Hi Raymond,

In case you didn't know, Galaxy likes to keep all BAM files in
coordinate sorted order with a BAI index (using samtools).
Somehow this is failing on your system (perhaps a suitable
version of samtools is not on the $PATH).

I'm sure a Galaxy expert can and will comment, but it looks like
while trying to sort the BAM file in order to index it, something
fails on the cluster side. This means the BAI index does not
exist, so Galaxy cannot access the BAM file metadata. I'm
still surprised if this is why Galaxy is not starting up - but
perhaps you've found a new bug?

If no one else has any suggestions and this is urgent, I would
try manually sorting and indexing the problem BAM file(s) outside
of Galaxy using samtools, and see if after that Galaxy can restart?

Peter

On Tue, May 24, 2016 at 11:07 AM, Raymond Wan <rwan.w...@gmail.com> 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
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