Re: [Gusdev-gusdev] uploading P. falciparum data

[Steve F. <sfi...@pc...>]

i have never run the GBParser.    The plasmoDB folks have used it to=20
load data.

the funny thing is that P. falciparum is much smaller than human.

unfortunately the guy who know this coded best, Angel, is in europe this=20
week.

maybe somebody else i'll pick this up.

steve

Fidel Salas wrote:

>I tried uploding P. falciparum chromosome data using the GBParser and
>ran out of memory in all cases.  setMaximumNumberOfObjects is set to
>4000000.  The verbose output files contain the line:
>VLD     CBIL::Bio::GenBank::Origin      1
>more than 20 million times before an =A8out of memory=A8 message is
>output.
>
>Here are some of some of the numbers for some of the files:
>bash-2.05$ grep VLD NC_004325.gbk-gbparser.out | grep -c Origin
>20479965
>bash-2.05$ grep VLD NC_004314.gbk-gbparser.out | grep -c Origin
>20356504
>bash-2.05$ grep VLD NC_004315.gbk-gbparser.out | grep -c Origin
>20335688
>
>Has anyone run into something similar before?  How did the people
>working on P. falciparum upload the data into GUS?
>
>Thanks
>
>Fidel
>
>
>
>
>
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