Question: Attempting To Use Parallelism In Bwa
0
Kevin C. Dorff • 10 wrote:
Hi,
I am using Python 2.7. I am running with an hg checked out, up to date
version of "https://bitbucket.org/galaxy/galaxy-dist/".
I am very new to Galaxy. I have an instance setup *and running*
locally. I
am able to perform routine actions such as uploading files, processing
with
Picard, and aligning with BWA. I have been able to make the jobs
execute
out our SGE cluster.
In order to better utilize my cluster, I attempted to enable
parallelism of
the tasks that support it (such as BWA) by configuring the *
universe_wsgi.ini* file with the parameter
use_tasked_jobs = True
When I do this and attempt execute a BWA alignment on a 4.1Gb fastq
file, I
am given the error
Result 256 from mv
/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-
python/database/job_working_directory/000/21/task_1/dataset_21.dat
/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-
python/database/files/000/dataset_21.dat
/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-
python/database/job_working_directory/000/21/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 25, in ?
import galaxy.model.mapping #need to load this before we unpickle,
in
order to setup properties assigned by the mappers
File
"/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-
python/lib/galaxy/model/__init__.py",
line 13, in ?
import galaxy.datatypes.registry
File
"/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-
python/lib/galaxy/datatypes/registry.py",
line 146
finally:
^
SyntaxError: invalid syntax
The alignment failed.
If you need the complete error message, contact me and I can supply
you
with it. It's too large to paste in-line and attachments aren't
allowed.
Is there more I need to do to enable parallel jobs (splitting of
input,
align, then merge)?
Any suggestions are greatly appreciated.
Kevin
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modified 6.4 years ago
by
Dannon Baker ♦ 3.7k
•
written
6.4 years ago by
Kevin C. Dorff • 10
