Hey @ChristianEdwardson,
Sorry for taking so long to get back to this. Your conda looks to be up-to-date, so that’s good.
From your first file, I see this:
PATH: /home/christian/miniconda3/bin:/home/christian/MyTaxa-master:/home/christian/.rbenv/plugins/ruby-build/bin:/home/christian/.rbenv/shims:/home/christian/.rbenv/bin:/home/christian/miniconda3/bin:/home/christian/biobakery-metaphlan2-5ea2bdea8b78:/home/christian/biobakery-metaphlan2-5ea2bdea8b78/utils/:/home/christian/pipits/bin:/usr/lib/:/home/christian/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer:/home/christian/qiime_software/chimeraslayer-4.29.2010-release/NAST-iEr:/home/christian/qiime_software/cytoscape-2.7.0-release/.:/home/christian/qiime_software/rdpclassifier-2.2-release/.:/home/christian/qiime_software/muscle-3.8.31-release/.:/home/christian/qiime_software/ea-utils-1.1.2-537-release/.:/home/christian/qiime_software/blast-2.2.22-release/bin:/home/christian/qiime_software/qiime-galaxy-0.0.1-repository-de3646d3/scripts:/home/christian/qiime_software/ampliconnoise-1.27-release/Scripts:/home/christian/qiime_software/ampliconnoise-1.27-release/bin:/home/christian/qiime_software/raxml-7.3.0-release/.:/home/christian/qiime_software/drisee-1.2-release/.:/home/christian/qiime_software/clearcut-1.0.9-release/.:/home/christian/qiime_software/cdbtools-10.11.2010-release/.:/home/christian/qiime_software/pprospector-1.0.1-release/bin:/home/christian/qiime_software/rtax-0.984-release/.:/home/christian/qiime_software/sourcetracker-1.0.0-release/.:/home/christian/qiime_software/tax2tree-1.0-release/bin:/home/christian/qiime_software/blat-34-release/.:/home/christian/bin:/home/christian/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/christian/bbmap_37.66:/home/christian/ngsutils-ngsutils-0.5.9/bin:/home/christian/mothur:/home/christian/sratoolkit.2.8.1-2-ubuntu64/bin:/home/christian/SPAdes-3.11.1-Linux/bin:/home/christian/ncbi-blast-2.7.1+/bin:/home/christian/bowtie2-2.3.3.1-linux-x86_64:/home/christian/MUMmer3.23:/home/christian/arb/bin:/home/christian/edirect:/home/christian/centrifuge/centrifuge:/home/christian/eggnog-mapper-1.0.3:/home/christian/apache-maven-3.5.2/bin:/home/christian/ESOM/bin:/home/christian/prokka/bin:/home/christian/barrnap-0.8/bin:/home/christian/FastTree:/home/christian/phylophlan:/home/christian/phyloskeleton::/home/christian/phyloskeleton/utils:/home/christian/miniconda3/bin
PYTHONPATH: /home/christian/qiime_software/qiime-galaxy-0.0.1-repository-de3646d3/lib/:/home/christian/qiime_software/pprospector-1.0.1-release/lib/python2.7/site-packages:/home/christian/qiime_software/tax2tree-1.0-release/lib/python2.7/site-packages:
It looks like you have a PYTHONPATH set as well as a lot of other things in your PATH. While I don’t know that this is the issue, it can cause trouble sometimes. Since you have QIIME 2018.2, I’m not sure why it would suddenly be an issue.
Your root environment is a bit polluted with other packages, but once again, nothing stands out as really being a problem.
The number of clobberwarnings from your install output is pretty impressive.
Let’s try a few other things, because other than the ENV variables potentially being an issue, nothing else seems terribly out of place.
I guess the first step is to entirely rule out the path situation.
In a new terminal, run:
export PATH='/home/christian/miniconda3/bin:/home/christian/bin:/home/christian/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
unset PYTHONPATH
That will make things more “normal” for the remainder of that terminal session.
Then try reinstalling.
If you get the same issue, we’ll try another more extreme thing:
rm -r /home/christian/miniconda3/pkgs
This will entirely remove the conda package cache (conda will remake the directory).
Then try reinstalling again.