Hello
I've just installed BWA ((Galaxy Version 0.7.17.3) , Galaxy itself is On branch release_17.09).
The first run is not a success.
I can see that the BAM is created, but job is tagged as fail (Unable to finish job).
It looks like close to this issue: https://github.com/galaxyproject/galaxy/issues/2083 I've checked, samtools is in the path.
Do you have any ideas ?
Thank you
Fred
Here is what I see in the log:
galaxy.jobs.runners.drmaa DEBUG 2018-01-17 10:57:23,787 (7062/86331.universe) state change: job finished normally galaxy.model.metadata DEBUG 2018-01-17 10:57:23,993 setting metadata externally failed for HistoryDatasetAssociation 11537: 'invalidated' galaxy.jobs.runners ERROR 2018-01-17 10:57:24,108 (7062/86331.universe) Job wrapper finish method failed Traceback (most recent call last): File "/softs/bioinfo/galaxy-prod/lib/galaxy/jobs/runners/__init__.py", line 630, in finish_job job_state.job_wrapper.finish(stdout, stderr, exit_code) File "/softs/bioinfo/galaxy-prod/lib/galaxy/jobs/__init__.py", line 1287, in finish dataset.datatype.set_meta(dataset, overwrite=False) File "/softs/bioinfo/galaxy-prod/lib/galaxy/datatypes/binary.py", line 424, in set_meta exit_code = subprocess.call(args=command, stderr=open(stderr_name, 'wb')) File "/softs/add-ons/Python-2.7.12/lib/python2.7/subprocess.py", line 523, in call return Popen(*popenargs, **kwargs).wait() File "/softs/add-ons/Python-2.7.12/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/softs/add-ons/Python-2.7.12/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
--- Frederic Sapet Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Centre de Recherche de Chappes CS 90126 63720 CHAPPES FRANCE Tel : +33 (0)4 73 67 88 54 Fax : +33 (0)4 73 67 88 99 E-mail : frederic.sapet@biogemma.commailto:frederic.sapet@biogemma.com