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/76277761807306ec2be3f1e4059dd7cde6fd2dc6#comment-820648

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:
ralo...@cipf.es
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