[Bio-Linux] cdhit in qiime

[Joanna Schroeder]

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