Branden,

Which revision of Galaxy are you using? What this sounds like is that it is taking a long time to set the metadata on the resulting SAM file, i.e., after the Bowtie job has run. Prior to 4698:48a81f235356 (12/1/10), all the lines in a large SAM file would be read to determine how many lines there were--this could take a very long time. But that changeset made it so that it gave up if the file was too large and did not set the number of lines. However, in 4842:7933d9312c38 (1/12/11), this was changed so that if the file is too large, it generates a rough estimate of the number of lines.

Regards,
Kelly

On Jan 12, 2011, at 5:32 PM, Branden Timm wrote:

> 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
> btimm@glbrc.wisc.edu
>
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