Hi Marius Ok, nice, it works. My bad, samtools was not really in the path at galaxy startup.
The job is fine, but I still see these messages : galaxy.model.metadata DEBUG 2018-01-17 16:37:34,295 setting metadata externally failed for HistoryDatasetAssociation 11543: 'invalidated' galaxy.jobs INFO 2018-01-17 16:38:03,242 Collecting metrics for Job 7068 galaxy.jobs DEBUG 2018-01-17 16:38:03,262 job 7068 ended (finish() executed in (29086.817 ms)) galaxy.model.metadata DEBUG 2018-01-17 16:38:03,267 Cleaning up external metadata files galaxy.model.metadata DEBUG 2018-01-17 16:38:03,317 Failed to cleanup MetadataTempFile temp files from /softs/bioinfo/galaxy-prod/database/job_working_directory/007/7068/metadata_out_HistoryDatasetAssociation_11543_s8UGmV: No JSON object could be decoded Fred De : Marius van den Beek [mailto:[email protected]] Envoyé : mercredi 17 janvier 2018 15:33 À : SAPET, Frederic <[email protected]> Cc : Galaxy-dev <[email protected]> Objet : Re: [galaxy-dev] Error at the end of a BWA job 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]<mailto:[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<tel:+33%204%2073%2067%2088%2054> Fax : +33 (0)4 73 67 88 99<tel:+33%204%2073%2067%2088%2099> E-mail : [email protected]<mailto:[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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