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.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to