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

[Chris Fields]

Florent,

The Bio::Assembly error is documented in Bugzilla:

http://bugzilla.open-bio.org/show_bug.cgi?id=2577

Switching to a Bio::SeqFeature::CollectionI capable of distinguishing features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way to go.

chris

On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:

> 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
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>>> 
>>> 
>> 
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