<div dir="ltr"><div><div><div><div>Dear Whom It May Concern,<br><br></div>I may have accidentally sent this email to the wrong place initially, I apologize. I upgraded to
Ubuntu 16.04 and now there are items within qiime that are not working.
I imagine I may have removed some essential items during the upgrade?
What would be the best way to fix this? Below are some of the errors I
am encountering with the print_qiime_config_all and join_paired_ends commands. <br><br></div>Thank you for your time and help, <br><br></div>Sincerely, <br><br></div>David Bradshaw<br><br><br>microbiology@microbiology-<wbr>OptiPlex-9020[microbiology] qiime [ 1:35PM]<br>join_paired_ends.py<br>Setting up ZSH (/bin/zsh) environment to run QIIME commands.<br><br>You have QIIME version UNKNOWN.<br>Note that this will not produce identical results to the official QIIME release<br>as it uses updated versions of several tools.<br><br>Type 'help' for help, 'print_qiime_config_all' to see the current QIIME<br>settings, or 'exit' to return to regular shell.<br><br>microbiology@microbiology-<wbr>OptiPlex-9020[microbiology] qiime > print_qiime_config_all<br>/usr/lib/python2.7/dist-<wbr>packages/matplotlib/font_<wbr>manager.py:273:
UserWarning: Matplotlib is building the font cache using fc-list. This
may take a moment.<br> warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')<br>Traceback (most recent call last):<br> File "/usr/lib/qiime/bin/print_<wbr>qiime_config.py", line 57, in <module><br> raise ImportError("%s\n%s" % (e, core_dependency_missing_msg))<br>ImportError: cannot import name OrdinationResults<br>See the QIIME Installation Guide: <a href="http://qiime.org/install/install.html" target="_blank" rel="nofollow">http://qiime.org/install/<wbr>install.html</a><br><br>Here are the versions of the packages that QIIME depends on as reported by<br>the system package manager:<br><br>ampliconnoise : 1.29-5build1<br>blast2 : 1:2.2.26.20120620-10<br>bwa : 0.7.12-5<br>cd-hit : 4.6.4-1<br>chimeraslayer : 20101212+dfsg1-1<br>clearcut : 1.0.9-1<br>clustalw : 2.1+lgpl-4<br>ea-utils : 1.1.2+dfsg-3<br>emperor : 0.9.51-0biolinux1<br>fasttree : 2.1.8-2<br>infernal : 1.1.1-3<br>mafft : 7.271-1<br>mothur : 1.36.1-1build1<br>muscle : 1:3.8.31+dfsg-1<br>parsinsert : 1.04-1biolinux1.1<br>pynast : 1.2.2-1<br>python : 2.7.11-1<br>python-biom-format : 2.1.5+dfsg-1<br>python-burrito : 0.9.1-1<br>python-burrito-fillings : 0.1.0-0biolinux4<br>python-cogent : 1.5.3-10<br>python-matplotlib : 1.5.1-1ubuntu1<br>python-mpi4py : 1.3.1+hg20131106-2ubuntu5<br>python-numpy : 1:1.11.0-1ubuntu1<br>python-pandas : 0.17.1-3ubuntu2<br>python-qcli : 0.1.0-1<br>python : 2.7.11-1<br>qiime-data : 1.9.0+dfsg-0biolinux5<br>qiime-default-reference : 0.1.1-0biolinux2<br>r-cran-optparse : 1.3.0-1cran1ppa0<br>raxml : 8.2.4-1<br>rdp-classifier : 2.10.2-1<br>seqprep : 1.1-4ubuntu1<br>sortmerna : 2.0-1<br>sumatra : 1.0.10-1<br>swarm : 2.1.6-1<br>vsearch : 1.1.3+dfsg-1<br><br>OK<br>microbiology@microbiology-<wbr>OptiPlex-9020[microbiology]
qiime > join_paired_ends.py -f
DCH2_062216/4653_C1S616-515wF-<wbr>806bR_R1.fastq -r
DCH2_062216/4653_C1S616-515wF-<wbr>806bR_R2.fastq -o C1S616<br>/usr/lib/python2.7/dist-<wbr>packages/matplotlib/font_<wbr>manager.py:273:
UserWarning: Matplotlib is building the font cache using fc-list. This
may take a moment.<br> warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')<br>Traceback (most recent call last):<br> File "/usr/lib/qiime/bin/join_<wbr>paired_ends.py", line 11, in <module><br> from qiime.join_paired_ends import (join_method_names,<br> File "/usr/lib/python2.7/dist-<wbr>packages/qiime/join_paired_<wbr>ends.py", line 11, in <module><br> from skbio.parse.sequences import parse_fastq<br>ImportError: No module named parse.sequences</div>