[Bio-Linux] cdhit in qiime

[Tim Booth]

Hi,

I think the problem is more mundane.  CD-HIT always used to leave behind
a certain temporary file, and so QIIME (or rather the Cogent library it
uses) manually cleans it up after each run.  A recent update to CD-HIT
removes this bug and the file is now cleaned up within CD-HIT.

But when QIIME tries to remove the file and can't find it, it craps out.
What it should do it just press on regardless.

I'm applying and testing a simple patch just now.  Will push it as an
update if it works.

Cheers,

TIM

On Tue, 2013-10-08 at 16:15 +0100, Daniel Pass wrote:
> I don't know for certain, but I'm wondering if having such a high ram
> allocation could be knocking it over. Is this server based as 2gb
> could be pushing it for an oldish desktop? Also, I've known on
> occasion that if you've got multiple cores specified in a parameters
> file qiime would run it parallel even if not specified specifically in
> the command and this would duplicate the ram.
> 
> 
> If you turn the -M down or to default does that stop the error?
> 
> 
> Also, the qiime forum is pretty quick to help with things like
> this: https://groups.google.com/forum/#!forum/qiime-forum
> 
> 
> Dan
> 
> 
> On 8 October 2013 15:28, Joanna Schroeder <joasch at mba.ac.uk> wrote:
>         Hello Tim and/or the Biolinux team,
>         
>         I'm struggling to get the cdhit otu picking method working
>         within Qiime.  I wondered if you had any suggestions or
>         recommendations of how to proceed with this.  e.g I use the
>         command
>         
>         pick_otus.py
>         -i /home/joasch/Rarefaction/Data/Pro/BacCombined.fa -m cdhit
>         -t -M 2000 -o /home/joasch/Rarefaction/Data/Pro/OpenOTU
>         
>         and the error I get is
>         
>         Traceback (most recent call last):
>           File "/usr/lib/qiime/bin/pick_otus.py", line 771, in
>         <module>
>             main()
>           File "/usr/lib/qiime/bin/pick_otus.py", line 579, in main
>             trie_prefilter=trie_prefilter)
>           File "/usr/lib/python2.7/dist-packages/qiime/pick_otus.py",
>         line 697, in __call__
>             seqs=seqs,moltype=moltype,params=cd_hit_params)
>           File
>         "/usr/lib/python2.7/dist-packages/cogent/app/cd_hit.py", line
>         260, in cdhit_clusters_from_seqs
>             remove(params['-o'] + '.bak.clstr')
>         OSError: [Errno 2] No such file or directory:
>         '/tmp/tmpwmVbfmpFIo2z0DnhDWhm.txt.bak.clstr'
>         
>         I'm not quite sure how to interpret or get round this.  I'd
>         really appreciate any recommendations,
>         
>         Thanks and best regards,
>         Jo
>         
>         
>         Dr Jo Schroeder
>         Research Assistant (Bioinformatics and Statistics)
>         The Marine Biological Association of the UK, Plymouth
>         joasch at mba.ac.uk
>         _______________________________________________
>         Bio-Linux mailing list
>         Bio-Linux at nebclists.nerc.ac.uk
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> 
> 
> 
> -- 
> 
> 
> 
> Daniel Pass
> 
> Tel: (029208)76680
> Mob: 07735658687
> http://www.kille-morgan.org.uk
> 
> Room 0.39,
> School of Biosciences,
> Biological Sciences Building,
> Museum Avenue,
> Cardiff,
> CF10 3AT
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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OX10 8BB 

http://nebc.nerc.ac.uk
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