Generating .biom tables with taxonomy

The scripts just don’t seem to be working for most of the 18S_chimera and GOM_illumina runs. Did a bit of poking on the QIIME forums and it seems like the easier way to do this (confirmed via my fiddling) is just re-generating the OTU tables using and passing in the taxonomy mapping file using the -t flag. This is quick and easy to do on my MacBook Retina:

Commands run: -i /Users/hollybik/Desktop/Alaska\
 Analyses/GOM_Illumina/uclust_openref99_rev_16Sept/final_otu_map_mc2.txt -o /Users/hol
lybik/Desktop/Alaska\ Analyses/GOM_Illumina/uclust_openref99_rev_16Sept/otu_table_mc2_
w_tax.biom -t /Users/hollybik/Desktop/Alaska\ Analyses/GOM_Illumina/uclust_openref99_r
ev_16Sept/rdp_assigned_taxonomy/rep_set_tax_assignments.txt -i /Users/hollybik/Desktop/Alaska\
 Analyses/GOM_Illumina/uclust_openref96_fwd_16Sept/final_otu_map_mc2.txt -o /Users/hol
lybik/Desktop/Alaska\ Analyses/GOM_Illumina/uclust_openref96_fwd_16Sept/otu_table_mc2_
w_tax.biom -t /Users/hollybik/Desktop/Alaska\ Analyses/GOM_Illumina/uclust_openref96_f
wd_16Sept/rdp_assigned_taxonomy/rep_set_tax_assignments.txt -i /Users/hollybik/Desktop/Alaska\
 Analyses/GOM_Illumina/uclust_openref99_fwd_20Sept/final_otu_map_mc2.txt -o /Users/hol
lybik/Desktop/Alaska\ Analyses/GOM_Illumina/uclust_openref99_fwd_20Sept/otu_table_mc2_
w_tax.biom -t /Users/hollybik/Desktop/Alaska\ Analyses/GOM_Illumina/uclust_openref99_f

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