MACS3 is reporting that 100 paired reads are needed, even when single end data is used as input
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- Nextflow
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Description
Description of the bug
I have some low quality data where the second paired read had very low quality. As such, I tried to run chipseq version 2.1.0 with single-ended data as input.
This results in an error with the MACS3 step. MACS3 is reporting that 100 paired reads are needed:
WARNING @ 09 Jul 2026 02:09:00: [86 MB] #2 MACS3 needs at least 100 paired peaks at + and - strand to build the model, but can only find 0! Please make your MFOLD range broader and try again. If MACS3 still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead.
Command used and terminal output
nextflow run nf-core/chipseq --input samplesheet.csv --read_length 150 --outdir mouse_output_single_end2 --genome GRCm38 -profile singularity -r 2.1.0
Relevant files
No response
System information
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Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the report with the provided nf-core/chipseq command and single-end samples, then inspect the MACS3 step's handling of paired versus single-end input. Done means a single-end run no longer reports that paired reads are required and the MACS3 step proceeds successfully.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100