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Re: [wgs-assembler-users] Error in gateKeeper on pacbioToCa...
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From: Francois S. <fra...@ir...> - 2013-07-24 07:22:55
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Hi guys Ok, it was a problem in manes of library. Everuthing is running fine now Thanks for all Francois On 23/07/2013 15:53, Serge Koren wrote: > 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 >>> 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. >>> Start your free trial of AppDynamics Pro today! >>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> wgs-assembler-users mailing list >>> wgs...@li... >>> <mailto:wgs...@li...> >>> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users >>> >>> >> >> -- >> -------------------------------------------------------- >> 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. >> Start your free trial of AppDynamics Pro today! >> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________ >> wgs-assembler-users mailing list >> wgs...@li... >> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users > > > -- -------------------------------------------------------- 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 ----------------------------------------- |
