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  • 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.

  • #2
    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?

    Comment


    • #3
      Thanks for the reply. I was going to add memory to my machine soon. I think now is a good time.

      Comment

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