[Bio-Linux] Circos? And a question or two!

[Rowena Stern]

Hi Tim,
I don't this question came from me, but in any case you reminded me to update you.
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?  

rowena at 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
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 172, in <module>
    main()
  File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 169, in main
    keep_intermediates=keep_intermediates)
  File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 148, in chimeraSlayer_identify_chimeras
    keep_intermediates=keep_intermediates):
  File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 133, in __call__
    keep_intermediates=keep_intermediates)
  File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 592, in get_chimeras_from_Nast_aligned
    app_results = app()
  File "/usr/lib/pymodules/python2.6/cogent/app/util.py", line 269, in __call__
    result_paths=self._get_result_paths(data)) 
  File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 405, in _get_result_paths
    raise ApplicationError,"Calling ChimeraSlayer failed."
cogent.app.util.ApplicationError: Calling ChimeraSlayer failed.

Thanks
Rowena

-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
Sent: 08 March 2012 15:10
To: Cox, Michael J
Cc: Bio-Linux mailing list
Subject: Re: [Bio-Linux] Circos? And a question or two!

Hi Mike,

Part of your e-mail is probably of broader interest so I've taken the
liberty of copying this first part of the reply back to the BL mailing
list.

> Was wondering whether you'd come across Circos http://circos.ca/ the
> boss has a hankering after pretty pictures and I was wondering whether
> it was something that you might consider biolinuxing.  From the forum
> it seems impenetrably complicated to use and still in beta, so perhaps
> not!

I've heard of Circos several years ago - nice to see the project is
still going even if they haven't declared a version 1 release yet.  The
software is already being packaged for Debian but the version is out of
date and also won't install directly on BL - see:

http://packages.debian.org/sid/circos

I could try and backport/update that package but I have so much on the
TODO list I can't see it happening before the Bio-Linux 7 release late
in the summer.  At least the page above shows the dependency packages
you need to install, so maybe it will help you if you want to try just
grabbing the download from the website directly?

> Also, I wanted to ask about R packages - are these distributed as
> packages, or are some included with biolinux?  

A mixture.  Some come from CRAN, a few come from us, some are not
packaged but just loaded manually.

> I was guessing bioconductor would be?  

Nope, Bioconductor is all loaded manually at present - see
http://nebc.nerc.ac.uk/tools/bioinformatics-docs/other-bioinf/r-and-bioconductor#rpack

> I came across phyloseq, which looks great for integrating QIIME and
> mothur (and even rubbish old pyrotagger and the RDP) with R
> https://github.com/joey711/phyloseq I'm starting to play with it at
> the moment, just in case you're interested.

Thanks for the hint.  Definitely one to watch - I wonder who else on
this list might be interested in the thing?

Cheers,

TIM

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

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

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