Cutandrun pipeline help :(

Hi! I’m beginner in nf-core pipelines world. I recently have a cut and run seq data for analysis, but I can’t get past the alignment step when using nf-core/cutandrun pipeline. The error is next: Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN. And I try many times but error is not always in the same sample. The pipeline configuration is:

revision 3.2.2
Profile Singularity
Genome GRCh38

and the execution script is:

nohup nextflow run
nf-core/cutandrun -r 3.2.2
–input /home/jjsantillan/cutandrun_org/concat_org/samplesheet_org.csv
–outdir /home/jjsantillan/cutandrun_org/resultados
–genome GRCh38
-profile singularity -with-report reporte_org06.html

Thank you for your help!

Hi, @FideoEspacial. Welcome to the forum :smiley:

Please, share a file with the full output and the .nextflow.log file.

Does it work when you run the test profile -profile singularity,test?

Hi @mribeirodantas

Thanks for your reply. When I run the test, the pipeline works “succesfully” (but with some errors) here is the report of the test (
pipeline_report_test_singularity.txt (3,0 KB))

The problem is when I work with my own data. Here’s the report:
pipeline_report_my_data.txt (4,3 KB)
I’m having trouble finding the .nextflow.log file, but I found the bowtie2.log file which has no info.
I hope this information helps, if not could you explain how to get the documents you need?

Thank you

The .nextflow.log file is stored where you ran your nextflow command. Pay attention to the . before, as it’s a hidden file.

What are the errors that you get when you run with the test profile?

Thank you so much @mribeirodantas !

I found the file:
.nextflow.log (237,1 KB)

and the errors in the test are:

I hope this information helps.

Does it work if you run without Nextflow (but with the same command in the script block) the samples that errored out?

I didn’t try this

Could you please try? So that we can exclude it’s not a bowtie2/data/parameters issue.