pipeline fails at same step each time

[lo-schwartz]

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]

Hi @lo-schwartz, I think your issue is related to using singularity and might be related to this: nextflow-io/nextflow#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]

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]

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: nextflow-io/nextflow#4272.

[apeltzer]

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 :-(