[Bio-Linux] cdhit in qiime

[Daniel Pass]

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
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>



-- 



Daniel Pass

Tel: (029208)76680
Mob: 07735658687
http://www.kille-morgan.org.uk

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