[Bio-Linux] Bio-Linux Digest, Vol 47, Issue 3

[Cox, Michael J]

To update,

I've fixed this by eliminating a rogue colon in my .qiime_config file.  A copy of what I'm now using is below for reference in case you're having the same problem - each user needs to update their copy:

# qiime_config
# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config
# To overwrite defaults, copy this file to $HOME/.qiime_config or a full path
# specified by $QIIME_CONFIG_FP and edit that copy of the file.

cluster_jobs_fp
python_exe_fp python
working_dir .
blastmat_dir /usr/share/ncbi/data
blastall_fp blastall
rdp_classifier_fp /usr/software/rdp_classifier/rdp_classifier_2.0.1/rdp_classifier-2.0.jar
pynast_template_alignment_fp /home/db/qiime/core_set_aligned.fasta.imputed
pynast_template_alignment_blastdb
template_alignment_lanemask_fp /home/db/qiime/lanemask_in_1s_and_0s
jobs_to_start 4
seconds_to_sleep 60
qiime_scripts_dir /usr/lib/qiime/bin/
temp_dir /tmp
pyronoise_data_fp /usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat
assign_taxonomy_reference_seqs_fp       /home/db/qiime/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta
assign_taxonomy_id_to_taxonomy_fp       /home/db/qiime/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt
cloud_environment False

Cheers

Mike

On 19 Mar 2012, at 12:00, <bio-linux-request at nebclists.nerc.ac.uk<mailto:bio-linux-request at nebclists.nerc.ac.uk>>
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Today's Topics:

  1. QIIME 1.4 assign taxonomy issue (Cox, Michael J)


----------------------------------------------------------------------

Message: 1
Date: Mon, 19 Mar 2012 11:48:25 +0000
From: "Cox, Michael J" <michael.cox1 at imperial.ac.uk>
Subject: [Bio-Linux] QIIME 1.4 assign taxonomy issue
To: "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
Message-ID: <DDC77D15-1C92-4F4A-802C-7AC890477663 at imperial.ac.uk>
Content-Type: text/plain; charset="us-ascii"

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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