Il 13.02.2015 03:17 Peter Cock ha scritto:
Hi Roberto,
It looks like this is a known issue with FASTQ splitting,
https://trello.com/c/qRHLFSzd/1522-issues-with-tasked-jobs-parallelism
I originally broke it during a refactor, but it looks like the discussion died about that that method was meant to do (e.g. FQTOC = FASTQ table of contents?):
https://bitbucket.org/galaxy/galaxy-central/commits/76277761807306ec2be3f1e4...
I'm away from the office so can't try this, but probably all that is needed is to copy and paste the old method get_split_commands_sequential and the old method get_split_commands_with_toc (removed from the base Sequence class in the above commit) into the base Fastq class instead.
Nicola - did you fix this locally after noticing the problem last year?
No, sorry, we disabled Galaxy parallelism because it was using too many cluster nodes. Nicola
Peter
On Wed, Feb 11, 2015 at 3:45 PM, Roberto Alonso CIPF wrote:
Hello, I am trying to map a a fastqsanger file and map it with bwa, my bwa tool config file is this:map with bwabwa mem /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa $input > $output 2>xxbwaAnd when I see the stderr I see this error: type object 'Sequence' has no attribute 'get_split_commands_sequential' It seems that this command that I see in the log is not working galaxy.jobs.runners DEBUG 2015-02-11 16:33:48,738 (74) command is: /home/ralonso/galaxy-dist/extract_dataset_parts.sh
/home/ralonso/galaxy-dist/database/job_working_directory/000/74/task_0; bwa mem /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa
/home/ralonso/galaxy-dist/database/job_working_directory/000/74/task_0/dataset_8.dat/home/ralonso/galaxy-dist/database/job_working_directory/000/74/task_0/dataset_75.dat
When I go directly to the code, around line 559 of class galaxy.datatypes.sequence I can't find this function get_split_commands_sequential anywhere. Any idea? Thank you very much Regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso@cipf.es ___________________________________________________________ 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/mailinglists/
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