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

[Fungazid]

Scott, Jason, hi,

I replaced my code with:

for(...) {system("bp_seqfeature_load.pl -d contigs -u root -p xxxx ./$file[$i]")==0 or die;}

run it, and it went smoothly (or seem to be like that ).

The reason I used an alternative script is that it is almost identical to bp_seqfeature_load.pl but it calls the following functions only once:

Bio::DB::SeqFeature::Store->new(..)
Bio::DB::SeqFeature::Store::GFF3Loader->new(...)


Thanks,
Avi


--- On Fri, 2/5/10, Scott Cain <scott at scottcain.net> wrote:

> From: Scott Cain <scott at scottcain.net>
> Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm
> To: "Fungazid" <fungazid at yahoo.com>
> Cc: Bioperl-l at lists.open-bio.org
> Date: Friday, February 5, 2010, 5:38 AM
> 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
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.           
>                
>        scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)         
>            216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>