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

[Ole K. T. <ol...@st...>]

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...> 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.
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