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<div>To update,</div>
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>
<div><font class="Apple-style-span" face="Courier"># qiime_config</font></div>
<div><font class="Apple-style-span" face="Courier"># WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config</font></div>
<div><font class="Apple-style-span" face="Courier"># To overwrite defaults, copy this file to $HOME/.qiime_config or a full path</font></div>
<div><font class="Apple-style-span" face="Courier"># specified by $QIIME_CONFIG_FP and edit that copy of the file.</font></div>
<div><font class="Apple-style-span" face="Courier"><br>
</font></div>
<div><font class="Apple-style-span" face="Courier">cluster_jobs_fp</font></div>
<div><font class="Apple-style-span" face="Courier">python_exe_fp<span class="Apple-tab-span" style="white-space:pre">
</span>python</font></div>
<div><font class="Apple-style-span" face="Courier">working_dir<span class="Apple-tab-span" style="white-space:pre">
</span>.</font></div>
<div><font class="Apple-style-span" face="Courier">blastmat_dir<span class="Apple-tab-span" style="white-space:pre">
</span>/usr/share/ncbi/data</font></div>
<div><font class="Apple-style-span" face="Courier">blastall_fp<span class="Apple-tab-span" style="white-space:pre">
</span>blastall</font></div>
<div><font class="Apple-style-span" face="Courier">rdp_classifier_fp<span class="Apple-tab-span" style="white-space:pre">
</span>/usr/software/rdp_classifier/rdp_classifier_2.0.1/rdp_classifier-2.0.jar</font></div>
<div><font class="Apple-style-span" face="Courier">pynast_template_alignment_fp<span class="Apple-tab-span" style="white-space:pre">
</span>/home/db/qiime/core_set_aligned.fasta.imputed</font></div>
<div><font class="Apple-style-span" face="Courier">pynast_template_alignment_blastdb</font></div>
<div><font class="Apple-style-span" face="Courier">template_alignment_lanemask_fp<span class="Apple-tab-span" style="white-space:pre">
</span>/home/db/qiime/lanemask_in_1s_and_0s</font></div>
<div><font class="Apple-style-span" face="Courier">jobs_to_start<span class="Apple-tab-span" style="white-space:pre">
</span>4</font></div>
<div><font class="Apple-style-span" face="Courier">seconds_to_sleep<span class="Apple-tab-span" style="white-space:pre">
</span>60</font></div>
<div><font class="Apple-style-span" face="Courier">qiime_scripts_dir<span class="Apple-tab-span" style="white-space:pre">
</span>/usr/lib/qiime/bin/</font></div>
<div><font class="Apple-style-span" face="Courier">temp_dir<span class="Apple-tab-span" style="white-space:pre">
</span>/tmp</font></div>
<div><font class="Apple-style-span" face="Courier">pyronoise_data_fp<span class="Apple-tab-span" style="white-space:pre">
</span>/usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat</font></div>
<div><font class="Apple-style-span" face="Courier">assign_taxonomy_reference_seqs_fp /home/db/qiime/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta</font></div>
<div><font class="Apple-style-span" face="Courier">assign_taxonomy_id_to_taxonomy_fp /home/db/qiime/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt</font></div>
<div><font class="Apple-style-span" face="Courier">cloud_environment<span class="Apple-tab-span" style="white-space:pre">
</span>False</font></div>
</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Mike</div>
<br>
<div>
<div>On 19 Mar 2012, at 12:00, <<a href="mailto:bio-linux-request@nebclists.nerc.ac.uk">bio-linux-request@nebclists.nerc.ac.uk</a>></div>
<div> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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<div>You can reach the person managing the list at<br>
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When replying, please edit your Subject line so it is more specific<br>
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Today's Topics:<br>
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1. QIIME 1.4 assign taxonomy issue (Cox, Michael J)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 19 Mar 2012 11:48:25 +0000<br>
From: "Cox, Michael J" <michael.cox1@imperial.ac.uk><br>
Subject: [Bio-Linux] QIIME 1.4 assign taxonomy issue<br>
To: "bio-linux@nebclists.nerc.ac.uk" <bio-linux@nebclists.nerc.ac.uk><br>
Message-ID: <DDC77D15-1C92-4F4A-802C-7AC890477663@imperial.ac.uk><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi Tim,<br>
<br>
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:<br>
<br>
assign_taxonomy_reference_seqs_fp<br>
assign_taxonomy_id_to_taxonomy_fp<br>
<br>
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.<br>
<br>
I wish they'd document things like this<br>
<br>
Cheers<br>
<br>
Mike<br>
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