[Bio-linux-list] Updated to Ubuntu 16.04 and now I am having problems with qiime

David Bradshaw dbradshaw3366 at gmail.com
Fri Aug 12 16:00:50 EDT 2016


Dear Whom It May Concern,

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.

Thank you for your time and help,

Sincerely,

David Bradshaw


microbiology at microbiology-OptiPlex-9020[microbiology] qiime           [
1:35PM]
join_paired_ends.py
Setting up ZSH (/bin/zsh) environment to run QIIME commands.

You have QIIME version UNKNOWN.
Note that this will not produce identical results to the official QIIME
release
as it uses updated versions of several tools.

Type 'help' for help, 'print_qiime_config_all' to see the current QIIME
settings, or 'exit' to return to regular shell.

microbiology at microbiology-OptiPlex-9020[microbiology]  qiime >
print_qiime_config_all
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273:
UserWarning: Matplotlib is building the font cache using fc-list. This may
take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This
may take a moment.')
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 57, in <module>
    raise ImportError("%s\n%s" % (e, core_dependency_missing_msg))
ImportError: cannot import name OrdinationResults
See the QIIME Installation Guide: http://qiime.org/install/install.html

Here are the versions of the packages that QIIME depends on as reported by
the system package manager:

ampliconnoise             : 1.29-5build1
blast2                    : 1:2.2.26.20120620-10
bwa                       : 0.7.12-5
cd-hit                    : 4.6.4-1
chimeraslayer             : 20101212+dfsg1-1
clearcut                  : 1.0.9-1
clustalw                  : 2.1+lgpl-4
ea-utils                  : 1.1.2+dfsg-3
emperor                   : 0.9.51-0biolinux1
fasttree                  : 2.1.8-2
infernal                  : 1.1.1-3
mafft                     : 7.271-1
mothur                    : 1.36.1-1build1
muscle                    : 1:3.8.31+dfsg-1
parsinsert                : 1.04-1biolinux1.1
pynast                    : 1.2.2-1
python                    : 2.7.11-1
python-biom-format        : 2.1.5+dfsg-1
python-burrito            : 0.9.1-1
python-burrito-fillings   : 0.1.0-0biolinux4
python-cogent             : 1.5.3-10
python-matplotlib         : 1.5.1-1ubuntu1
python-mpi4py             : 1.3.1+hg20131106-2ubuntu5
python-numpy              : 1:1.11.0-1ubuntu1
python-pandas             : 0.17.1-3ubuntu2
python-qcli               : 0.1.0-1
python                    : 2.7.11-1
qiime-data                : 1.9.0+dfsg-0biolinux5
qiime-default-reference   : 0.1.1-0biolinux2
r-cran-optparse           : 1.3.0-1cran1ppa0
raxml                     : 8.2.4-1
rdp-classifier            : 2.10.2-1
seqprep                   : 1.1-4ubuntu1
sortmerna                 : 2.0-1
sumatra                   : 1.0.10-1
swarm                     : 2.1.6-1
vsearch                   : 1.1.3+dfsg-1

OK
microbiology at microbiology-OptiPlex-9020[microbiology]  qiime >
join_paired_ends.py -f DCH2_062216/4653_C1S616-515wF-806bR_R1.fastq -r
DCH2_062216/4653_C1S616-515wF-806bR_R2.fastq -o C1S616
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273:
UserWarning: Matplotlib is building the font cache using fc-list. This may
take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This
may take a moment.')
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/join_paired_ends.py", line 11, in <module>
    from qiime.join_paired_ends import (join_method_names,
  File "/usr/lib/python2.7/dist-packages/qiime/join_paired_ends.py", line
11, in <module>
    from skbio.parse.sequences import parse_fastq
ImportError: No module named parse.sequences
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