On Feb 13, 2012, at 9:45 AM, Nate Coraor wrote:

> On Feb 8, 2012, at 9:32 PM, Fields, Christopher J wrote:
>> 'samtools sort' seems to be running on our server end as well (not on the 
>> cluster).  I may look into it a bit more myself.  Snapshot of top off our 
>> server (you can see our local runner as well):
>> PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND           
>> 3950 galaxy    20   0 1303m 1.2g  676 R 99.7 15.2 234:48.07 samtools sort 
>> /home/a-m/galaxy/dist-database/file/000/dataset_587.dat 
>> /home/a-m/galaxy/dist-database/tmp/tmp9tv6zc/sorted
>> 5417 galaxy    20   0 1186m 104m 5384 S  0.3  1.3   0:15.08 python 
>> ./scripts/paster.py serve universe_wsgi.runner.ini --server-name=runner0 
>> --pid-file=runner0.pid --log-file=runner0.log --daemon
> Hi Chris,
> 'samtools sort' is run by groom_dataset_contents, which should only be called 
> from within the upload tool, which should run on the cluster unless you still 
> have the default local override for it in your job runner's config file.

Yes, that is likely the problem.  Our cluster was running an old version of 
python (v2.4) that was also UCS2 (bx_python broke), so we were running locally. 
 That was rectified this past week (the admins insisted on not installing a 
python version locally, so we insisted back they install something modern using 
UCS4).  I tested a single upload with success off the cluster, so I would guess 
this is rectified (I'll confirm that).

Is there any information on data grooming on the wiki?  I only found info 
relevant to FASTQ grooming, not SAM/BAM.

> Ryan's instance is running 'samtools index' which is in set_meta which is 
> supposed to be run on the cluster if set_metadata_externally = True, but can 
> be run locally under certain conditions.
> --nate

Will have to check, but I believe we have not set that yet either.  We are in 
the midst of moving all jobs to the cluster, just rectifying the various issues 
with disparate python versions, etc. which now seem to be rectified, so that 
will shortly be resolved as well.


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