I am seeing a strange problem with Galaxy and bowtie. Here is the
1) I run bowtie for Illumina data (bowtie 0.12.5 Linux x86_64) on a
fastqsanger input generated by FASTQ-Groomer
2) On the system, I see the bowtie_wrapper and bowtie subprocesses
start, with bowtie distributing across the four cores in the system
3) The bowtie and bowtie_wrapper processes stop a few minutes later, but
the history item still shows that it is running. This happens for about
20 minutes. Paster.log show constant POST history_item_updates
activities every three seconds, and the Galaxy server process itself
hogs 100% of one of the system's cores.
I've tried this both on our production galaxy site (RHEL 5.5, Python
2.4.3) and my local workstation (RHEL 6, Python 2.6.5).
As part of my troubleshooting, I've extracted the bowtie_wrapper command
from paster.log and run it on the command line. The tool completes
successfully in a few minutes, which confirms that the Galaxy server
process seems to be the culprit in this situation, not bowtie_wrapper.
Any help would be greatly appreciated. Cheers
University of Wisconsin
Great Lakes Bioenergy Research Center
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