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 <frederic.sapet@biogemma.com> 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

Fax : +33 (0)4 73 67 88 99

E-mail : frederic.sapet@biogemma.com

 


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