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.
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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