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

[Jelle Scholtalbers]

Also specifying the -f(ast) option could be beneficial for you. Probably you
have a limit in how many files you can specify on the commandline, so could
it also be an idea for you to concatenate the files before loading them? Or
take a look at xargs when on linux: "find -maxdepth 1 -name '*.gff'  | xargs
bp_seqfeature_load.pl -d contigs -u root -p xxxx -f"

2010/2/5 Scott Cain <scott at scottcain.net>

> I believe you can call the loading script with more than one GFF file
> as the argument, eliminating the need for the for loop.
>
>
>
> On Fri, Feb 5, 2010 at 11:25 AM, Fungazid <fungazid at yahoo.com> wrote:
> > 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
> >>
> >
> >
> >
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> 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
>