Try other tools that use Samtools to ensure that is intact. On a local, you'll need to do some admin detective work: Re-running the job generally resolves this type of issue. If working at, this indicates an error from the cluster. Return Popen(*popenargs, **kwargs).wait()įile "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 711, in _init_įile "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 1343, in _execute_child Job_state.job_wrapper.finish( stdout, stderr, exit_code )įile "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/_init_.py", line 1265, in finishĭ_meta( dataset, overwrite=False )įile "/home/eclark28/galaxy_production/galaxy/lib/galaxy/datatypes/binary.py", line 347, in set_metaĮxit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )įile "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 523, in call Traceback (most recent call last):įile "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/_init_.py", line 609, in finish_job I am not sure what other issue could be causing hisat to fail. I attempt to run a job and receive the following near the end of the job from hisat. I installed hisat and added samtools to my PATH on my galaxy install machine. I believe I had posted this under another account but cannot seem to find a solution to this issue.
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