[Bioperl-l] Too many links at LoadHelper.pm

[Scott Cain]

Hi Avi,

Off hand, I have no idea what is happening.  Is there a reason you
aren't using bp_seqfeature_load.pl?

Scott


On Thu, Feb 4, 2010 at 9:52 PM, Fungazid <fungazid at yahoo.com> wrote:
> Bioperl hi,
>
> I have multiple gff3 files that look like:
>
> --------------------------------------------------------
> ##gff-version 3
> # file: temp1.gff3
> contig453278    hs    contig    1    699    .    +    .    Name=contig453278
> contig453278    hs    alignment    1    194    .    +    .    Name=hs.ENST00000258455
> contig453278    hs    alignment    252    699    .    +    .    Name=hs.ENST00000258455
> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
> contig453278    hs    transcript    104    183    .    +    .    Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
> contig453278    hs    transcript    1    9    .    +    .    Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
> contig453278    hs    transcript    73    103    .    +    .    Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
> contig453278    hs    transcript    10    72    .    +    .    Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
> ---------------------------------------------------------
>
>
>
> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>
> --------------------------------------------
> Bio::DB::SeqFeature::Store->new(...)
> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
> for($i=0; $i<$#files+1; $i++){
> $loader->load($file[$i]);
> }
> --------------------------------------------
>
> Eventually after uploading ~15000 small gff3 files I got the error:
>
> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory /tmp/9bbpdE5ibf: Too many links at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>
>
>
> I am trying to see what went wrong, maybe you can rescue me,
> Avi
>
>
>
>
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>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research