'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

chris

On Jan 20, 2012, at 10:43 AM, Shantanu Pavgi wrote:

> 
> Just wanted to add that we have consistently seen this issue of 'samtools 
> index' running locally on our install. We are using SGE scheduler. Thanks for 
> pointing out details in the code Nate. 
> 
> --
> Shantanu.
> 
> 
> 
> On Jan 20, 2012, at 9:35 AM, Nate Coraor wrote:
> 
>> On Jan 18, 2012, at 11:54 AM, Ryan Golhar wrote:
>> 
>>> Nate - Is there a specific place in the Galaxy code that forks the samtools 
>>> index on bam files on the cluster or the head node?  I really need to track 
>>> this down.
>> 
>> Hey Ryan,
>> 
>> Sorry it's taken so long, I've been pretty busy.  The relevant code is in 
>> galaxy-dist/lib/galaxy/datatypes/binary.py, in the Bam class.  When Galaxy 
>> runs a tool, it creates a Job, which is placed inside a JobWrapper in 
>> lib/galaxy/jobs/__init__.py.  After the job execution is complete, the 
>> JobWrapper.finish() method is called, which contains:
>> 
>>                   if not self.app.config.set_metadata_externally or \
>>                    ( not 
>> self.external_output_metadata.external_metadata_set_successfully( dataset, 
>> self.sa_session ) \
>>                      and self.app.config.retry_metadata_internally ):
>>                       dataset.set_meta( overwrite = False )
>> 
>> Somehow, this conditional is being entered.  Since set_metadata_externally 
>> is set to True, presumably the problem is 
>> external_metadata_set_successfully() is returning False and 
>> retry_metadata_internally is set to True.  If you leave behind the relevant 
>> job files (cleanup_job = never) and have a look at the PBS and metadata 
>> outputs you may be able to see what's happening.  Also, you'll want to set 
>> retry_metadata_internally = False.
>> 
>> --nate
>> 
>>> 
>>> On Fri, Jan 13, 2012 at 12:54 PM, Ryan Golhar <ngsbioinformat...@gmail.com> 
>>> wrote:
>>> I re-uploaded 3 BAM files using the "Upload system file paths.  runner0.log 
>>> shows:
>>> 
>>> galaxy.jobs DEBUG 2012-01-13 12:50:08,442 dispatching job 76 to pbs runner
>>> galaxy.jobs INFO 2012-01-13 12:50:08,555 job 76 dispatched
>>> galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,697 (76) submitting file 
>>> /home/galaxy/galaxy-dist-9/database/pbs/76.sh
>>> galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,697 (76) command is: 
>>> python /home/galaxy/galaxy-dist-9/tools/data_source/upload.py 
>>> /home/galaxy/galaxy-dist-9 /home/galaxy/galaxy-dist-9/datatypes_conf.xml 
>>> /home/galaxy/galaxy-dist-9/database/tmp/tmpqrVYY7         
>>> 208:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_208_files:None
>>>          
>>> 209:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_209_files:None
>>>          
>>> 210:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_210_files:None;
>>>  cd /home/galaxy/galaxy-dist-9; /home/galaxy/galaxy-dist-9/set_metadata.sh 
>>> ./database/files ./database/tmp . datatypes_conf.xml 
>>> ./database/job_working_directory/76/galaxy.json 
>>> galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,699 (76) queued in 
>>> default queue as 114.localhost.localdomain
>>> galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:09,037 
>>> (76/114.localhost.localdomain) PBS job state changed from N to R
>>> galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:09,205 
>>> (76/114.localhost.localdomain) PBS job state changed from R to E
>>> galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:10,206 
>>> (76/114.localhost.localdomain) PBS job state changed from E to C
>>> galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:10,206 
>>> (76/114.localhost.localdomain) PBS job has completed successfully
>>> 
>>> 76.sh shows:
>>> [galaxy@bic pbs]$ more 76.sh 
>>> #!/bin/sh
>>> GALAXY_LIB="/home/galaxy/galaxy-dist-9/lib"
>>> if [ "$GALAXY_LIB" != "None" ]; then
>>>   if [ -n "$PYTHONPATH" ]; then
>>>       export PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
>>>   else
>>>       export PYTHONPATH="$GALAXY_LIB"
>>>   fi
>>> fi
>>> cd /home/galaxy/galaxy-dist-9/database/job_working_directory/76
>>> python /home/galaxy/galaxy-dist-9/tools/data_source/upload.py 
>>> /home/galaxy/galaxy-dist-9 /home/galaxy/galaxy-dist-9/datatypes_conf.xml 
>>> /home/galaxy
>>> /galaxy-dist-9/database/tmp/tmpqrVYY7         
>>> 208:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_208_files:None
>>>          209:/
>>> home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_209_files:None
>>>          210:/home/galaxy/galaxy-dist-9/database/job_working_dire
>>> ctory/76/dataset_210_files:None; cd /home/galaxy/galaxy-dist-9; 
>>> /home/galaxy/galaxy-dist-9/set_metadata.sh ./database/files ./database/tmp 
>>> . dataty
>>> pes_conf.xml ./database/job_working_directory/76/galaxy.json 
>>> 
>>> Right as the job ended I check the job output files:
>>> 
>>> [galaxy@bic pbs]$ ll
>>> total 4
>>> -rw-rw-r-- 1 galaxy galaxy 950 Jan 13 12:50 76.sh
>>> [galaxy@bic pbs]$ ll
>>> total 4
>>> -rw------- 1 galaxy galaxy   0 Jan 13 12:50 76.e
>>> -rw------- 1 galaxy galaxy   0 Jan 13 12:50 76.o
>>> -rw-rw-r-- 1 galaxy galaxy 950 Jan 13 12:50 76.sh
>>> 
>>> samtools is now running on the head node.
>>> 
>>> 
>>> Where does Galaxy decide how to run samtools?  Maybe I can add a check of 
>>> some sort to see what's going on?
>>> 
>>> 
>>> On Fri, Jan 13, 2012 at 10:53 AM, Nate Coraor <n...@bx.psu.edu> wrote:
>>> On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote:
>>> 
>>>> Any ideas as to how to fix this?  We are interested in using Galaxy to 
>>>> host all our NGS data.  If indexing on the head node is going to happen, 
>>>> then this is going to be an extremely slow process.
>>> 
>>> Could you post the contents of 
>>> /home/galaxy/galaxy-dist-9/database/pbs/62.sh ?
>>> 
>>> Although I have to admit this is really baffling.  The presence of this 
>>> line without an error:
>>> 
>>>  galaxy.datatypes.metadata DEBUG 2012-01-11 10:22:40,162 Cleaning up 
>>> external metadata files
>>> 
>>> Indicates that metadata was set externally and the relevant metadata files 
>>> were present on disk.
>>> 
>>> --nate
>>> 
>>> 
>>> 
>> 
>> 
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