0
```

Standard Error:

47581 reads; of these:
  47581 (100.00%) were paired; of these:
    1344 (2.82%) aligned concordantly 0 times
    42961 (90.29%) aligned concordantly exactly 1 time
    3276 (6.89%) aligned concordantly >1 times
    ----
    1344 pairs aligned concordantly 0 times; of these:
      267 (19.87%) aligned discordantly 1 time
    ----
    1077 pairs aligned 0 times concordantly or discordantly; of these:
      2154 mates make up the pairs; of these:
        1304 (60.54%) aligned 0 times
        537 (24.93%) aligned exactly 1 time
        313 (14.53%) aligned >1 times
98.63% overall alignment rate

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6376fc76a05711f099ef6045bd007b6d"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmpusn_gcn_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 1, "aligned_file": false, "input_1": {"values": [{"id": 4, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
reference_genome	`{"__current_case__": 0, "index": "mm10", "source": "indexed"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 8: filter MAPQ30 concordent pairs:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpusn_gcn_/files/e/e/d/dataset_eed38044-70a8-4485-85df-16a07bf21b43.dat' input.bam && ln -s '/tmp/tmpusn_gcn_/files/_metadata_files/8/d/c/metadata_8dcece34-5157-4d77-be18-723810d056b4.dat' input.bai && samtools view -o '/tmp/tmpusn_gcn_/job_working_directory/000/5/outputs/dataset_98278229-032f-42a7-abf2-68f4c29f19cb.dat' -h   -b  -q 30 -f 0x2 input.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bam"`
__workflow_invocation_uuid__	`"6376fc76a05711f099ef6045bd007b6d"`
bed_file	`None`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
dbkey	`"mm10"`
flag	`{"__current_case__": 1, "filter": "yes", "reqBits": ["0x0002"], "skipBits": null}`
header	`"-h"`
library	`""`
mapq	`"30"`
outputtype	`"bam"`
possibly_select_inverse	`false`
read_group	`""`
regions	`""`

Step 9: Call Peaks with MACS2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

export PYTHON_EGG_CACHE=`pwd` &&   (macs2 callpeak   -t '/tmp/tmpusn_gcn_/files/9/8/2/dataset_98278229-032f-42a7-abf2-68f4c29f19cb.dat'  --name wt_H3K4me3    --format BAMPE   --gsize '1870000000'      --SPMR     --call-summits  --keep-dup '1'  --d-min 20 --buffer-size 100000  --bdg  --qvalue '0.05'  --mfold '5' '50'  --bw '300'  2>&1 > macs2_stderr) && cp wt_H3K4me3_peaks.xls '/tmp/tmpusn_gcn_/job_working_directory/000/6/outputs/dataset_9a0b34be-2fba-48d8-bef9-2d6fa95294af.dat'   && ( count=`ls -1 wt_H3K4me3* 2>/dev/null | wc -l`; if [ $count != 0 ]; then mkdir '/tmp/tmpusn_gcn_/job_working_directory/000/6/outputs/dataset_0f693c54-2fc4-4e23-805d-d7f1e7f9c2c2_files' && cp -r wt_H3K4me3* '/tmp/tmpusn_gcn_/job_working_directory/000/6/outputs/dataset_0f693c54-2fc4-4e23-805d-d7f1e7f9c2c2_files' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/macs2/86e2413cf3f8/macs2/dir2html.py' '/tmp/tmpusn_gcn_/job_working_directory/000/6/outputs/dataset_0f693c54-2fc4-4e23-805d-d7f1e7f9c2c2_files' macs2_stderr > '/tmp/tmpusn_gcn_/job_working_directory/000/6/outputs/dataset_0f693c54-2fc4-4e23-805d-d7f1e7f9c2c2.dat'; fi; ) && exit_code_for_galaxy=$? && cat macs2_stderr 2>&1 && (exit $exit_code_for_galaxy)

Exit Code:

```
0
```

Standard Output:

INFO  @ Fri, 03 Oct 2025 12:53:40: 
# Command line: callpeak -t /tmp/tmpusn_gcn_/files/9/8/2/dataset_98278229-032f-42a7-abf2-68f4c29f19cb.dat --name wt_H3K4me3 --format BAMPE --gsize 1870000000 --SPMR --call-summits --keep-dup 1 --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --mfold 5 50 --bw 300
# ARGUMENTS LIST:
# name = wt_H3K4me3
# format = BAMPE
# ChIP-seq file = ['/tmp/tmpusn_gcn_/files/9/8/2/dataset_98278229-032f-42a7-abf2-68f4c29f19cb.dat']
# control file = None
# effective genome size = 1.87e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Paired-End mode is on
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1 read fragment files... 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1 read treatment fragments... 
INFO  @ Fri, 03 Oct 2025 12:53:40: 42745 fragments have been read. 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1 mean fragment size is determined as 202.0 bp from treatment 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1 fragment size = 202.0 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1  total fragments in treatment: 42745 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1 user defined the maximum fragments... 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1 filter out redundant fragments by allowing at most 1 identical fragment(s) 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1  fragments after filtering in treatment: 42745 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1  Redundant rate of treatment: 0.00 
INFO  @ Fri, 03 Oct 2025 12:53:40: #1 finished! 
INFO  @ Fri, 03 Oct 2025 12:53:40: #2 Build Peak Model... 
INFO  @ Fri, 03 Oct 2025 12:53:40: #2 Skipped... 
INFO  @ Fri, 03 Oct 2025 12:53:40: #3 Call peaks... 
INFO  @ Fri, 03 Oct 2025 12:53:40: #3 Going to call summits inside each peak ... 
INFO  @ Fri, 03 Oct 2025 12:53:40: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 03 Oct 2025 12:53:40: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 03 Oct 2025 12:53:40: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... wt_H3K4me3_treat_pileup.bdg 
INFO  @ Fri, 03 Oct 2025 12:53:40: #3   Write bedGraph files for control lambda (after scaling if necessary)... wt_H3K4me3_control_lambda.bdg 
INFO  @ Fri, 03 Oct 2025 12:53:40: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 03 Oct 2025 12:53:40: #3 Call peaks for each chromosome... 
INFO  @ Fri, 03 Oct 2025 12:53:40: #4 Write output xls file... wt_H3K4me3_peaks.xls 
INFO  @ Fri, 03 Oct 2025 12:53:40: #4 Write peak in narrowPeak format file... wt_H3K4me3_peaks.narrowPeak 
INFO  @ Fri, 03 Oct 2025 12:53:40: #4 Write summits bed file... wt_H3K4me3_summits.bed 
INFO  @ Fri, 03 Oct 2025 12:53:40: Done!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6376fc76a05711f099ef6045bd007b6d"`
advanced_options	`{"broad_options": {"__current_case__": 1, "broad_options_selector": "nobroad", "call_summits": true}, "buffer_size": "100000", "d_min": "20", "keep_dup_options": {"__current_case__": 1, "keep_dup_options_selector": "1"}, "llocal": null, "nolambda": false, "ratio": null, "slocal": null, "spmr": true, "to_large": false}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
control	`{"__current_case__": 1, "c_select": "No"}`
cutoff_options	`{"__current_case__": 1, "cutoff_options_selector": "qvalue", "qvalue": "0.05"}`
dbkey	`"mm10"`
effective_genome_size_options	`{"__current_case__": 4, "effective_genome_size_options_selector": "user_defined", "gsize": "1870000000"}`
format	`"BAMPE"`
nomodel_type	`{"__current_case__": 0, "band_width": "300", "mfold_lower": "5", "mfold_upper": "50", "nomodel_type_selector": "create_model"}`
outputs	`["peaks_tabular", "summits", "bdg", "html"]`
treatment	`{"__current_case__": 0, "input_treatment_file": {"values": [{"id": 11, "src": "dce"}]}, "t_multi_select": "No"}`

Step 10: summary of MACS2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator  -i -- '^#' '/tmp/tmpusn_gcn_/files/9/a/0/dataset_9a0b34be-2fba-48d8-bef9-2d6fa95294af.dat' > '/tmp/tmpusn_gcn_/job_working_directory/000/7/outputs/dataset_113b5991-7369-4992-8975-1bc8cdb7cc70.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6376fc76a05711f099ef6045bd007b6d"`
case_sensitive	`"-i"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
color	`"NOCOLOR"`
dbkey	`"mm10"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"^#"`

Other invocation details
- history_id
  - 652e48125c8552a0
- history_state
  - ok
- invocation_id
  - 652e48125c8552a0
- invocation_state
  - scheduled
- workflow_id
  - 652e48125c8552a0

github-actions · 2025-10-03T13:06:10Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ chipseq-pe.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: PE fastq input:
- step_state: scheduled
Step 2: Percentage of bad quality bases per read:
- step_state: scheduled

Step 11: Bigwig from MACS2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -v "^track" '/tmp/tmpk6bgvnfr/files/0/9/e/dataset_09e13733-79d8-4976-bcba-de0dcd949304.dat' | wigToBigWig stdin '/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len' '/tmp/tmpk6bgvnfr/job_working_directory/000/8/outputs/dataset_37270be0-efa0-48f3-8b71-be5d927ac4d3.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__	`"4d3c3b50a05811f0a35e6045bd85fced"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
dbkey	`"mm10"`
settings	`{"__current_case__": 0, "settingsType": "preset"}`

Step 12: MultiQC:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpk6bgvnfr/files/a/c/8/dataset_ac8f8624-9bf4-4326-9fab-49c098a1d2b4.dat' 'multiqc_WDir/fastp_0/wt_H3K4me3fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/wt_H3K4me3fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/bowtie2_1 &&         grep -Pq '% overall alignment rate' /tmp/tmpk6bgvnfr/files/7/3/d/dataset_73df4e17-2ff0-4dcb-ae78-0751764c3cc3.dat || die "Module 'bowtie2: '% overall alignment rate' not found in the file 'wt_H3K4me3'" && ln -s '/tmp/tmpk6bgvnfr/files/7/3/d/dataset_73df4e17-2ff0-4dcb-ae78-0751764c3cc3.dat' 'multiqc_WDir/bowtie2_1/wt_H3K4me3'  &&    mkdir multiqc_WDir/macs2_2 &&    grep -q "# This file is generated by MACS" /tmp/tmpk6bgvnfr/files/b/6/8/dataset_b6812dad-dc53-4022-ad8c-957b48965c23.dat || die "'# This file is generated by MACS' not found in the file" && ln -s '/tmp/tmpk6bgvnfr/files/b/6/8/dataset_b6812dad-dc53-4022-ad8c-957b48965c23.dat' 'multiqc_WDir/macs2_2/wt_H3K4me3_peaks.xls' &&   multiqc multiqc_WDir --filename 'report'    --export   && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.27

     version_check | MultiQC Version v1.31 now available!
       file_search | Search path: /tmp/tmpk6bgvnfr/job_working_directory/000/9/working/multiqc_WDir

             macs2 | Found 1 logs
           bowtie2 | Found 1 reports
             fastp | Found 1 reports
     write_results | Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag

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

Standard Output:

total 704
-rw-r--r-- 1 1001 1001    199 Oct  3 13:04 bowtie2_pe_plot.txt
-rw-r--r-- 1 1001 1001   1530 Oct  3 13:04 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 1001   1089 Oct  3 13:04 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001   1048 Oct  3 13:04 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001   1100 Oct  3 13:04 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001   1048 Oct  3 13:04 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    679 Oct  3 13:04 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    703 Oct  3 13:04 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    786 Oct  3 13:04 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    835 Oct  3 13:04 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    858 Oct  3 13:04 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    863 Oct  3 13:04 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    856 Oct  3 13:04 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    863 Oct  3 13:04 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    102 Oct  3 13:04 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 1001    894 Oct  3 13:04 multiqc.log
-rw-r--r-- 1 1001 1001    393 Oct  3 13:04 multiqc_bowtie2.txt
-rw-r--r-- 1 1001 1001    422 Oct  3 13:04 multiqc_citations.txt
-rw-r--r-- 1 1001 1001 537217 Oct  3 13:04 multiqc_data.json
-rw-r--r-- 1 1001 1001  88291 Oct  3 13:04 multiqc_fastp.txt
-rw-r--r-- 1 1001 1001    393 Oct  3 13:04 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001    196 Oct  3 13:04 multiqc_macs.txt
-rw-r--r-- 1 1001 1001     47 Oct  3 13:04 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001    413 Oct  3 13:04 multiqc_sources.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4d3c3b50a05811f0a35e6045bd85fced"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
comment	`""`
dbkey	`"mm10"`
export	`true`
flat	`false`
image_content_input	`None`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 3, "input": {"values": [{"id": 6, "src": "hdca"}]}, "software": "bowtie2"}}, {"__index__": 2, "software_cond": {"__current_case__": 16, "input": {"values": [{"id": 8, "src": "hdca"}]}, "software": "macs2"}}]`
title	`""`

Step 3: Reference genome:
- step_state: scheduled
Step 4: Effective genome size:
- step_state: scheduled
Step 5: Normalize profile:
- step_state: scheduled

Step 6: Fastp (remove adapter and bad quality reads):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmpk6bgvnfr/files/0/4/9/dataset_04942af0-37c7-43c4-a66d-96a54a81f7d4.dat' 'wt_H3K4me3.fastqsanger.gz' && ln -sf '/tmp/tmpk6bgvnfr/files/6/9/7/dataset_6972a70c-0ab5-4d86-b1d7-638719adebbe.dat' 'wt_H3K4me3_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for wt_H3K4me3.fastqsanger.gz'  -i 'wt_H3K4me3.fastqsanger.gz'   -I 'wt_H3K4me3_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                       -q 30 -u 70                            && mv first.fastqsanger.gz '/tmp/tmpk6bgvnfr/job_working_directory/000/3/outputs/dataset_525a8b83-d6d3-4edc-b676-3065dcc91983.dat' && mv second.fastqsanger.gz '/tmp/tmpk6bgvnfr/job_working_directory/000/3/outputs/dataset_f05e03e5-e28a-4bee-9dc5-d3d68bcc6210.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 50000
total bases: 2550000
Q20 bases: 2486726(97.5187%)
Q30 bases: 2377575(93.2382%)
Q40 bases: 936574(36.7284%)

Read2 before filtering:
total reads: 50000
total bases: 2550000
Q20 bases: 2388223(93.6558%)
Q30 bases: 2254599(88.4156%)
Q40 bases: 860843(33.7585%)

Read1 after filtering:
total reads: 47581
total bases: 2425445
Q20 bases: 2380779(98.1584%)
Q30 bases: 2290757(94.4469%)
Q40 bases: 924416(38.1133%)

Read2 after filtering:
total reads: 47581
total bases: 2425445
Q20 bases: 2354909(97.0918%)
Q30 bases: 2237103(92.2347%)
Q40 bases: 859699(35.445%)

Filtering result:
reads passed filter: 95162
reads failed due to low quality: 4810
reads failed due to too many N: 28
reads failed due to too short: 0
reads with adapter trimmed: 198
bases trimmed due to adapters: 2404

Duplication rate: 0.002%

Insert size peak (evaluated by paired-end reads): 36

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

fastp --thread 1 --report_title fastp report for wt_H3K4me3.fastqsanger.gz -i wt_H3K4me3.fastqsanger.gz -I wt_H3K4me3_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz -q 30 -u 70 
fastp v1.0.1, time used: 1 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4d3c3b50a05811f0a35e6045bd85fced"`
chromInfo	`"/tmp/tmpk6bgvnfr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "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": "70"}}`
output_options	`{"report_html": true, "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": null, "adapter_sequence2": null, "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 7: Bowtie2 map on reference:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;   ln -f -s '/tmp/tmpk6bgvnfr/files/5/2/5/dataset_525a8b83-d6d3-4edc-b676-3065dcc91983.dat' input_f.fastq.gz &&  ln -f -s '/tmp/tmpk6bgvnfr/files/f/0/5/dataset_f05e03e5-e28a-4bee-9dc5-d3d68bcc6210.dat' input_r.fastq.gz &&   THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x '/cvmfs/data.galaxyproject.org/byhand/mm10/bowtie2_index/mm10'   -1 'input_f.fastq.gz' -2 'input_r.fastq.gz'                2> >(tee '/tmp/tmpk6bgvnfr/job_working_directory/000/4/outputs/dataset_73df4e17-2ff0-4dcb-ae78-0751764c3cc3.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpk6bgvnfr/job_working_directory/000/4/outputs/dataset_4449fb76-447d-4e61-9ee5-2021f27f8474.dat'

Exit Code:

```
0
```

Standard Error:

47581 reads; of these:
  47581 (100.00%) were paired; of these:
    1344 (2.82%) aligned concordantly 0 times
    42961 (90.29%) aligned concordantly exactly 1 time
    3276 (6.89%) aligned concordantly >1 times
    ----
    1344 pairs aligned concordantly 0 times; of these:
      267 (19.87%) aligned discordantly 1 time
    ----
    1077 pairs aligned 0 times concordantly or discordantly; of these:
      2154 mates make up the pairs; of these:
        1304 (60.54%) aligned 0 times
        537 (24.93%) aligned exactly 1 time
        313 (14.53%) aligned >1 times
98.63% overall alignment rate

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4d3c3b50a05811f0a35e6045bd85fced"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmpk6bgvnfr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 1, "aligned_file": false, "input_1": {"values": [{"id": 4, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
reference_genome	`{"__current_case__": 0, "index": "mm10", "source": "indexed"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 8: filter MAPQ30 concordent pairs:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpk6bgvnfr/files/4/4/4/dataset_4449fb76-447d-4e61-9ee5-2021f27f8474.dat' input.bam && ln -s '/tmp/tmpk6bgvnfr/files/_metadata_files/e/b/d/metadata_ebd8dc46-5ad7-410f-96bd-8ec7cc320977.dat' input.bai && samtools view -o '/tmp/tmpk6bgvnfr/job_working_directory/000/5/outputs/dataset_6bc8a3d2-99a8-4a5a-ac4d-e5f3bdebbb08.dat' -h   -b  -q 30 -f 0x2 input.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"bam"`
__workflow_invocation_uuid__	`"4d3c3b50a05811f0a35e6045bd85fced"`
bed_file	`None`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
dbkey	`"mm10"`
flag	`{"__current_case__": 1, "filter": "yes", "reqBits": ["0x0002"], "skipBits": null}`
header	`"-h"`
library	`""`
mapq	`"30"`
outputtype	`"bam"`
possibly_select_inverse	`false`
read_group	`""`
regions	`""`

Step 9: Call Peaks with MACS2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

export PYTHON_EGG_CACHE=`pwd` &&   (macs2 callpeak   -t '/tmp/tmpk6bgvnfr/files/6/b/c/dataset_6bc8a3d2-99a8-4a5a-ac4d-e5f3bdebbb08.dat'  --name wt_H3K4me3    --format BAMPE   --gsize '1870000000'      --SPMR     --call-summits  --keep-dup '1'  --d-min 20 --buffer-size 100000  --bdg  --qvalue '0.05'  --mfold '5' '50'  --bw '300'  2>&1 > macs2_stderr) && cp wt_H3K4me3_peaks.xls '/tmp/tmpk6bgvnfr/job_working_directory/000/6/outputs/dataset_b6812dad-dc53-4022-ad8c-957b48965c23.dat'   && ( count=`ls -1 wt_H3K4me3* 2>/dev/null | wc -l`; if [ $count != 0 ]; then mkdir '/tmp/tmpk6bgvnfr/job_working_directory/000/6/outputs/dataset_0f60534c-85f0-4d8f-98d8-ba84e0107d6e_files' && cp -r wt_H3K4me3* '/tmp/tmpk6bgvnfr/job_working_directory/000/6/outputs/dataset_0f60534c-85f0-4d8f-98d8-ba84e0107d6e_files' && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/macs2/86e2413cf3f8/macs2/dir2html.py' '/tmp/tmpk6bgvnfr/job_working_directory/000/6/outputs/dataset_0f60534c-85f0-4d8f-98d8-ba84e0107d6e_files' macs2_stderr > '/tmp/tmpk6bgvnfr/job_working_directory/000/6/outputs/dataset_0f60534c-85f0-4d8f-98d8-ba84e0107d6e.dat'; fi; ) && exit_code_for_galaxy=$? && cat macs2_stderr 2>&1 && (exit $exit_code_for_galaxy)

Exit Code:

```
0
```

Standard Output:

INFO  @ Fri, 03 Oct 2025 13:03:54: 
# Command line: callpeak -t /tmp/tmpk6bgvnfr/files/6/b/c/dataset_6bc8a3d2-99a8-4a5a-ac4d-e5f3bdebbb08.dat --name wt_H3K4me3 --format BAMPE --gsize 1870000000 --SPMR --call-summits --keep-dup 1 --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --mfold 5 50 --bw 300
# ARGUMENTS LIST:
# name = wt_H3K4me3
# format = BAMPE
# ChIP-seq file = ['/tmp/tmpk6bgvnfr/files/6/b/c/dataset_6bc8a3d2-99a8-4a5a-ac4d-e5f3bdebbb08.dat']
# control file = None
# effective genome size = 1.87e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Paired-End mode is on
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1 read fragment files... 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1 read treatment fragments... 
INFO  @ Fri, 03 Oct 2025 13:03:54: 42745 fragments have been read. 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1 mean fragment size is determined as 202.0 bp from treatment 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1 fragment size = 202.0 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1  total fragments in treatment: 42745 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1 user defined the maximum fragments... 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1 filter out redundant fragments by allowing at most 1 identical fragment(s) 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1  fragments after filtering in treatment: 42745 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1  Redundant rate of treatment: 0.00 
INFO  @ Fri, 03 Oct 2025 13:03:54: #1 finished! 
INFO  @ Fri, 03 Oct 2025 13:03:54: #2 Build Peak Model... 
INFO  @ Fri, 03 Oct 2025 13:03:54: #2 Skipped... 
INFO  @ Fri, 03 Oct 2025 13:03:54: #3 Call peaks... 
INFO  @ Fri, 03 Oct 2025 13:03:54: #3 Going to call summits inside each peak ... 
INFO  @ Fri, 03 Oct 2025 13:03:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 03 Oct 2025 13:03:54: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 03 Oct 2025 13:03:54: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... wt_H3K4me3_treat_pileup.bdg 
INFO  @ Fri, 03 Oct 2025 13:03:54: #3   Write bedGraph files for control lambda (after scaling if necessary)... wt_H3K4me3_control_lambda.bdg 
INFO  @ Fri, 03 Oct 2025 13:03:54: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 03 Oct 2025 13:03:54: #3 Call peaks for each chromosome... 
INFO  @ Fri, 03 Oct 2025 13:03:54: #4 Write output xls file... wt_H3K4me3_peaks.xls 
INFO  @ Fri, 03 Oct 2025 13:03:54: #4 Write peak in narrowPeak format file... wt_H3K4me3_peaks.narrowPeak 
INFO  @ Fri, 03 Oct 2025 13:03:54: #4 Write summits bed file... wt_H3K4me3_summits.bed 
INFO  @ Fri, 03 Oct 2025 13:03:54: Done!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4d3c3b50a05811f0a35e6045bd85fced"`
advanced_options	`{"broad_options": {"__current_case__": 1, "broad_options_selector": "nobroad", "call_summits": true}, "buffer_size": "100000", "d_min": "20", "keep_dup_options": {"__current_case__": 1, "keep_dup_options_selector": "1"}, "llocal": null, "nolambda": false, "ratio": null, "slocal": null, "spmr": true, "to_large": false}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
control	`{"__current_case__": 1, "c_select": "No"}`
cutoff_options	`{"__current_case__": 1, "cutoff_options_selector": "qvalue", "qvalue": "0.05"}`
dbkey	`"mm10"`
effective_genome_size_options	`{"__current_case__": 4, "effective_genome_size_options_selector": "user_defined", "gsize": "1870000000"}`
format	`"BAMPE"`
nomodel_type	`{"__current_case__": 0, "band_width": "300", "mfold_lower": "5", "mfold_upper": "50", "nomodel_type_selector": "create_model"}`
outputs	`["peaks_tabular", "summits", "bdg", "html"]`
treatment	`{"__current_case__": 0, "input_treatment_file": {"values": [{"id": 11, "src": "dce"}]}, "t_multi_select": "No"}`

Step 10: summary of MACS2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator  -i -- '^#' '/tmp/tmpk6bgvnfr/files/b/6/8/dataset_b6812dad-dc53-4022-ad8c-957b48965c23.dat' > '/tmp/tmpk6bgvnfr/job_working_directory/000/7/outputs/dataset_4b8d48dd-65b3-479e-8272-44856a49d223.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4d3c3b50a05811f0a35e6045bd85fced"`
case_sensitive	`"-i"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len"`
color	`"NOCOLOR"`
dbkey	`"mm10"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"^#"`

Other invocation details
- history_id
  - a1de22bd2a454ce8
- history_state
  - ok
- invocation_id
  - a1de22bd2a454ce8
- invocation_state
  - scheduled
- workflow_id
  - a1de22bd2a454ce8

planemo-autoupdate and others added 2 commits September 29, 2025 05:16

Updating workflows/epigenetics/chipseq-pe from 0.15 to 0.16

7a0aff8

use fastp instead of cutadapt

f39f445

lldelisle mentioned this pull request Oct 3, 2025

Updating workflows/epigenetics/chipseq-pe from 0.15 to 0.16 #958

Closed

add the release

bc42806

fix test

c812e4b

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