Error at the end of a BWA job

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Error at the end of a BWA job

SAPET, Frederic

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 : [hidden email]

 


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Re: Error at the end of a BWA job

Marius van den Beek
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 <[hidden email]> 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 : <a href="tel:+33%204%2073%2067%2088%2054" value="+33473678854" target="_blank">+33 (0)4 73 67 88 54

Fax : <a href="tel:+33%204%2073%2067%2088%2099" value="+33473678899" target="_blank">+33 (0)4 73 67 88 99

E-mail : [hidden email]

 


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Re: Error at the end of a BWA job

SAPET, Frederic

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:[hidden email]]
Envoyé : mercredi 17 janvier 2018 15:33
À : SAPET, Frederic <[hidden email]>
Cc : Galaxy-dev <[hidden email]>
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 <[hidden email]> 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 : <a href="tel:&#43;33%204%2073%2067%2088%2054" target="_blank"> +33 (0)4 73 67 88 54

Fax : <a href="tel:&#43;33%204%2073%2067%2088%2099" target="_blank"> +33 (0)4 73 67 88 99

E-mail : [hidden email]

 


___________________________________________________________
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/

 


___________________________________________________________
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:
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