<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Tim,</div><div><br></div><div>That's excellent, thanks. A user found another issue - looks like there are still some dependencies lurking around that aren't available. This time it's with check_id_map.py (which hardly does anything - how QIIME can make this complicated I've no idea).</div><div><br></div><div>The error is:</div><div><br></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier">qiime > check_id_map.py -m aran.r2.map.txt -o mapping_output</font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> <o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier">Traceback (most recent call last):<o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> File "/usr/lib/qiime/bin/check_id_map.py", line 149, in <module><o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> main()<o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> File "/usr/lib/qiime/bin/check_id_map.py", line 145, in main<o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> disable_primer_check, added_demultiplex_field)<o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> File "/usr/lib/python2.7/dist-packages/qiime/check_id_map.py", line 112, in check_mapping_file<o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> 'js/overlib.js'), join(output_dir,'overlib.js'))<o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> File "/usr/lib/python2.7/shutil.py", line 82, in copyfile<o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier"> with open(src, 'rb') as fsrc:<o:p></o:p></font></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; "><font face="Courier">IOError: [Errno 2] No such file or directory: '/usr/lib/python2.7/dist-packages/qiime/support_files/js/overlib.js'</font></div></div><br><div><div>Thanks</div><div><br></div><div>Mike</div><div><br></div><div>PS</div><div><br></div><div>Locally the bioinformatics support service here have written a wrapper that stops ampliconnoise.py from failing (or at least, starts it going again from where it left off) when it hits a sample with no good reads. I've asked whether they're happy for me to share it with you in case it's of use as you're having to do a lot of patching anyway in QIIME. Will pass it on if they OK.</div><div><br></div><div>On 14 Nov 2012, at 15:43, Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Mike,<br><br>Thanks for reporting the problems with QIIME. I've patched the code to<br>make it work with the newer RDP classifier and I've also fixed the issue<br>with KING not working.<br><br>I've also applied the patch that I saw on the QIIME blog to fix the<br>problem with compare_alpha_diversity reporting the wrong t-statistic.<br><br>The new packages are now on the package server for BL7.<br><br>Cheers,<br><br>TIM<br><br>On Wed, 2012-11-07 at 16:12 +0000, Michael Cox wrote:<br><blockquote type="cite">Hi Tim,<br><br><br>it looks like something else is going on too - King is now not working<br>within the pipeline to generate the kinemage files for PCoA analysis.<br> Here's the error:<br><br><br>Qiime> beta_diversity_through_plots.py -i otus/otu_table.biom -m<br>aran.r1.map.txt -o wf_bdiv_even692/ -t otus/rep_set.tre -e 692 <br><br><br>Traceback (most recent call last):<br> File "/usr/lib/qiime/bin/beta_diversity_through_plots.py", line 166,<br>in <module><br> main()<br> File "/usr/lib/qiime/bin/beta_diversity_through_plots.py", line 163,<br>in main<br> status_update_callback=status_update_callback)<br> File "/usr/lib/python2.7/dist-packages/qiime/workflow.py", line 867,<br>in run_beta_diversity_through_plots<br> close_logger_on_success=close_logger_on_success)<br> File "/usr/lib/python2.7/dist-packages/qiime/workflow.py", line 135,<br>in call_commands_serially<br> raise WorkflowError, msg<br>qiime.workflow.WorkflowError: <br><br>*** ERROR RAISED DURING STEP: Make 3D plots (continuous coloring,<br>weighted_unifrac)<br>Command run was:<br>python /usr/lib/qiime/bin//make_3d_plots.py -p<br>wf_bdiv_even692//prefs.txt -i wf_bdiv_even692//weighted_unifrac_pc.txt<br>-o wf_bdiv_even692//weighted_unifrac_3d_continuous/ -m<br>aran.r1.map.txt <br>Command returned exit status: 1<br>Stdout:<br><br>Stderr<br>Traceback (most recent call last):<br> File "/usr/lib/qiime/bin//make_3d_plots.py", line 443, in <module><br> main()<br> File "/usr/lib/qiime/bin//make_3d_plots.py", line 419, in main<br> shutil.copyfile(os.path.join(jar_path,'king.jar'),<br>os.path.join(jar_dir_path,'king.jar'))<br> File "/usr/lib/python2.7/shutil.py", line 82, in copyfile<br> with open(src, 'rb') as fsrc:<br>IOError: [Errno 2] No such file or directory:<br>'/usr/lib/python2.7/dist-packages/qiime/support_files/jar/king.jar'<br><br><br>There is no "support_files" directory in that directory. I have<br>installed King myself independently in /usr/local/bioinf/king/king and<br>this available as king from the command line. I guess I could create<br>a symlink to this, but it would break on update? For the moment I'm<br>going to get this user to load his distance matrices into R as they<br>will have been generated and I'm evil ;)<br><br><br>Cheers<br><br><br>Mike<br><br>On 7 Nov 2012, at 10:27, Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>> wrote:<br><br><blockquote type="cite">Hi Mike,<br><br>Well, if I'd actually tested the thing I guess I'd have found this<br>out<br>for myself. I just couldn't quite believe that Qiime would find the<br>JAR<br>that you've told it to run but then refuse to run it because it<br>doesn't<br>like the name.<br><br>The discussion on the forum makes it quite clear that they added<br>this<br>check because they wanted to stop people using the older version of<br>the<br>classifier. It is highly likely that the new version works fine.<br> Maybe<br>the 2.2 RDP version added some option that Qiime relies on, in which<br>case it's unlikely this would be removed in a later version.<br><br>My "normalised" comment means that the rdp-classifier package now<br>meets<br>proper packaging standards. It was a bit of a fudge before, and I<br>couldn't put all the configuration bits in one place. It also means<br>that the version of the package given by dpkg gives you the version<br>of<br>the classifier - ie. 2.5.<br><br>My inclination is to do a bit more testing and then if 2.5 seems to<br>work<br>I'll patch Qiime to accept it. I'll also add a warning when Qiime<br>is<br>started that the classifier being used is not the default. Let me<br>know<br>if you have any problems with the renamed 2.5 classifier or if you<br>think<br>you need to switch back to 2.2 in order to ensure a "standard"<br>analysis.<br><br>Cheers,<br><br>TIM<br><br><blockquote type="cite">I did say below! :P<br><br>assign_taxonomy.py does a crappy name check<br><a href="https://groups.google.com/d/msg/qiime-forum/o7CaXnfS1J0/DgsFm-Q-s6YJ">https://groups.google.com/d/msg/qiime-forum/o7CaXnfS1J0/DgsFm-Q-s6YJ</a><br>hence the problem<br><br>Apparently they only support 2.2 as well, do you know whether<br>Biolinux<br>has the most recent version of RDP classifier installed? I tried<br>to<br>determine the version number, but helpfully it's not included in<br>the<br>help output :) <br><br>I am fairly sure other versions aren't supported, and after<br>changing<br>the name to rdp_classifier-2.2.jar<br><br>and the path to<br><br># This was previously set in bio-linux-rdp-classifier but can now<br>live<br>here<br># as the rdp-classifier package has been normalised.<br>export RDP_JAR_PATH=<br>${RDP_JAR_PATH:-/usr/share/rdp-classifier/rdp_classifier-2.2.jar}<br><br>It does seem to run and produce a sensible result, but I've not<br>checked within the context of the whole pipeline yet. Will let<br>you<br>know if I hit a problem with it and have to install 2.2. What<br>does<br>the normalised comment refer to?<br><br>Thanks! QIIME is such fun isn't it? Is Galaxy more or less fun?<br><br></blockquote><br>-- <br>This message (and any attachments) is for the recipient only. NERC<br>is subject to the Freedom of Information Act 2000 and the contents<br>of this email and any reply you make may be disclosed by NERC unless<br>it is exempt from release under the Act. Any material supplied to<br>NERC may be stored in an electronic records management system.<br></blockquote><br></blockquote><br>-- <br>Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>NERC Environmental Bioinformatics Centre <br><br>Centre for Ecology and Hydrology<br>Maclean Bldg, Benson Lane<br>Crowmarsh Gifford<br>Wallingford, England<br>OX10 8BB <br><br><a href="http://nebc.nerc.ac.uk">http://nebc.nerc.ac.uk</a><br>+44 1491 69 2705<br></blockquote></div><br></body></html>