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Old 09-17-2014, 07:15 AM   #1
Location: North Carolina

Join Date: Sep 2011
Posts: 38
Default 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:
[2014-09-12 16:32:42] Checking for Samtools
Samtools version:
[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!

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Old 09-17-2014, 07:35 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You need to request more time from the scheduler. Tophat takes hours to run, so try requesting a day to be safe.
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Old 09-17-2014, 09:19 AM   #3
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

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.
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