Issues with "bamtools split", running jobs don't show up in history (and fail after several hours)

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

Issues with "bamtools split", running jobs don't show up in history (and fail after several hours)


Dear all,

I've been trying to properly install the "BAMTools split" tool in our local DKFZ-Galaxy instance, but it doesn't work properly.

The strange thing is that you can launch a bamtools splitter job on our cluster, but it never shows up in the history...until it fails with following


"tool error

An error occurred with this dataset:
Unable to finish job"

All versions (Galaxy, bamtools 2.4.0,samtools 1.3.1) are up to date and this is what I installed:

Repository                bamtools_split
Name:                      bamtools_split
Owner:                     devteam
Synopsis:                  Tool for splitting BAM files
Detailed description: Utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett.
Content homepage:

Development repository:

Revision: 2:e2c1b62e1db1

Thanks and best regards,


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

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434


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:

To search Galaxy mailing lists use the unified search at: