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