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).

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