Samtools running on submit-node and as a slurm job

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Samtools running on submit-node and as a slurm job

Previti

Dear all,

We found something strange with our Galaxy instance...

Our Galaxy server is configured as a submit node using slurm to submit to our cluster.

This works fine for the most part, but today we saw a samtools index job running "locally" on the submit node instead of a  cluster node.

Is there any way of stopping this behavior? The submit nodes are not configured for data-intensive computation and everything runs significantly slower.

I was running bamtools (splitting a bam-file into mapped into unmapped) at the time and the output bam-files were being indexed. 

Thanks and best regards,

Christopher

--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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Re: Samtools running on submit-node and as a slurm job

Marius van den Beek
Hi Christopher,

If your galaxy is configured to set metadata externally then you shouldn't
see samtools index being run on the node that runs galaxy 
(On a side-note galaxy will use pysam starting from release 18.01).
One possibility is that the metadata setting failed, and it has been tried again internally.
You can control this with the `retry_metadata_internally` option in your galaxy.yml / galaxy.ini
file.

Best,
Marius

On 24 April 2018 at 15:55, Previti <[hidden email]> wrote:

Dear all,

We found something strange with our Galaxy instance...

Our Galaxy server is configured as a submit node using slurm to submit to our cluster.

This works fine for the most part, but today we saw a samtools index job running "locally" on the submit node instead of a  cluster node.

Is there any way of stopping this behavior? The submit nodes are not configured for data-intensive computation and everything runs significantly slower.

I was running bamtools (splitting a bam-file into mapped into unmapped) at the time and the output bam-files were being indexed. 

Thanks and best regards,

Christopher

--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.



    

___________________________________________________________
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:
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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:
  http://galaxyproject.org/search/