iPython Notebook 18S Chimera

Started a new iPython notebook for the 18S Chimera project. Running open ref OTU picking over the weekend:

!pick_open_reference_otus.py -i /Users/hollybik/Desktop/Data/18S_chimera/chim_demux.extendedFrags_primersremoved_fastxtrimmed.fasta -o /Users/hollybik/Desktop/Data/18S_chimera/uclust_99_merged -r /macqiime/silva_111/eukaryotes_only/rep_set_euks/99_Silva_111_rep_set_euk.fasta --parallel -O 2 -s 0.1 --suppress_taxonomy_assignment --suppress_align_and_tree --prefilter_percent_id 0.0

OTU picking finished over the weekend (yay!) on my Desktop iMac for an input file that was ~2GB in size. Running taxonomy assignment next:

!assign_taxonomy.py -i /Users/hollybik/Desktop/Data/18S_chimera/uclust_99_merged/rep_set.fna -r /macqiime/silva_111/eukaryotes_only/rep_set_euks/99_Silva_111_rep_set_euk.fasta -t /macqiime/silva_111/eukaryotes_only/taxonomy_euks/99_Silva_111_taxa_map_RDP_7_levels_euks.txt -m rdp -c 0.5
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