search

RitchieLabIGH / IRFinder

MIT License
13 stars 10 forks source link

Segmentation fault (core dumped) when run IRfinder BAM #32

Open yalanyang opened 1 year ago

yalanyang commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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:

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 commented 1 year ago

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