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
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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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