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

[Chris Fields]

The only place I can think of tempfiles being generated offhand are Bio::SeqFeature::Collection (actually, tied handles), but as you mention this may not be related.  There are calls to tempfile from Bio::Assembly::IO::sam/bowtie (one using Root::IO, one using File::Temp directly).

chris

On Feb 5, 2010, at 9:24 PM, Florent Angly wrote:

> It can't be, Chris, because I use the workaround mentioned here: http://bugzilla.open-bio.org/show_bug.cgi?id=2577#c5
> 
> It seems like temporary files keep accumulating assembly after assembly. Looking at the lsof command, I get a lot of files described as "(deleted)". I am thinking that maybe some filehandle is not closed or something.
> 
> I'll investigate...
> 
> Florent
> 
> On 06/02/10 13:13, Chris Fields wrote:
>> 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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>>>>> 
>>>>> 
>>>>>         
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>>   
> 
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