[Bio-Linux] QIIME 1.4 assign taxonomy issue

[Cox, Michael J]

Hi Tim,

I've noticed an issue with QIIME 1.4 - according to this thread on the forum https://groups.google.com/forum/?fromgroups#!topic/qiime-forum/dCwvX1HWi_E it should be defaulting to using greengenes with the the RDP classifier for assigning taxonomy whereas in 1.3 it was using RDP's own database.  With the biolinux install we're still on RDP.  I have a feeling this is an issue with old .qiime_config files lurking around in profiles that might be over-riding the default behaviour, I've tried updating the .qiime_config in my profile to a version that includes:

assign_taxonomy_reference_seqs_fp
assign_taxonomy_id_to_taxonomy_fp

and paths to the gg reference files in /home/db/qiime but with no luck.  I'm still trying, but thought I'd let you know in case it's something that has implications for the package.

I wish they'd document things like this

Cheers

Mike
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