QIIME open ref OTU picking

Been trying to use the new QIIME 1.7 scripts on the GOM Illumina data (running out of memory so this is still a work in progress though…heading over to Amazon Cloud soon):pick_open_reference_otus.py -i

Standard workflow:

/Users/hollybik/Desktop/Data/Illumina_GOM/demultiplexed_qiime1.7/GOM_concat1.7_fwd_demulti_1to12_1.fna -o /Users/hollybik/Desktop/Data/Illumina_GOM/uclust_99_fwd -r /macqiime/silva_111/rep_set/Silva_111_full_unique.fasta --parallel -O 2 -s 0.1 --suppress_taxonomy_assignment --suppress_align_and_tree

Skipping prefiltering (thought this would speed things up but no…)

pick_open_reference_otus.py -i /Users/hollybik/Desktop/Data/Illumina_GOM/demultiplexed_qiime1.7/GOM_concat1.7_fwd_demulti_1to12_1.fna -o /Users/hollybik/Desktop/Data/Illumina_GOM/uclust_99_fwd -r /macqiime/silva_111/rep_set/Silva_111_full_unique.fasta --parallel -O 2 -s 0.1 --suppress_taxonomy_assignment --suppress_align_and_tree --prefilter_percent_id 0.0
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