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.
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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