Hello Ray
One of my colleagues encountered a similar-sounding error on our local test instance, where an unsorted BAM file seemed to crash the Galaxy handler processes and prevented them from restarting.
In our case the default samtools version in the Galaxy environment was 0.1.18; we found that updating this to samtools 1.2 fixed the crash problem.
Hope this helps,
Best wishes
Peter
On 24/05/16 11:07, Raymond Wan wrote:
Dear all,
We are experiencing a crash of our Galaxy instance (latest git log is early January 2016) and it seems unable to restart. The last entries in paster.log says the following:
galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,593 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,622 Enabling 'history_contents' API controller, class: HistoryContentsController [bam_index_core] the alignment is not sorted (XXX): 21-th chr > 11-th chr [bam_index_build2] fail to index the BAM file. galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,632 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController [bam_index_core] the alignment is not sorted (XXX): 24-th chr > 9-th chr [bam_index_build2] fail to index the BAM file. galaxy.datatypes.metadata DEBUG 2016-05-24 17:46:42,638 setting metadata externally failed for HistoryDatasetAssociation 442: External set_meta() not called galaxy.jobs.runners.slurm WARNING 2016-05-24 17:46:42,642 (313/189770) Job not found, assuming job check exceeded MinJobAge and completing as successful
So, the system cannot start and if we visit the site, it says "503 Service Temporarily Unavailable".
The log file seems to indicate some problem with the sorting of the BAM file. The problem looks a bit like something from 9 months ago (https://www.biostars.org/p/159336/), but the messages I've seen do not indicate that the problem prevents Galaxy from starting up.
I would have thought if there is a problem with the input file, the job would have failed, but not affect Galaxy from starting up again. So, I'm wondering if that is the problem or maybe it's the line after about,
"setting metadata externally failed"
Has anyone seen this problem before or might have an idea about what to do about it?
Thank you in advance!
Ray ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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