i'm used to run gangstr on my bam files but recently we tried experiment by trimming our fastq sequences from 150bp to 100bp and 75bp and with these new bams i get this error :
2021-11-08_15-23-42: START
[GangSTR-2.4] ProgressMeter: Loading read group id 4 for sample 20
terminate called after throwing an instance of 'std::out_of_range'
what(): vector::_M_range_check
/usr/ccub/sge-8.1.8/ccub/spool/davis004/job_scripts/6443774 : ligne 23 : 4850 Abandon (core dumped)"$GANGSTR" --bam $OUTPUTDIR/$SAMPLE/$SAMPLE".RG.sort.mark.bam" --ref "$REF" --regions "$GANGSTR_REGIONS" --out $OUTPUTDIR/$SAMPLE/gangstr --verbose --readlength 75
gangstr exit code : 134
2021-11-08_15-23-45: END
i can send you my bam file if needed
do you have any idea what can be the problem?
thanks!
Marine
Hi,
i'm used to run gangstr on my bam files but recently we tried experiment by trimming our fastq sequences from 150bp to 100bp and 75bp and with these new bams i get this error :
2021-11-08_15-23-42: START [GangSTR-2.4] ProgressMeter: Loading read group id 4 for sample 20 terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check /usr/ccub/sge-8.1.8/ccub/spool/davis004/job_scripts/6443774 : ligne 23 : 4850 Abandon (core dumped)"$GANGSTR" --bam $OUTPUTDIR/$SAMPLE/$SAMPLE".RG.sort.mark.bam" --ref "$REF" --regions "$GANGSTR_REGIONS" --out $OUTPUTDIR/$SAMPLE/gangstr --verbose --readlength 75 gangstr exit code : 134 2021-11-08_15-23-45: END
i can send you my bam file if needed do you have any idea what can be the problem? thanks! Marine