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nf-core / smrnaseq

A small-RNA sequencing analysis pipeline
https://nf-co.re/smrnaseq
MIT License
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pipeline fails at same step each time #453

Open lo-schwartz opened 1 month ago

lo-schwartz commented 1 month ago

I have tried this pipeline multiple times but it fails at the same step every time. It does not complete and I am not sure why. 09_30_nextflow.log.1.pdf

atrigila commented 1 month ago

Hi @lo-schwartz, I think your issue is related to using singularity and might be related to this: https://github.com/nextflow-io/nextflow/discussions/4272. Could you try running the pipeline with docker to see if you still see the same issue? Also, could you try running the -dev version instead of master? Thank you

lo-schwartz commented 1 month ago

I tried using it with -r 2.3.1 \ but I am on an HPC and I do not think I will be able to use docker. I tried it again with singularity and it failed again the same way even with the version change.

nschcolnicov commented 1 month ago

Hi @lo-schwartz I tried to run the pipeline using your settings and wasn't able to reproduce the error.

Also. looking at the log: `NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMT OOLS_FLAGSTAT (BT474-7_mature_hairpin) terminated with an error exit status (151)` I think that the issue seems to be related to what @atrigila posted: https://github.com/nextflow-io/nextflow/discussions/4272.

apeltzer commented 1 month ago

Looks indeed like an issue with LSF + Singularity and not with the pipeline. Also tried your parameters with some samples and it passed / worked fine for me :-(