Samtools running on submit-node and as a slurm job
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@dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://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.
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 <christopher.previti@dkfz-heidelberg.de> 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@dkfz.de <http://www.dkfz.de/> 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.
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participants (2)
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Marius van den Beek -
Previti