[Bio-Linux] help with denoise wrapper

[Tim Booth]

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

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