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Old 11-09-2009, 09:04 AM   #1
spb2003
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Location: seattle

Join Date: Feb 2009
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Default Alloc error in Tophat

Hello All,

I have been running tophat on Solexa RNAseq data. A few times, tophat crashes for certain lane data with the following error:

Found 0 potential split-segment junctions
Indexing extensions in tophat_s3/tmp//left_kept_reads_missing.fq
Total extensions: 132496606
Looking for junctions by island end pairings
Adding hits from segment file 0 to coverage map
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Aborted

Is this an out of memory error? I am inclined to think so but wanted to check if somebody has come across this problem before and it was not due to memory allocation. I am working with a small memory size, 4 GB and this has happened maybe in 5% of all my tophat runs.

Looking at the logs, the command being run when this happens is:

/usr/local/bin/segment_juncs --fastq --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.0 --output-dir tophat_s3/ --max-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --no-closure-search --no-microexon-search --ium-reads tophat_s3/tmp//left_kept_reads_missing.fq /home/solexa/bowtie/indexes/hg18andsplice.fa tophat_s3/tmp//segment.juncs tophat_s3/left_kept_reads.fq tophat_s3/tmp//left_kept_reads.bwtout

Thanks in advance for your help.
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Old 11-09-2009, 09:47 AM   #2
Cole Trapnell
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Yes, this is an out of memory error, and the error is occuring duing one of TopHat's more memory intensive phases (assuming you are using reads shorter than 75bp). Do you have access to a larger memory machine?
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Old 11-09-2009, 01:03 PM   #3
spb2003
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Thanks for the reply. I was going to add memory to my machine soon. I think now is a good time.
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