Hi,

I just noticed that this was another case of a tool that needs more then the 1GB memory that is default on our cluster. After adjusting the job_runner settings everything seems fine.


regards, Andreas

On 15.11.2012 09:08, Andreas Kuntzagk wrote:
Hi,

when I start a lastz job it submits a job to GridEngine. But this job seems to 
hang.
The process running is

python /data/galaxy/galaxy-dist/tools/sr_mapping/lastz_wrapper.py --ref_source= 
...

This wrapper seems to not start a lastz but lastz is in the path.
After 2 days then Galaxy shows "Job did not produce output"

Here is the paster.log from the start of the job.


galaxy.jobs DEBUG 2012-11-15 09:03:07,539 (254) Working directory for job is:
/data/galaxy/galaxy-dist/database/job_working_directory/000/254
galaxy.jobs.handler DEBUG 2012-11-15 09:03:07,540 dispatching job 254 to drmaa 
runner
galaxy.jobs.handler INFO 2012-11-15 09:03:07,688 (254) Job dispatched
galaxy.tools DEBUG 2012-11-15 09:03:07,980 Building dependency shell command 
for dependency 'lastz'
galaxy.tools WARNING 2012-11-15 09:03:07,981 Failed to resolve dependency on 
'lastz', ignoring
galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,669 (254) submitting file
/data/galaxy/galaxy-dist/database/pbs/galaxy_254.sh
galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,670 (254) command is: python
/data/galaxy/galaxy-dist/tools/sr_mapping/lastz_wrapper.py       
--ref_source=cached
--source_select=pre_set       --out_format=sam
--input2=/data/galaxy/galaxy-dist/database/files/027/dataset_27795.dat
--input1="/data/galaxy/galaxy-dist/tool-data/shared/ucsc/hg18/seq/hg18.2bit"
--ref_sequences="None"          --pre_set_options=yasra98       --identity_min=0
--identity_max=100       --coverage=0
--output=/data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy_dataset_27800.dat
     --unmask=yes       --lastzSeqsFileDir=/data/galaxy/galaxy-dist/tool-data; 
cd
/data/galaxy/galaxy-dist; /data/galaxy/galaxy-dist/set_metadata.sh 
./database/files
/data/galaxy/galaxy-dist/database/job_working_directory/000/254 .
/data/galaxy/galaxy-dist/universe_wsgi.ini 
/data/galaxy/galaxy-dist/database/tmp/tmpL4MMJV
/data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy.json
/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_in_HistoryDatasetAssociation_288_9ynzEN,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_kwds_HistoryDatasetAssociation_288_AEIseO,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_out_HistoryDatasetAssociation_288_RhsufT,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_results_HistoryDatasetAssociation_288_86DYsR,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy_dataset_27800.dat,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_override_HistoryDatasetAssociation_288_HMRNEG

galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,676 run as user 
['kuntzagk', '600']
galaxy.jobs DEBUG 2012-11-15 09:03:08,676 (254) Changing ownership of working 
directory with:
/usr/bin/sudo -E scripts/external_chown_script.py
/data/galaxy/galaxy-dist/database/job_working_directory/000/254 kuntzagk 600
galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:09,148 (254) Job script for 
external submission is:
/data/galaxy/galaxy-dist/database/pbs/254.jt_json
141.80.188.178 - - [15/Nov/2012:09:03:10 +0200] "POST 
/galaxy/root/history_item_updates HTTP/1.1"
200 - "http://bbc.mdc-berlin.de/galaxy/history"; "Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:16.0)
Gecko/20100101 Firefox/16.0"
galaxy.jobs.runners.drmaa INFO 2012-11-15 09:03:11,553 (254) queued as 1282605
galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:11,767 (254/1282605) state 
change: job is running


--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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