Hi All,
I am seeing a strange problem with Galaxy and bowtie. Here is the scenario:

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

Branden Timm
University of Wisconsin
Great Lakes Bioenergy Research Center

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