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  • Brian Bushnell
    replied
    You could also switch to something faster, such as BBMap or Star. A few minutes would probably still be way too short, depending on the input size.

    Leave a comment:


  • dpryan
    replied
    You need to request more time from the scheduler. Tophat takes hours to run, so try requesting a day to be safe.

    Leave a comment:


  • bbm
    started a topic tophat job killed by run time limit

    tophat job killed by run time limit

    I got my tophat running, and then it was killed after a few minutes.


    My output file said the job was killed after reaching LSF run time limit.
    Exited with exit code 140.


    This is the error file:
    [2014-09-12 16:32:42] Beginning TopHat run (v2.0.12)
    -----------------------------------------------
    [2014-09-12 16:32:42] Checking for Bowtie
    Bowtie version: 2.2.1.0
    [2014-09-12 16:32:42] Checking for Samtools
    Samtools version: 0.1.19.0
    [2014-09-12 16:32:42] Checking for Bowtie index files (genome)..
    [2014-09-12 16:32:42] Checking for reference FASTA file
    [2014-09-12 16:32:42] Generating SAM header for /gpfs_share/hlibyar/tophat/Am_genome
    [2014-09-12 16:33:03] Preparing reads
    left reads: min. length=12, max. length=100, 35244255 kept reads (1989 discarded)
    Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
    [2014-09-12 16:49:20] Mapping left_kept_reads to genome Am_genome with Bowtie2
    User defined signal 2


    --

    I appreciate any insights you can give!

    Regards,
    bbm

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