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Old 02-29-2016, 01:04 AM   #1
Him26
Member
 
Location: California US

Join Date: Aug 2011
Posts: 19
Default STAR mapping error

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.
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Old 02-29-2016, 08:17 AM   #2
alexdobin
Senior Member
 
Location: NY

Join Date: Feb 2009
Posts: 161
Default

Quote:
Originally Posted by Him26 View Post
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
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Old 03-09-2016, 03:17 PM   #3
Him26
Member
 
Location: California US

Join Date: Aug 2011
Posts: 19
Default 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.
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