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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Cheers Dan! Will try this<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Rowena<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> bio-linux-bounces@nebclists.nerc.ac.uk [mailto:bio-linux-bounces@nebclists.nerc.ac.uk] <b>On Behalf Of </b>Daniel Pass<br><b>Sent:</b> 08 March 2012 21:58<br><b>To:</b> Bio-Linux help and discussion<br><b>Subject:</b> Re: [Bio-Linux] Circos? And a question or two!<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Rowena<br><br>If you run: 'print_qiime_config.py -t' does it say that ChimeraSlayer is installed properly?<br><br>I'd recomend running through the steps <a href="https://groups.google.com/forum/?fromgroups#!topic/qiime-forum/cP6ibzfNqRU">here</a>, where someone else seems to have had the same problem. I think it's probably qiime looking in the wrong place for it, with new versions and all.<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Let me (us!) know how it goes. I haven't ran this myself since the update as the sequencers seem to have gone missing with my data, but if they ever turn up I'll be following in your footsteps!<br><br>Dan<br><br>On 8 March 2012 15:44, Rowena Stern <<a href="mailto:rost@sahfos.ac.uk">rost@sahfos.ac.uk</a>> wrote:<br>><br>> Hi Tim,<br>> I don't this question came from me, but in any case you reminded me to update you.<br>> I had a problem doing denoising and using sffinfo command. I have updated biolinux and everything is fine now except for ChimeraSlayer, which after about 30 seconds tells me there is an application failure- see below. Any thoughts how I can fix this?<br>><br>> rowena@biolinux[454WSFeb_May] qiime > identify_chimeric_seqs.py -m ChimeraSlayer -i SternA_total/pynast_108_EukA7_aligned/EukA7_rep_set_aligned.fasta -a Silva_108_rep_set.fna -o EukA7_108_chimeric_seqs.txt<br>> Traceback (most recent call last):<br>> File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 172, in <module><br>> main()<br>> File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 169, in main<br>> keep_intermediates=keep_intermediates)<br>> File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 148, in chimeraSlayer_identify_chimeras<br>> keep_intermediates=keep_intermediates):<br>> File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 133, in __call__<br>> keep_intermediates=keep_intermediates)<br>> File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 592, in get_chimeras_from_Nast_aligned<br>> app_results = app()<br>> File "/usr/lib/pymodules/python2.6/cogent/app/util.py", line 269, in __call__<br>> result_paths=self._get_result_paths(data))<br>> File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 405, in _get_result_paths<br>> raise ApplicationError,"Calling ChimeraSlayer failed."<br>> cogent.app.util.ApplicationError: Calling ChimeraSlayer failed.<br>><br>> Thanks<br>> Rowena<br>><br>> -----Original Message-----<br>> From: <a href="mailto:bio-linux-bounces@nebclists.nerc.ac.uk">bio-linux-bounces@nebclists.nerc.ac.uk</a> [mailto:<a href="mailto:bio-linux-bounces@nebclists.nerc.ac.uk">bio-linux-bounces@nebclists.nerc.ac.uk</a>] On Behalf Of Tim Booth<br>> Sent: 08 March 2012 15:10<br>> To: Cox, Michael J<br>> Cc: Bio-Linux mailing list<br>> Subject: Re: [Bio-Linux] Circos? And a question or two!<br>><br>> Hi Mike,<br>><br>> Part of your e-mail is probably of broader interest so I've taken the<br>> liberty of copying this first part of the reply back to the BL mailing<br>> list.<br>><br>> > Was wondering whether you'd come across Circos <a href="http://circos.ca/">http://circos.ca/</a> the<br>> > boss has a hankering after pretty pictures and I was wondering whether<br>> > it was something that you might consider biolinuxing. From the forum<br>> > it seems impenetrably complicated to use and still in beta, so perhaps<br>> > not!<br>><br>> I've heard of Circos several years ago - nice to see the project is<br>> still going even if they haven't declared a version 1 release yet. The<br>> software is already being packaged for Debian but the version is out of<br>> date and also won't install directly on BL - see:<br>><br>> <a href="http://packages.debian.org/sid/circos">http://packages.debian.org/sid/circos</a><br>><br>> I could try and backport/update that package but I have so much on the<br>> TODO list I can't see it happening before the Bio-Linux 7 release late<br>> in the summer. At least the page above shows the dependency packages<br>> you need to install, so maybe it will help you if you want to try just<br>> grabbing the download from the website directly?<br>><br>> > Also, I wanted to ask about R packages - are these distributed as<br>> > packages, or are some included with biolinux?<br>><br>> A mixture. Some come from CRAN, a few come from us, some are not<br>> packaged but just loaded manually.<br>><br>> > I was guessing bioconductor would be?<br>><br>> Nope, Bioconductor is all loaded manually at present - see<br>> <a href="http://nebc.nerc.ac.uk/tools/bioinformatics-docs/other-bioinf/r-and-bioconductor#rpack">http://nebc.nerc.ac.uk/tools/bioinformatics-docs/other-bioinf/r-and-bioconductor#rpack</a><br>><br>> > I came across phyloseq, which looks great for integrating QIIME and<br>> > mothur (and even rubbish old pyrotagger and the RDP) with R<br>> > <a href="https://github.com/joey711/phyloseq">https://github.com/joey711/phyloseq</a> I'm starting to play with it at<br>> > the moment, just in case you're interested.<br>><br>> Thanks for the hint. Definitely one to watch - I wonder who else on<br>> this list might be interested in the thing?<br>><br>> Cheers,<br>><br>> TIM<br>><br>> --<br>> Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>> NERC Environmental Bioinformatics Centre<br>><br>> Centre for Ecology and Hydrology<br>> Maclean Bldg, Benson Lane<br>> Crowmarsh Gifford<br>> Wallingford, England<br>> OX10 8BB<br>><br>> <a href="http://nebc.nerc.ac.uk">http://nebc.nerc.ac.uk</a><br>> +44 1491 69 2705<br>><br>> --<br>> This message (and any attachments) is for the recipient only. NERC<br>> is subject to the Freedom of Information Act 2000 and the contents<br>> of this email and any reply you make may be disclosed by NERC unless<br>> it is exempt from release under the Act. Any material supplied to<br>> NERC may be stored in an electronic records management system.<br>><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">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</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">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><br><br><br><br><br>--<br><br><br><br>Daniel Pass<br><br>Tel: (029208)76680<br>Mob: 07735658687<br><br>Room 0.39,<br>School of Biosciences,<br>Biological Sciences Building,<br>Museum Avenue,<br>Cardiff,<br>CF10 3AT<o:p></o:p></p></div></div></body></html>