18S Chimera – rerunning relabeled files

Wrote a script last night to label chimeric sequences with >chimera_ – now rerunning QIIME analyses locally on my iMac

pick_open_reference_otus.py -i /Users/hollybik/Desktop/Data/18S_chimera/chim_demux.extendedFrags_primersremoved_fastxtrimmed_chimeraslabelled.fasta -o /Users/hollybik/Desktop/Data/18S_chimera/chimera_openref96_18Sept -r /macqiime/silva_111/eukaryotes_only/rep_set_euks/99_Silva_111_rep_set_euk.fasta --parallel -O 2 -s 0.1 --prefilter_percent_id 0.0 -p /Users/hollybik/Dropbox/QIIME/qiime_parameters_18Schimera_96_iMac.txt 

Update (10/3/13) – iMac taking way too long for OTU picking, so moved over to Amazon AWS. Command for 96% open ref:

pick_open_reference_otus.py -i /home/ubuntu/data/chim_demux.extendedFrags_primersremoved_fastxtrimmed_chimeraslabelled.fasta -o /home/ubuntu/data/18S_chimera_openref96_3oct13 -r /home/ubuntu/data/silva_111/99_Silva_111_rep_set_euk.fasta --parallel -O 8 -s 0.1 --prefilter_percent_id 0.0 -p /home/ubuntu/data/qiime_parameters_18Schimera_96_amazon.txt

Command for 99% open ref:

pick_open_reference_otus.py -i /home/ubuntu/data/chim_demux.extendedFrags_primersremoved_fastxtrimmed_chimeraslabelled.fasta -o /home/ubuntu/data/18S_chimera_openref99_5oct13 -r /home/ubuntu/data/silva_111/99_Silva_111_rep_set_euk.fasta --parallel -O 8 -s 0.1 --prefilter_percent_id 0.0 -p /home/ubuntu/data/qiime_parameters_18Schimera_99_amazon.txt
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