<div dir="ltr">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.<div>
<br></div><div>If you turn the -M down or to default does that stop the error?</div><div><br></div><div>Also, the qiime forum is pretty quick to help with things like this: <a href="https://groups.google.com/forum/#!forum/qiime-forum">https://groups.google.com/forum/#!forum/qiime-forum</a></div>
<div><br></div><div>Dan</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 8 October 2013 15:28, Joanna Schroeder <span dir="ltr"><<a href="mailto:joasch@mba.ac.uk" target="_blank">joasch@mba.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello Tim and/or the Biolinux team,<br>
<br>
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<br>
<br>
pick_otus.py -i /home/joasch/Rarefaction/Data/Pro/BacCombined.fa -m cdhit -t -M 2000 -o /home/joasch/Rarefaction/Data/Pro/OpenOTU<br>
<br>
and the error I get is<br>
<br>
Traceback (most recent call last):<br>
File "/usr/lib/qiime/bin/pick_otus.py", line 771, in <module><br>
main()<br>
File "/usr/lib/qiime/bin/pick_otus.py", line 579, in main<br>
trie_prefilter=trie_prefilter)<br>
File "/usr/lib/python2.7/dist-packages/qiime/pick_otus.py", line 697, in __call__<br>
seqs=seqs,moltype=moltype,params=cd_hit_params)<br>
File "/usr/lib/python2.7/dist-packages/cogent/app/cd_hit.py", line 260, in cdhit_clusters_from_seqs<br>
remove(params['-o'] + '.bak.clstr')<br>
OSError: [Errno 2] No such file or directory: '/tmp/tmpwmVbfmpFIo2z0DnhDWhm.txt.bak.clstr'<br>
<br>
I'm not quite sure how to interpret or get round this. I'd really appreciate any recommendations,<br>
<br>
Thanks and best regards,<br>
Jo<br>
<br>
<br>
Dr Jo Schroeder<br>
Research Assistant (Bioinformatics and Statistics)<br>
The Marine Biological Association of the UK, Plymouth<br>
<a href="mailto:joasch@mba.ac.uk">joasch@mba.ac.uk</a><br>
_______________________________________________<br>
Bio-Linux mailing list<br>
<a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><br>
<a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux" target="_blank">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><br><br><br>Daniel Pass<br><br>Tel: (029208)76680<br>Mob: 07735658687<div><a href="http://www.kille-morgan.org.uk" target="_blank">http://www.kille-morgan.org.uk</a><br>
<br>Room 0.39,<br>School of Biosciences,<br>Biological Sciences Building,<br>Museum Avenue,<br>Cardiff,<br>CF10 3AT<br></div>
</div>