OK, I have played around some more with the pick_open_reference_otus.py script. Figured out that I do need a parameter file to tweak things the way I wanted. Template QIIME parameter files are now posted to Dropbox folder “QIIME” (need to post these to website too). Commands I ran are as follows:

18S Chimera – rerun locally at 99% cutoff:

!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_redo_21Aug -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_18Sopenref_iMac.txt

GOM Illumina – Starcluster/Amazon run on the cloud:

!pick_open_reference_otus.py -i /gom_data/GOM_concat1.7_rev_demulti_1to12_2.fna -o /gom_data/uclust_openref99_rev_21Aug -r /gom_data/99_Silva_111_rep_set_euk.fasta --parallel -O 6 -s 0.1 --prefilter_percent_id 0.0 -p /gom_data/qiime_parameters_18Sopenref_GOMamazon.txt

One Response to Pick_open_reference_otus.py

  1. arnstrm says:

    Thanks for these posts! It is great to see posts how you systematically troubleshoot a problem by tinkering around the options. I have a related question: How long will it take to run open OTU picking to finish for 11 million sequences? I will be using the standard greengenes as reference and I have access to HPC (32 procs/512Gb RAM). Thanks in advance!

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