[Bio-Linux] help with denoise wrapper

[Tim Booth]

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

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