Hi Frederic, samtools couldn't be found, which is required for creating the bam index files during the metadata setting. You can install it globally or in the admin panel -> Manage tool dependencies -> Find the "Set External Metadata" tool and hit "Install checked dependencies via Conda".
Best, Marius On 17 January 2018 at 15:23, SAPET, Frederic <[email protected]> wrote: > 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 <+33%204%2073%2067%2088%2054> > > Fax : +33 (0)4 73 67 88 99 <+33%204%2073%2067%2088%2099> > > E-mail : [email protected] > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ >
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