Ok, I think I understand the line:
beginning merge: bwa mem
/home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa
/home/ralonso/galaxy-dist/database/files/000/dataset_8.dat >
/home/ralonso/galaxy-dist/database/files/000/dataset_94.dat 2> /dev/null
it refers to the original command, so everything is fine with this line.
The other problem still remains
Regards, sorry for the confusion

On 25 February 2015 at 11:40, Roberto Alonso CIPF <ralo...@cipf.es> wrote:

> Hello again,
>
> this is something that I consider important, when I see the log I see this
> output:
> galaxy.jobs.runners.tasks DEBUG 2015-02-25 11:33:30,989 execution finished
> -* beginning merge: bwa mem*
> /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa
> /home/ralonso/galaxy-dist/database/files/000/dataset_8.dat >
> /home/ralonso/galaxy-dist/database/files/000/dataset_94.dat 2> /dev/null
> I think the merge should be done with samtools. I don't know how is this
> programmed in Galaxy, but I didn't indicate anywhere the path to samtools,
> is it maybe the problem related with this?
>
> Thanks a lot,
>
> Regards
>
>
> On 25 February 2015 at 11:13, Roberto Alonso CIPF <ralo...@cipf.es> wrote:
>
>> Hello,
>>
>> I just changed for the CDATA format, but the problem still remains. When
>> I split by 2, there is no problem, but when I go for 3, it happens the
>> problem commented before. Here it is the link to the sam/bam file:
>>  https://dl.dropboxusercontent.com/u/1669701/ejemplo_split.bam
>>
>> Best regards
>>
>> On 24 February 2015 at 17:49, Peter Cock <p.j.a.c...@googlemail.com>
>> wrote:
>>
>>> On Tue, Feb 24, 2015 at 4:43 PM, Roberto Alonso CIPF <ralo...@cipf.es>
>>> wrote:
>>> > Hello again,
>>> >
>>> > first of all thanks for your help, it is being very useful.
>>> >
>>> > What I have done up to now is to copy this method to the class Sequence
>>> >
>>> > def get_split_commands_sequential(is_compressed, input_name,
>>> output_name,
>>> > start_sequence, sequence_count):
>>> >         ...
>>> >         return [cmd]
>>> >     get_split_commands_sequential =
>>> > staticmethod(get_split_commands_sequential)
>>> >
>>> > This is something that you suggested.
>>>
>>> Good.
>>>
>>> > When I run the tool with this configuration:
>>> >
>>> > <tool id="bwa_mio" name="map with bwa">
>>> >   <description>map with bwa</description>
>>> >   <parallelism method="basic" split_size="3"
>>> > split_mode="number_of_parts"></parallelism>
>>> >
>>> >   <command>
>>> >       bwa mem
>>> /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa
>>> > $input > $output 2>/dev/null</command>
>>> >   <inputs>
>>> >     <param format="fastqsanger" name="input" type="data"
>>> label="fastq"/>
>>> >   </inputs>
>>> >   <outputs>
>>> >       <data format="sam" name="output" />
>>> >   </outputs>
>>> >
>>> >   <help>
>>> >   bwa
>>> >   </help>
>>> >
>>> > </tool>
>>>
>>> One minor improvement would be to escape the ">" as "&gt;" in
>>> your XML, or use the CDATA approach documented here:
>>>
>>> https://wiki.galaxyproject.org/Tools/BestPractices
>>>
>>> > Everything ends ok, but when I go to check how is the sam, I see that
>>> in the
>>> > alingments it is the path of the file, i.e
>>> > example_split.sam:
>>> >
>>> /home/ralonso/galaxy-dist/database/job_working_directory/000/90/task_2/dataset_91.dat:SRR098409.1113446
>>> > 4 * 0 0 * * 0 0
>>> >
>>> TCTGGGTGAGGGAGTGGGGAGTGGGTTTTTGAGGGTGTGTGAGGATGTGTAAGTGGATGGAAGTAGATTGAATGTT
>>> >
>>> ############################################################################
>>> > AS:i:0 XS:i:0
>>> >
>>> > you know what  may be going on?
>>> > If i don't split the file, everything goes correctly.
>>>
>>> This sounds to me like there may be a problem with SAM merging?
>>> Could you share the entire example_split.sam file (e.g. as a gist
>>> on GitHub, or via dropbox)?
>>>
>>> Peter
>>>
>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> 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
>



-- 
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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