Re: [wgs-assembler-users] Error in gateKeeper on pacbioToCa...

[Serge K. <se...@um...>]

Hi,

I think the library name specified to pacBioToCA is the issue. The library name given is lluminaTog5681 and, based on the Illumina FRG file name, I am guessing the Illumina library has the same name. The correction pipeline uses library attributes to figure out which library needs to be corrected and which are the short-read data. If the two have the same library name, it will get confused as the same library will be both short-read and pacbio data. Double-check that the library name in the Illumina_Tog5681_clean.frg file is not the same as the library name specified to pacBioToCA.

Sergey

On Jul 23, 2013, at 7:42 AM, Francois Sabot <fra...@ir...> wrote:

> Hi
> 
> The frg file
> /data/projects/assembling-glab/tempIlluminaTog5681/IlluminaTog5681.frg
> has been created during the run.
> 
> Here the frg file
> /data/projects/assembling-glab/Illumina_Tog5681_clean.frg was created
> using fastqToCA from an Illumina file, as recommended on the wiki
> 
> The command line was:
> 
> /home/sabotf/sources/wgs/Linux-amd64/bin/pacBioToCA -s
> /data/projects/assembling-glab/pacbio_SGE_PACBIODEV.spec -l
> IlluminaTog5681 -partitions 13 -t 6 -fastq
> /data/projects/assembling-glab/PacBio_Tog5681/filtered_subreads.fastq
> /data/projects/assembling-glab/Illumina_Tog5681_clean.frg
> 
> 
> 
> Francois
> 
> On 23/07/2013 13:32, Ole Kristian Tørresen wrote:
>> Hi Francois.
>> 
>> Which frg file contain the PacBio sequences? You point to two frg
>> files, /data/projects/assembling-glab/Illumina_Tog5681clean.frg
>> and /data/projects/assembling-glab//tempIlluminaTog5681/IlluminaTog5681.frg,
>> and it seems
>> that /data/projects/assembling-glab/Illumina_Tog5681clean.frg is the one
>> containing the PacBio reads. You just need to add them in the oposite
>> order, the PacBio reads needs to be the last loaded.  
>> 
>> Ole
>> 
>> 
>> On 23 July 2013 10:09, Francois Sabot <fra...@ir...
>> <mailto:fra...@ir...>> wrote:
>> 
>>    Dear all,
>> 
>>    We are using Illumina data to correct PacBio runs, as everyone those
>>    days...
>> 
>>    After creating (successufll) the frg file for the illumina, we launched
>>    the pacbioToCa system, and it started to run.
>> 
>>    However after a while, gatekeeper stopped with the following error:
>> 
>>    "/home/sabotf/sources/wgs/Linux-amd64/bin/gatekeeper  -o
>>    /data/projects/assembling-glab/tempIlluminaTog5681/asm.gkpStore.BUILDING
>>     -F  /data/projects/assembling-glab/Illumina_Tog5681clean.frg
>>    /data/projects/assembling-glab//tempIlluminaTog5681/IlluminaTog5681.frg
>>> 
>>    /data/projects/assembling-glab/tempIlluminaTog5681/asm.gkpStore.err 2>&1
>>    ----------------------------------------END Tue Jul 23 09:56:39 2013
>>    (3084 seconds)
>>    numFrags = 291073268
>>    Stop requested after 'initialstorebuilding'.
>>    ----------------------------------------END Tue Jul 23 09:56:45 2013
>>    (3090 seconds)
>>    Error: The PacBio library 0 must be the last library loaded but it
>>    preceedes 1. Please double-check your input files and try again. at
>>    /home/sabotf/sources/wgs/Linux-amd64/bin/pacBioToCA line 1084."
>> 
>> 
>>    Any idea ?
>>    The pacbio input file come from the provider directly, we did not make
>>    any change on it
>> 
>>    Cheers
>> 
>>    Francois
>> 
>>    --
>>    --------------------------------------------------------
>>    Francois Sabot, PhD
>> 
>>    Be realistic. Demand the Impossible.
>>    http://bioinfo.mpl.ird.fr/
>>    http://www.mpl.ird.fr/rice
>>    -----------------------------------------
>>    UMR DIversity, Adaptation & DEvelopment
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>>    34394 Montpellier Cedex 5
>>    France
>>    Phone: +33 4 67 41 64 18
>>    -----------------------------------------
>> 
>> 
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>> 
> 
> -- 
> --------------------------------------------------------
> Francois Sabot, PhD
> 
> Be realistic. Demand the Impossible.
> http://bioinfo.mpl.ird.fr/
> http://www.mpl.ird.fr/rice
> -----------------------------------------
> UMR DIversity, Adaptation & DEvelopment
> Centre IRD
> 911, Av Agropolis BP 64501
> 34394 Montpellier Cedex 5
> France
> Phone: +33 4 67 41 64 18
> -----------------------------------------
> 
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
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