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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/