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

[Mark A. Jensen]

Dan has been partial to temp in Root::IO (bowtie); I scurried off to File::Temp 
(sam)--
any issues with tempfile handles, Dan?
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Florent Angly" <florent.angly at gmail.com>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 11:41 PM
Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm


> 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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