Hi Georgios I am just guessing here, but the error looks familiar: Do you have samtools installed? and is it in $PATH? (for a similar case, see: https://biostar.usegalaxy.org/p/19938/ ) Regards, Hans-Rudolf On 05/19/2017 10:03 AM, Georgios Nikolis wrote:
Dear all, we are currently working on a new local Galaxy instance (17.01) and we encounter an error when running bwa-mem jobs. The jobs fail with a python subprocess OSError triggered in the module lib/galaxy/datatypes/binary.py Here is the traceback:
Traceback (most recent call last): File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 624, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/opt/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1350, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/opt/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 391, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' )) File "/usr/lib64/python2.7/subprocess.py", line 524, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory Has anyone seen this error before? Is there anything we can do to get rid of it?
Thanks a lot!
Best, Georgios
-- *Georgios Nikolis* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) IT Management Genomics Proteomics
German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-4659
g.nikolis@dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/>
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