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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoPlainText>Hello,<o:p></o:p></p><p class=MsoPlainText>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. <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>rowena@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):<o:p></o:p></p><p class=MsoPlainText><o:p></o:p></p><p class=MsoPlainText> File "/usr/lib/qiime/bin/denoise_wrapper.py", line 159, in <module><o:p></o:p></p><p class=MsoPlainText> main()<o:p></o:p></p><p class=MsoPlainText> File "/usr/lib/qiime/bin/denoise_wrapper.py", line 145, in main<o:p></o:p></p><p class=MsoPlainText> titanium=opts.titanium)<o:p></o:p></p><p class=MsoPlainText> File "/usr/lib/python2.6/dist-packages/qiime/denoise_wrapper.py", line 37, in fast_denoiser<o:p></o:p></p><p class=MsoPlainText> verbose=verbose, titanium=titanium)<o:p></o:p></p><p class=MsoPlainText> File "/usr/lib/python2.6/dist-packages/qiime/denoiser/flowgram_clustering.py", line 612, in denoise_seqs<o:p></o:p></p><p class=MsoPlainText> verbose=verbose, squeeze=squeeze, primer=primer)<o:p></o:p></p><p class=MsoPlainText> File "/usr/lib/python2.6/dist-packages/qiime/denoiser/preprocess.py", line 197, in preprocess<o:p></o:p></p><p class=MsoPlainText> flowgrams, header = cat_sff_files(map(open, sff_fp.split(',')))<o:p></o:p></p><p class=MsoPlainText> File "/usr/lib/python2.6/dist-packages/qiime/denoiser/utils.py", line 378, in cat_sff_files<o:p></o:p></p><p class=MsoPlainText> 'produced by sffinfo. The binary .sff will not work here.'<o:p></o:p></p><p class=MsoPlainText>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.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>I tried using sffinfo and it can't find this command either, see below (although it worked on my individual sample sff files).<o:p></o:p></p><p class=MsoPlainText>rowena@biolinux[454WSFeb_May] qiime > sffinfo SternA_total/EukA7/454Reads.1-EukA7.sff > SternA_total/EukA7/454Reads.1-EukA7.sff.txt <o:p></o:p></p><p class=MsoPlainText>zsh: command not found: sffinfo<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Many thanks<o:p></o:p></p><p class=MsoNormal>Rowena<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>SAHFOS<o:p></o:p></p><p class=MsoNormal style='punctuation-wrap:simple;text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Times New Roman","serif"'>The Laboratory,<o:p></o:p></span></p><p class=MsoNormal style='punctuation-wrap:simple;text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Times New Roman","serif"'>Citadel Hill, <o:p></o:p></span></p><p class=MsoNormal style='punctuation-wrap:simple;text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Times New Roman","serif"'>The Hoe,<o:p></o:p></span></p><p class=MsoNormal style='punctuation-wrap:simple;text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Times New Roman","serif"'>Plymouth, <o:p></o:p></span></p><p class=MsoNormal style='punctuation-wrap:simple;text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Times New Roman","serif"'>PL1 2PB, UK<o:p></o:p></span></p><p class=MsoNormal style='punctuation-wrap:simple;text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Times New Roman","serif"'>Tel: 01752 633294<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>