STAR mapping error

[Him26]

Hi, I am using STAR to find fusion transcripts and may be use cufflinks to quantify the transcripts. below is my command for 2ndpass mapping.

$STAR_HOME/STAR --runThreadN $CORE \
--genomeDir $GDIR \
--readFilesIn $READ1 $READ2 \
--readFilesCommand zcat \
--sjdbGTFfile $GTF \
--quantMode TranscriptomeSAM GeneCounts \
--outSAMattributes NH HI NM MD AS nM XS \
--chimSegmentMin 12 \
--chimJunctionOverhangMin 12 \
--alignSJDBoverhangMin 10 \
--outSAMtype BAM Unsorted

I gave 40gb of memory. It ran fine with one sample test but when I generated index with multisample and tried the 2nd pass mapping
it gave me the following error

terminate called after throwing an instance of 'std:ut_of_range'
what(): vector::_M_range_check
/opt/gridengine/default/spool/r-slave-1-3/job_scripts/581271: line 76: 26016 Aborted (core dumped) $ST

This happens while processing the gtf file.
Is there somthing wrong with my new SAindex ? how do I fix this?
If I want to try the option --alignMatesGapMax --alignIntronMax with bigger numbers the process would get killed. Is there a limit on this?
Thank you.

[alexdobin]

Hi, I am using STAR to find fusion transcripts and may be use cufflinks to quantify the transcripts. below is my command for 2ndpass mapping.

$STAR_HOME/STAR --runThreadN $CORE \
--genomeDir $GDIR \
--readFilesIn $READ1 $READ2 \
--readFilesCommand zcat \
--sjdbGTFfile $GTF \
--quantMode TranscriptomeSAM GeneCounts \
--outSAMattributes NH HI NM MD AS nM XS \
--chimSegmentMin 12 \
--chimJunctionOverhangMin 12 \
--alignSJDBoverhangMin 10 \
--outSAMtype BAM Unsorted

I gave 40gb of memory. It ran fine with one sample test but when I generated index with multisample and tried the 2nd pass mapping
it gave me the following error

terminate called after throwing an instance of 'std:ut_of_range'
what(): vector::_M_range_check
/opt/gridengine/default/spool/r-slave-1-3/job_scripts/581271: line 76: 26016 Aborted (core dumped) $ST

This happens while processing the gtf file.
Is there somthing wrong with my new SAindex ? how do I fix this?
If I want to try the option --alignMatesGapMax --alignIntronMax with bigger numbers the process would get killed. Is there a limit on this?
Thank you.

Hi @Him26,

please post or send me the Log.out file, and also a few hundred lines. It's likely that the problem is with GTF file formatting.

Cheers
Alex

[Him26]

My dumb mistake

Hi Alex,

Thank you for your reply.
I was looking through the gtf file and found that gtf file I was using had different 'chr' naming.
Gtf file I was using for the 1st mapping and 2nd mapping was different.
My bad for not checking this from the first place.

Thank you for your advice.