Error exit status (1) in NFCORE_CHIPSEQ:CHIPSEQ:CUSTOM_DUMPSOFTWAREVERSIONS

[nayem-haque]

Description of the bug

Hi all, I am trying to process my ChIP-seq data using the nf-core pipeline. It is pretty much finished but running into an error in the second to last step:

The error code I received was this:

I went to the work directory and opened the collated_versions.yml file and went to line 79, column 4 and found this (indicated by red star):

So it looks like the text here is shifted and should be in column 1, however, I cannot find how to fix this issue, and it seems to be doing this for all collated_versions.yml files. If it helps, I added --nomodel and --extsize 147 in the main.nf file in macs2/callpeak since there were too few peaks to build a shifting model. I dont know if this is the cause of the error:

Any help would be greatly appreciated.

Command used and terminal output

No response

Relevant files

*Changed file format to .txt so it can upload here. Please find attached the dumpsoftwareversions.py and the main.nf files.

dumpsoftwareversions.txt
main.txt

System information

Nextflow version: 22.10.4.5836
Hardware: HPC
Executor: Slurm
Container engine: Singularity
Version of nf-core/chipseq: 2.0.0

[JoseEspinosa]

Sorry for the late reply, for what I understand you are modifying the dumpsoftwareversions.py in principle the original script is working without any issue in most of the nf-core pipelines, and I have never seen the error you reported. I will advice you to use the original released pipeline and if you keep having issues, do not hesitate to ask again.

[nayem-haque]

I didn't modify dumpsoftwareversions.py . I ended up having to shift the two lines of code I entered for main.nf and that fixed the issue.

The original released pipeline did not work for my data, as MACS2 was unable to call peaks. So I had to add --nomodel and --extsize 147 to main.nf .