Segmentation fault (core dumped) when run IRfinder BAM

[yalanyang]

Hi, when I run IRfinder BAM using: IRFinder BAM -r Hg38 Sorted.bam
There is an error reported:
IRFinderBAM: line 163: 51805 Segmentation fault (core dumped) ${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}:${AI_INTRON}:${AI_RATIO}" "${JITTER}" $1 >> $OUTPUTDIR/logs/irfinder.stdout 2>> $OUTPUTDIR/logs/irfinder.stderr

Could you help me to solve this problem?
Thank you very much.
Best,
Yalan

[CloXD]

Hi Yalan,
It's a generic error, I would appreciate more information to help you.
Could you provide the content of the files in the output directory /logs/irfinder.stderr and /logs/irfinder.stdout?
Was the bam file generated using the same reference in the folder Hg38?
Cheers
Claudio

[yalanyang]

Hi, Claudio,
Thank you for your reply.
There was no content in the /logs/irfinder.stderr file. and the content in /logs/irfinder.stdout are:

| IRFinder v. 2.0.0 |

---

IRFinder version: 2.0.0
IRFinder start: Tue Aug 1 16:23:23 CDT 2023
IRFinder runmode: BAM
IRFinder working dir: /IRfinder
IRFinder reference: Hg38
IRFinder file 1: Sorted.bam

[ Tue Aug 1 16:23:23 CDT 2023 ] Processing the BAM file with IRFinder

IRFinder run with options:

• Output Dir: IRfinder
• Main intron ref.: Hg38/IRFinder/ref-cover.bed
• Splice junction ref.: Hg38/IRFinder/ref-sj.ref
• Read spans ref.: Hg38/IRFinder/ref-read-continues.ref
• Optional ROI ref.: Hg38/IRFinder/ref-ROI.bed
• Read type: SR
• AI levels: 1:1
• Input BAM: Sorted.bam

Yes, I used the same reference. Actually, I could run IRfinder-S successfully a month ago, I don't know why it's doesn't work now.

Best,
Yalan

[CloXD]

Hi Yalan,
that's quite strange... few more questions:

• Are you using Singularity, Docker or a local installation?
• Does the command run for a while and then it stops or it stops immediately?
• Have you tried with the unsorted ( sort by name ) bam file? it might help in case of low memory issues
• Could you copy-paste the exact command you are using?
  Sorry for the inconvenience, I hope we can solve the issue.
  Cheers,
  Claudio