20881 Segmentation fault

[mguaita]

Hello,

I am trying to run IRFinder on a cluster (Linux) and got this issue:

IRFinderBAM: line 141: 20881 Segmentation fault ${LIBEXEC}/irfinder ${OUTPUTDIR} ${REF}/IRFinder/ref-cover.bed ${REF}/IRFinder/ref-sj.ref ${REF}/IRFinder/ref-read-continues.ref ${REF}/IRFinder/ref-ROI.bed ${READ_TYPE} "${AI_WARN}:${AI_INTRON}" $1 >> $OUTPUTDIR/logs/irfinder.stdout 2>> $OUTPUTDIR/logs/irfinder.stderr

The irfinder.stderr is empty and the irfinder.stdout has the following output:

 --------------------
|  IRFinder v. 2.0.0 |
 --------------------

---
IRFinder version: 2.0.0
IRFinder start:  Thu Apr 28 14:20:46 CEST 2022
IRFinder runmode: BAM
IRFinder user@host: user @ node-c02
IRFinder working dir:  /IRFinder
IRFinder reference: /IRFinder/REF/hg38_ensembl
IRFinder file 1:  /mydir/test.bam
---
[  Thu Apr 28 14:20:46 CEST 2022  ] Processing the BAM file with IRFinder
---
WARNING! The given bam file is sorted by coordinate and is paired. The process will be slightly slower.
IRFinder run with options:
 - Output Dir:                 /IRFinder/RES/test
 - Main intron ref.:           /IRFinder/REF/hg38_ensembl/IRFinder/ref-cover.bed
 - Splice junction ref.:       /IRFinder/REF/hg38_ensembl/IRFinder/ref-sj.ref
 - Read spans ref.:            /IRFinder/REF/hg38_ensembl/IRFinder/ref-read-continues.ref
 - Optional ROI ref.:          /IRFinder/REF/hg38_ensembl/IRFinder/ref-ROI.bed
 - Read type:                  SR
 - AI levels:                  1:1
 - Input BAM:                  /mydir/test.bam

It seems that it doesn't even start to run.

Thank you!

[CloXD]

Hello @mguaita , sorry for the issue. I guess you are using the docker or singularity image given your stdout. I think the issue is related to the directory you are using to run your experiment, /IRFinder/, that is the same of the IRFinder source in the image. Another thing could be the position of the bam file: be sure to mount the directory correctly if you are using docker or singularity. Try moving the reference to another directory, such as /IRFinder_REF/ For example with singularity you can use the environmental variable SINGULARITY_BINDPATH:

export SINGULARITY_BINDPATH="/mydir/,/IRFinder_REF/"

I hope this will help. Keep me updated if you can ;) Cheers Claudio