Question: Attempting To Use Parallelism In Bwa
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gravatar for Kevin C. Dorff
6.1 years ago by
Kevin C. Dorff10 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
bwa alignment • 1.1k views
ADD COMMENTlink modified 6.1 years ago by Dannon Baker3.7k • written 6.1 years ago by Kevin C. Dorff10
0
gravatar for Scott McManus
6.1 years ago by
Scott McManus130
Scott McManus130 wrote:
Hi Kevin- That's truly odd. The error happens when the offending file is imported, which means that it is a syntax issue that should have been seen earlier. I'll take a look at this soon (unless someone else beats me to it). In the meantime, of course, do not use the use_tasked_jobs on this instance of Galaxy. If others have seen similar issues, then please speak up. -Scott
ADD COMMENTlink written 6.1 years ago by Scott McManus130
0
gravatar for Dannon Baker
6.1 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:
Hi Kevin, I'm not able to reproduce this with python 2.7. Can you confirm that galaxy is indeed using the installed python 2.7 and not, perhaps, 2.4? The structure of python's try/except/finally clause changed with python 2.5 and if you were unintentionally running 2.4 that would explain this error. And lastly, regarding the parallelization of BWA, there's nothing else you need to do; setting use_tasked_jobs = True should handle it. -Dannon
ADD COMMENTlink written 6.1 years ago by Dannon Baker3.7k
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