Error using test profile

[youpze]

Description of the bug

Hi,

When I tried to run the test profile provided from nf-core the pipeline crashed in the ISOSEQ3_REFINE process. Command exit status 139 and the command error was this:
.command.sh: line 8: 38 Segmentation fault isoseq3 refine -j 2 alz.chunk3_flnc.NEB_5p--NEB_Clontech_3p.bam primers.fasta alz.chunk3.bam

The nexflow logfile is added as a file.

I tried running the command provided below, using the containers singularity and conda. Both encountered the exact same issue.

nextflow run nf-core/isoseq -profile test,singularity --outdir /exports/sascstudent/yezegers/results/test/isoseq

I hope this helps to locate the issue.

Command used and terminal output

No response

Relevant files

nextflow_log_isoseq.txt

System information

I'm using the newest version of nextflow:

N E X T F L O W
      version 23.10.1 build 5891
      created 12-01-2024 22:01 UTC (23:01 CEST)
      cite doi:10.1038/nbt.3820
      http://nextflow.io

[gawxyz]

I got this error,too.

[gawxyz]

I solved this problem, which was caused by isoseq3 container
! image
modify the container tag 3.8.2 -->4.0.0 (or other version worked) in modules/nf-core/isoseq3/refine/main.nf

[sguizard]

Fixed with version 2.0.0