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?

Peter

On Wed, Feb 11, 2015 at 3:45 PM, Roberto Alonso CIPF <ralo...@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: ralo...@cipf.es
>
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