Hi Mike,

Can you share the parameters you used for the qiime otu picker? Also, has the procedure changed since the last time you updated this repo?

Thanks,

Alex

Getting strange problem with prep_silva_taxonomy script. I run the prep_silva_data and everything appears fine:

head -1 trunc_rawtax.txt
HE610125.2844.7343 Eukaryota;Viridiplantae;Chlorophyta;Trebouxiophyceae;Microthamniales;Stichococcus;Stichococcus bacillaris

head -2 trunc_seqs.fas

HE610125.2844.7343
TTTTGACCTGAGATCAGACAAGACCACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAA

Seqs are in sync with tax lines.

But after running prep_silva_taxonomy_file, the tax file is totally out of order:

head -1 trunc_tax.txt
AKZY01000201.42379.45235 D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;D_3__Rhizobiales;D_4__Rhizobiaceae;D_5__Ensifer;D_6__Sinorhizobium meliloti A0641M;D_7__;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__;D_17__;D_18__;D_19__;D_20__;D_21__

Everything is listed as domain level as well which doesn't bother me as much.