From rost at sahfos.ac.uk  Thu Mar  1 05:53:29 2012
From: rost at sahfos.ac.uk (Rowena Stern)
Date: Thu, 1 Mar 2012 10:53:29 +0000
Subject: [Bio-Linux] help with denoise wrapper
Message-ID: <C2F0F2B71A1597459E7FE37EE92E95680F6627C1B3@exchange>

Hello,

Would anyone be able to help me with Denoise wrapper command which gives me an error message- see below. I had previously got this command to work and the only error I can think of is my mapping files.



rowena at biolinux[454WSFeb_May]  qiime > denoise_wrapper.py -v -i SternA_total/EukA7/454Reads.1-EukA7.sff -f SternA_total/Split_library_output_WSallEukA7/seqs.fna -o Denoise_WSallEuKA7/ -m SternA_total/SternE_EukA7_map.txt Traceback (most recent call last):

  File "/usr/lib/qiime/bin/denoise_wrapper.py", line 159, in <module>

    main()

  File "/usr/lib/qiime/bin/denoise_wrapper.py", line 145, in main

    titanium=opts.titanium)

  File "/usr/lib/python2.6/dist-packages/qiime/denoise_wrapper.py", line 37, in fast_denoiser

    verbose=verbose, titanium=titanium)

  File "/usr/lib/python2.6/dist-packages/qiime/denoiser/flowgram_clustering.py", line 612, in denoise_seqs

    verbose=verbose, squeeze=squeeze, primer=primer)

  File "/usr/lib/python2.6/dist-packages/qiime/denoiser/preprocess.py", line 197, in preprocess

    flowgrams, header = cat_sff_files(map(open, sff_fp.split(',')))

  File "/usr/lib/python2.6/dist-packages/qiime/denoiser/utils.py", line 378, in cat_sff_files

    'produced by sffinfo. The binary .sff will not work here.'

qiime.util.FileFormatError: Wrong flogram file format. Make sure you pass the sff.txt format produced by sffinfo. The binary .sff will not work here.





I tried using sffinfo and it can't find this command either, see below (although it worked on my individual sample sff files).

rowena at biolinux[454WSFeb_May]  qiime > sffinfo SternA_total/EukA7/454Reads.1-EukA7.sff > SternA_total/EukA7/454Reads.1-EukA7.sff.txt

zsh: command not found: sffinfo

Many thanks
Rowena

SAHFOS
The Laboratory,
Citadel Hill,
The Hoe,
Plymouth,
PL1 2PB, UK
Tel: 01752 633294

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From tbooth at ceh.ac.uk  Thu Mar  1 12:07:09 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 01 Mar 2012 17:07:09 +0000
Subject: [Bio-Linux] help with denoise wrapper
In-Reply-To: <C2F0F2B71A1597459E7FE37EE92E95680F6627C1B3@exchange>
References: <C2F0F2B71A1597459E7FE37EE92E95680F6627C1B3@exchange>
Message-ID: <1330621629.3981.25376.camel@barsukas.nwl.ac.uk>

Hi Rowena,

The sffinfo tool is part of the Roche toolkit and is proprietary so we
can't redistribute it, but in fact Qiime can do the flowgram
preprocessing for you using process_sff.py.  I think the command you
need is:

process_sff.py -f -i SternA_total/EukA7

Any joy?

Cheers,

TIM

On Thu, 2012-03-01 at 10:53 +0000, Rowena Stern wrote:
> Hello,
> 
> Would anyone be able to help me with Denoise wrapper command which
> gives me an error message- see below. I had previously got this
> command to work and the only error I can think of is my mapping
> files. 
> 
>  
> 
> rowena at biolinux[454WSFeb_May]  qiime > denoise_wrapper.py -v -i
> SternA_total/EukA7/454Reads.1-EukA7.sff -f
> SternA_total/Split_library_output_WSallEukA7/seqs.fna -o
> Denoise_WSallEuKA7/ -m SternA_total/SternE_EukA7_map.txt Traceback
> (most recent call last):
> 
>   File "/usr/lib/qiime/bin/denoise_wrapper.py", line 159, in <module>
> 
>     main()
> 
>   File "/usr/lib/qiime/bin/denoise_wrapper.py", line 145, in main
> 
>     titanium=opts.titanium)
> 
>   File "/usr/lib/python2.6/dist-packages/qiime/denoise_wrapper.py",
> line 37, in fast_denoiser
> 
>     verbose=verbose, titanium=titanium)
> 
>   File
> "/usr/lib/python2.6/dist-packages/qiime/denoiser/flowgram_clustering.py", line 612, in denoise_seqs
> 
>     verbose=verbose, squeeze=squeeze, primer=primer)
> 
>   File
> "/usr/lib/python2.6/dist-packages/qiime/denoiser/preprocess.py", line
> 197, in preprocess
> 
>     flowgrams, header = cat_sff_files(map(open, sff_fp.split(',')))
> 
>   File "/usr/lib/python2.6/dist-packages/qiime/denoiser/utils.py",
> line 378, in cat_sff_files
> 
>     'produced by sffinfo. The binary .sff will not work here.'
> 
> qiime.util.FileFormatError: Wrong flogram file format. Make sure you
> pass the sff.txt format produced by sffinfo. The binary .sff will not
> work here.
> 
>  
> 
>  
> 
> I tried using sffinfo and it can't find this command either, see below
> (although it worked on my individual sample sff files).
> 
> rowena at biolinux[454WSFeb_May]  qiime > sffinfo
> SternA_total/EukA7/454Reads.1-EukA7.sff >
> SternA_total/EukA7/454Reads.1-EukA7.sff.txt 
> 
> zsh: command not found: sffinfo
> 
>  
> 
> Many thanks
> 
> Rowena
> 
>  
> 
> SAHFOS
> 
> The Laboratory,
> 
> Citadel Hill, 
> 
> The Hoe,
> 
> Plymouth, 
> 
> PL1 2PB, UK
> 
> Tel: 01752 633294
> 
>  
> 
> 

-- 
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

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From tbooth at ceh.ac.uk  Thu Mar  1 13:33:10 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 01 Mar 2012 18:33:10 +0000
Subject: [Bio-Linux] help with denoise wrapper
In-Reply-To: <C2F0F2B71A1597459E7FE37EE92E95680F6627C32F@exchange>
References: <C2F0F2B71A1597459E7FE37EE92E95680F6627C1B3@exchange>
	<1330621629.3981.25376.camel@barsukas.nwl.ac.uk>
	<C2F0F2B71A1597459E7FE37EE92E95680F6627C32F@exchange>
Message-ID: <1330626790.3981.25502.camel@barsukas.nwl.ac.uk>

Hi Rowena,

When calling denoise_wrapper.py you need to explicitly reference
the .sff.txt file for the -i parameter.  In the output you sent below,
you just gave the path to the .sff file.  Or is there still an error
with the .sff.txt file, in which case can you please send the output?

Cheers,

TIM

On Thu, 2012-03-01 at 18:19 +0000, Rowena Stern wrote:
> HI Tim,
> Yes, thanks i did use process_sff.py initially but somehow qiime can't
> recognise the flowgram output. Any other ideas?
> 
> Many thanks
> Rowena
> 
> -----Original Message-----
> From: Tim Booth [mailto:tbooth at ceh.ac.uk] 
> Sent: 01 March 2012 17:07
> To: Bio-Linux help and discussion
> Cc: Rowena Stern
> Subject: Re: [Bio-Linux] help with denoise wrapper
> 
> Hi Rowena,
> 
> The sffinfo tool is part of the Roche toolkit and is proprietary so we
> can't redistribute it, but in fact Qiime can do the flowgram
> preprocessing for you using process_sff.py.  I think the command you
> need is:
> 
> process_sff.py -f -i SternA_total/EukA7
> 
> Any joy?
> 
> Cheers,
> 
> TIM
> 
> On Thu, 2012-03-01 at 10:53 +0000, Rowena Stern wrote:
> > Hello,
> > 
> > Would anyone be able to help me with Denoise wrapper command which
> > gives me an error message- see below. I had previously got this
> > command to work and the only error I can think of is my mapping
> > files. 
> > 
> >  
> > 
> > rowena at biolinux[454WSFeb_May]  qiime > denoise_wrapper.py -v -i
> > SternA_total/EukA7/454Reads.1-EukA7.sff -f
> > SternA_total/Split_library_output_WSallEukA7/seqs.fna -o
> > Denoise_WSallEuKA7/ -m SternA_total/SternE_EukA7_map.txt Traceback
> > (most recent call last):
> > 
> >   File "/usr/lib/qiime/bin/denoise_wrapper.py", line 159, in <module>
> > 
> >     main()
> > 
> >   File "/usr/lib/qiime/bin/denoise_wrapper.py", line 145, in main
> > 
> >     titanium=opts.titanium)
> > 
> >   File "/usr/lib/python2.6/dist-packages/qiime/denoise_wrapper.py",
> > line 37, in fast_denoiser
> > 
> >     verbose=verbose, titanium=titanium)
> > 
> >   File
> > "/usr/lib/python2.6/dist-packages/qiime/denoiser/flowgram_clustering.py", line 612, in denoise_seqs
> > 
> >     verbose=verbose, squeeze=squeeze, primer=primer)
> > 
> >   File
> > "/usr/lib/python2.6/dist-packages/qiime/denoiser/preprocess.py", line
> > 197, in preprocess
> > 
> >     flowgrams, header = cat_sff_files(map(open, sff_fp.split(',')))
> > 
> >   File "/usr/lib/python2.6/dist-packages/qiime/denoiser/utils.py",
> > line 378, in cat_sff_files
> > 
> >     'produced by sffinfo. The binary .sff will not work here.'
> > 
> > qiime.util.FileFormatError: Wrong flogram file format. Make sure you
> > pass the sff.txt format produced by sffinfo. The binary .sff will not
> > work here.
> > 
> >  
> > 
> >  
> > 
> > I tried using sffinfo and it can't find this command either, see below
> > (although it worked on my individual sample sff files).
> > 
> > rowena at biolinux[454WSFeb_May]  qiime > sffinfo
> > SternA_total/EukA7/454Reads.1-EukA7.sff >
> > SternA_total/EukA7/454Reads.1-EukA7.sff.txt 
> > 
> > zsh: command not found: sffinfo
> > 
> >  
> > 
> > Many thanks
> > 
> > Rowena
> > 
> >  
> > 
> > SAHFOS
> > 
> > The Laboratory,
> > 
> > Citadel Hill, 
> > 
> > The Hoe,
> > 
> > Plymouth, 
> > 
> > PL1 2PB, UK
> > 
> > Tel: 01752 633294
> > 
> >  
> > 
> > 
> 
> -- 
> 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
> 

-- 
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

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From tbooth at ceh.ac.uk  Thu Mar  8 10:10:22 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 08 Mar 2012 15:10:22 +0000
Subject: [Bio-Linux] Circos? And a question or two!
In-Reply-To: <8B478F1C-65F5-46B5-A937-E5D0F5DC88B7@imperial.ac.uk>
References: <8B478F1C-65F5-46B5-A937-E5D0F5DC88B7@imperial.ac.uk>
Message-ID: <1331219422.27116.5752.camel@barsukas.nwl.ac.uk>

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

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From rost at sahfos.ac.uk  Thu Mar  8 10:44:41 2012
From: rost at sahfos.ac.uk (Rowena Stern)
Date: Thu, 8 Mar 2012 15:44:41 +0000
Subject: [Bio-Linux] Circos? And a question or two!
In-Reply-To: <1331219422.27116.5752.camel@barsukas.nwl.ac.uk>
References: <8B478F1C-65F5-46B5-A937-E5D0F5DC88B7@imperial.ac.uk>
	<1331219422.27116.5752.camel@barsukas.nwl.ac.uk>
Message-ID: <C2F0F2B71A1597459E7FE37EE92E95680F6627D081@exchange>

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

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


From daniel.antony.pass at googlemail.com  Thu Mar  8 16:58:28 2012
From: daniel.antony.pass at googlemail.com (Daniel Pass)
Date: Thu, 8 Mar 2012 21:58:28 +0000
Subject: [Bio-Linux] Circos? And a question or two!
In-Reply-To: <C2F0F2B71A1597459E7FE37EE92E95680F6627D081@exchange>
References: <8B478F1C-65F5-46B5-A937-E5D0F5DC88B7@imperial.ac.uk>
	<1331219422.27116.5752.camel@barsukas.nwl.ac.uk>
	<C2F0F2B71A1597459E7FE37EE92E95680F6627D081@exchange>
Message-ID: <CACwm78Ops9550ytCSCO1TjfOEoxAGNNBynLJi9pWGbtacHJ1-A@mail.gmail.com>

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
>
> --
> This message (and any attachments) is for the recipient only. NERC
> is subject to the Freedom of Information Act 2000 and the contents
> of this email and any reply you make may be disclosed by NERC unless
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux




--



Daniel Pass

Tel: (029208)76680
Mob: 07735658687

Room 0.39,
School of Biosciences,
Biological Sciences Building,
Museum Avenue,
Cardiff,
CF10 3AT
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From rost at sahfos.ac.uk  Fri Mar  9 04:58:05 2012
From: rost at sahfos.ac.uk (Rowena Stern)
Date: Fri, 9 Mar 2012 09:58:05 +0000
Subject: [Bio-Linux] Circos? And a question or two!
In-Reply-To: <CACwm78Ops9550ytCSCO1TjfOEoxAGNNBynLJi9pWGbtacHJ1-A@mail.gmail.com>
References: <8B478F1C-65F5-46B5-A937-E5D0F5DC88B7@imperial.ac.uk>
	<1331219422.27116.5752.camel@barsukas.nwl.ac.uk>
	<C2F0F2B71A1597459E7FE37EE92E95680F6627D081@exchange>
	<CACwm78Ops9550ytCSCO1TjfOEoxAGNNBynLJi9pWGbtacHJ1-A@mail.gmail.com>
Message-ID: <C2F0F2B71A1597459E7FE37EE92E95680F664C193B@exchange>

Cheers Dan! Will try this
Rowena

From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Daniel Pass
Sent: 08 March 2012 21:58
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] Circos? And a question or two!

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<mailto: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> [mailto: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<mailto: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
>
> --
> This message (and any attachments) is for the recipient only. NERC
> is subject to the Freedom of Information Act 2000 and the contents
> of this email and any reply you make may be disclosed by NERC unless
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux




--



Daniel Pass

Tel: (029208)76680
Mob: 07735658687

Room 0.39,
School of Biosciences,
Biological Sciences Building,
Museum Avenue,
Cardiff,
CF10 3AT
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From michael.cox1 at imperial.ac.uk  Mon Mar 19 07:48:25 2012
From: michael.cox1 at imperial.ac.uk (Cox, Michael J)
Date: Mon, 19 Mar 2012 11:48:25 +0000
Subject: [Bio-Linux] QIIME 1.4 assign taxonomy issue
Message-ID: <DDC77D15-1C92-4F4A-802C-7AC890477663@imperial.ac.uk>

Hi Tim,

I've noticed an issue with QIIME 1.4 - according to this thread on the forum https://groups.google.com/forum/?fromgroups#!topic/qiime-forum/dCwvX1HWi_E it should be defaulting to using greengenes with the the RDP classifier for assigning taxonomy whereas in 1.3 it was using RDP's own database.  With the biolinux install we're still on RDP.  I have a feeling this is an issue with old .qiime_config files lurking around in profiles that might be over-riding the default behaviour, I've tried updating the .qiime_config in my profile to a version that includes:

assign_taxonomy_reference_seqs_fp
assign_taxonomy_id_to_taxonomy_fp

and paths to the gg reference files in /home/db/qiime but with no luck.  I'm still trying, but thought I'd let you know in case it's something that has implications for the package.

I wish they'd document things like this

Cheers

Mike
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From michael.cox1 at imperial.ac.uk  Mon Mar 19 11:54:23 2012
From: michael.cox1 at imperial.ac.uk (Cox, Michael J)
Date: Mon, 19 Mar 2012 15:54:23 +0000
Subject: [Bio-Linux] Bio-Linux Digest, Vol 47, Issue 3
In-Reply-To: <mailman.1.1332158402.2999.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1332158402.2999.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <0EC231DB-CEB9-4E92-ABE2-C1C253F9CD8E@imperial.ac.uk>

To update,

I've fixed this by eliminating a rogue colon in my .qiime_config file.  A copy of what I'm now using is below for reference in case you're having the same problem - each user needs to update their copy:

# qiime_config
# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config
# To overwrite defaults, copy this file to $HOME/.qiime_config or a full path
# specified by $QIIME_CONFIG_FP and edit that copy of the file.

cluster_jobs_fp
python_exe_fp python
working_dir .
blastmat_dir /usr/share/ncbi/data
blastall_fp blastall
rdp_classifier_fp /usr/software/rdp_classifier/rdp_classifier_2.0.1/rdp_classifier-2.0.jar
pynast_template_alignment_fp /home/db/qiime/core_set_aligned.fasta.imputed
pynast_template_alignment_blastdb
template_alignment_lanemask_fp /home/db/qiime/lanemask_in_1s_and_0s
jobs_to_start 4
seconds_to_sleep 60
qiime_scripts_dir /usr/lib/qiime/bin/
temp_dir /tmp
pyronoise_data_fp /usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat
assign_taxonomy_reference_seqs_fp       /home/db/qiime/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta
assign_taxonomy_id_to_taxonomy_fp       /home/db/qiime/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt
cloud_environment False

Cheers

Mike

On 19 Mar 2012, at 12:00, <bio-linux-request at nebclists.nerc.ac.uk<mailto:bio-linux-request at nebclists.nerc.ac.uk>>
 wrote:

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Today's Topics:

  1. QIIME 1.4 assign taxonomy issue (Cox, Michael J)


----------------------------------------------------------------------

Message: 1
Date: Mon, 19 Mar 2012 11:48:25 +0000
From: "Cox, Michael J" <michael.cox1 at imperial.ac.uk>
Subject: [Bio-Linux] QIIME 1.4 assign taxonomy issue
To: "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
Message-ID: <DDC77D15-1C92-4F4A-802C-7AC890477663 at imperial.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Hi Tim,

I've noticed an issue with QIIME 1.4 - according to this thread on the forum https://groups.google.com/forum/?fromgroups#!topic/qiime-forum/dCwvX1HWi_E it should be defaulting to using greengenes with the the RDP classifier for assigning taxonomy whereas in 1.3 it was using RDP's own database.  With the biolinux install we're still on RDP.  I have a feeling this is an issue with old .qiime_config files lurking around in profiles that might be over-riding the default behaviour, I've tried updating the .qiime_config in my profile to a version that includes:

assign_taxonomy_reference_seqs_fp
assign_taxonomy_id_to_taxonomy_fp

and paths to the gg reference files in /home/db/qiime but with no luck.  I'm still trying, but thought I'd let you know in case it's something that has implications for the package.

I wish they'd document things like this

Cheers

Mike
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------------------------------

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End of Bio-Linux Digest, Vol 47, Issue 3
****************************************

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