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

[Daniel Pass]

Hi Rowena

If you run: 'print_qiime_config.py -t' does it say that ChimeraSlayer is
installed properly?

I'd recomend running through the steps
here<https://groups.google.com/forum/?fromgroups#!topic/qiime-forum/cP6ibzfNqRU>,
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.

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!

Dan

On 8 March 2012 15:44, Rowena Stern <rost at sahfos.ac.uk> wrote:
>
> 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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--



Daniel Pass

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