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

[Florent Angly]

I've run into this issue very recently, albeit working on something 
unrelated to loading GFF files: generating many small independent 
assemblies. Maybe there's a bug in the tempdir() code, or its 
documentation is not clear. I will take a look at it when I have some time.
Florent


On 05/02/10 22:27, Mark A. Jensen wrote:
> 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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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
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