I think newer versions of Galaxy give a better error message - I am pretty sure the problem is you are missing samtools. It needs to be available on the PATH for Galaxy if you use bam data. -John On Fri, Jun 3, 2016 at 1:00 PM, Anthony Underwood <Anthony.Underwood@phe.gov.uk> wrote:
Jobs that I run on a local Galaxy install on a Fedora 23 machine are completing but are erroring with the message below. Any idea why the metadata can not be written?
Thanks
galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished: /home/anthony.underwood/galaxy/database/jobs_directory/000/142/galaxy_142.sh galaxy.model.metadata DEBUG 2016-06-03 17:30:02,158 setting metadata externally failed for HistoryDatasetAssociation 158: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-06-03 17:30:02,235 Job wrapper finish method failed Traceback (most recent call last): File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/__init__.py", line 1257, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/anthony.underwood/galaxy/lib/galaxy/datatypes/binary.py", line 339, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
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