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

[Mark A. Jensen]

The tempfiles are not being unlinked before there are too many for the OS to 
handle.
Sounds like this may be your job, fungazid, if you're not employing the script 
(but
not sure about that)
----- Original Message ----- 
From: "Fungazid" <fungazid at yahoo.com>
To: <Bioperl-l at lists.open-bio.org>
Sent: Thursday, February 04, 2010 9:52 PM
Subject: [Bioperl-l] Too many links at LoadHelper.pm


> 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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