[Bio-Linux] help with denoise wrapper

[Rowena Stern]

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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