Rerunning GOM Illumina on QIIME 1.8

I’ve spent the last few day re-parsing data to get around some issues related to the way the sequencing facility handed me the GOM Illumina data (ended up needing to separate out primer sets and renumber demultiplexed sequences using the renumber_rev_reads_v2.pl script in the GOM_Illumina/QIIME_files/Dec_2013 folder on Dropbox). In any case, continuing with analysis on QIIME 1.8.

pick_open_reference_otus.py -i /home/ubuntu/data/GOM_co
ncat1.7_allF04combo_10Jan14.fna -o /home/ubuntu/data/uclust_openref99_F04_10Jan 
-r /home/ubuntu/data/silva_111/99_Silva_111_rep_set_euk.fasta --parallel -O 8 -s
 0.1 -p /home/ubuntu/data/qiime_parameters_18Sopenref99_GOMamazon_16sept.txt --p
refilter_percent_id 0.0

pick_open_reference_otus.py -i /home/ubuntu/data/GOM_co
ncat1.7_allR22combo_10Jan14.fna -o /home/ubuntu/data/uclust_openref99_R22_10Jan 
-r /home/ubuntu/data/silva_111/99_Silva_111_rep_set_euk.fasta --parallel -O 8 -s
 0.1 -p /home/ubuntu/data/qiime_parameters_18Sopenref99_GOMamazon_16sept.txt --p
refilter_percent_id 0.0

Got a weird error on AWS when I started ran these above script – “OpenBLAS : Your OS does not support AVX instructions. OpenBLAS is using Nehalem kernels as a fallback, which may give poorer performance.” Not sure if this will affect anything, but the open ref OTU picking seems to be progressing OK regardless (for now…).