Galaxy shouldn't be trying to do that, but it also shouldn't cause metadata to fail.
On Jan 20, 2012, at 10:52 AM, Ryan Golhar wrote: > Thanks Nate. I'll play with that. Could it be that Galaxy is trying to > reset the permissions or ownership of the imported BAM files. I'm not > copying them into Galaxy, rather I am linking to them. That is the only > error I see in runner0.log that indicates any type of failure. > > On Fri, Jan 20, 2012 at 10:35 AM, Nate Coraor <n...@bx.psu.edu> 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 > > > > > > > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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