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Old 09-07-2011, 04:09 AM   #1
Junior Member
Location: Cambridge

Join Date: Jan 2011
Posts: 7
Default Tophat cannot evoke bowtie from under qsub


I come across a strange problem. I have all the latest tophat, bowtie, samtools installed locally. All the tree programs are also in my $PATH.

When I run tophat on the test sequences it does not report any problems and produces the output files as expected.

however, when I run the same command but submitting it via qsub to the cluster, then tophat (which is evoked with the full path) starts up correctly but when it checks for bowtie it reports:
[Wed Sep 7 12:28:38 2011] Checking for Bowtie
Error locating program: bowtie
Any idea what could be wrong with the setup/configuration?
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