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? Peter On Wed, Feb 11, 2015 at 3:45 PM, Roberto Alonso CIPF <ralonso@cipf.es> wrote:
Hello,
I am trying to map a a fastqsacer file and map it with bwa, my bwa tool config file is this:
<tool id="bwa_mio" name="map with bwa"> <description>map with bwa</description> <parallelism method="basic" split_size="2" split_mode="number_of_parts"></parallelism>
<command> bwa mem /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa $input > $output 2>xx</command> <inputs> <param format="fastqsanger" name="input" type="data" label="fastq"/> </inputs> <outputs> <data format="sam" name="output" /> </outputs>
<help> bwa </help>
</tool>
And 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
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