[galaxy-dev] python subprocess OSError when running bwa-mem

[Georgios Nikolis]

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.niko...@dkfz.de www.dkfz.de Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537

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