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.
$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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