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

[Florent Angly]

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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