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…).

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2 Responses to Rerunning GOM Illumina on QIIME 1.8

  1. Kei says:

    Hello, I got the same strange error message in AWS about OS not supporting AVX instructions; I was wondering if you had any issues?
    Thanks – Kei

    • hollybik says:

      I never looked into it further, since the QIIME scripts seemed to be running OK despite the error message. If you figure out why that error pops up, please let me know!

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