Hi there,
I have the same plugin error as Nathan.
I removed and reinstalled fasttree, as well as q2-phylogeny, as suggested above.
Now ‘phylogeny’ is no longer recognized as a command, and the phylogeny plugin is not listed in the Installed Plugin list returned by qiime info.
Am I missing something? Is there another way to reinstall fasttree and q2-phylogeny? I am using a Linux.
Any help would be great! Thanks!
Hi @Adrian_08, it sounds like maybe you didn’t run all of the commands that @gregcaporaso suggested in your QIIME 2 conda environment. You need to make sure that your conda environment is activated first - if you followed our docs, that environment would be named qiime2-2017.4, so, you would run something like this:
source activate qiime2-2017.4
conda install -c bioconda fasttree
conda install -c qiime2 q2-phylogeny
Hope that helps!
Hi Matthew, thanks for the reply.
Yes I am working in my activated Qiime2 conda environment.
Both install commands run without any error messages.
Hmm, when you run qiime info in your conda environment you don’t see the phylogeny plugin listed? Can you provide the output from the following command: conda list (make sure to run this in your QIIME 2 conda environment)? Maybe your environment was corrupted somehow — perhaps you could try deleting the environment and reinstalling QIIME 2. Thanks!
Nope, phylogeny 2017.4.0 is gone from the plugin list.
This is the prompt I get with conda install c- qiime2 q2-phylogeny:
The following NEW packages will be INSTALLED:
arrow: 0.8.0-py35_0 qiime2
binaryornot: 0.3.0-0_ge797740 qiime2
cookiecutter: 1.4.0-py35_0 qiime2
ipymd: 0.1.2-py35_0 qiime2
jinja2-time: 0.2.0-py35_0 qiime2
jupyter: 1.0.0-py35_3
jupyter_console: 5.1.0-py35_0
poyo: 0.4.0-py35_0 qiime2
python-frontmatter: 0.2.1-py35_0 qiime2
q2-phylogeny: 0.0.6-py35_0 qiime2
qiime: 2.0.6-py35_0 qiime2
qtconsole: 4.3.0-py35_0
whichcraft: 0.4.0-py35_0 qiime2
And this is the conda list after removing and reinstalling fasttree and q2-phylogeny:
arrow 0.8.0 py35_0 qiime2 binaryornot 0.3.0 0_ge797740 qiime2 bioconductor-biobase 2.34.0 r3.3.1_0 bioconda bioconductor-biocgenerics 0.20.0 r3.3.1_0 bioconda bioconductor-biocparallel 1.6.6 r3.3.1_0 bioconda bioconductor-biostrings 2.40.2 r3.3.1_0 bioconda bioconductor-dada2 1.2 r3.3.1_0 bioconda bioconductor-genomeinfodb 1.8.7 r3.3.1_0 bioconda bioconductor-genomicalignments 1.8.4 r3.3.1_0 bioconda bioconductor-genomicranges 1.26.1 r3.3.1_1 bioconda bioconductor-iranges 2.8.0 r3.3.1_0 bioconda bioconductor-rsamtools 1.24.0 r3.3.1_0 bioconda bioconductor-s4vectors 0.12.0 r3.3.1_0 bioconda bioconductor-shortread 1.32.0 r3.3.1_0 bioconda bioconductor-summarizedexperiment 1.2.3 r3.3.1_0 bioconda bioconductor-xvector 0.12.1 r3.3.1_0 bioconda bioconductor-zlibbioc 1.20.0 r3.3.1_0 bioconda biom-format 2.1.5 py35_3 qiime2 blast 2.6.0 boost1.61_0 bioconda bleach 1.5.0 py35_0 bokeh 0.12.5 py35_0 boost 1.61.0 py35_0 bzip2 1.0.6 3 cachecontrol 0.11.7 py35_0 cairo 1.14.8 0 click 6.7 py35_0 cookiecutter 1.4.0 py35_0 qiime2 curl 7.52.1 0 cycler 0.10.0 py35_0 dbus 1.10.10 0 deblur 1.0.2 py35_0 biocore decorator 4.0.11 py35_0 emperor 1.0.0beta5 py35_2 conda-forge entrypoints 0.2.2 py35_1 expat 2.1.0 0 fasttree 2.1.9 1 bioconda fontconfig 2.12.1 3 freetype 2.5.5 2 future 0.16.0 py35_1 glib 2.50.2 1 gsl 2.2.1 0 gst-plugins-base 1.8.0 0 gstreamer 1.8.0 0 h5py 2.7.0 np112py35_0 harfbuzz 0.9.39 2 hdf5 1.8.17 1 html5lib 0.999 py35_0 icu 54.1 0 ijson 2.3 py35_0 qiime2 ipykernel 4.6.1 py35_0 ipymd 0.1.2 py35_0 qiime2 ipython 5.3.0 py35_0 ipython_genutils 0.2.0 py35_0 ipywidgets 6.0.0 py35_0 jbig 2.1 0 jinja2 2.9.6 py35_0 jinja2-time 0.2.0 py35_0 qiime2 jpeg 9b 0 jsonschema 2.6.0 py35_0 jupyter 1.0.0 py35_3 jupyter_client 5.0.1 py35_0 jupyter_console 5.1.0 py35_0 jupyter_core 4.3.0 py35_0 libffi 3.2.1 1 libgcc 5.2.0 0 libgfortran 3.0.0 1 libiconv 1.14 0 libpng 1.6.27 0 libsodium 1.0.10 0 libtiff 4.0.6 3 libxcb 1.12 1 libxml2 2.9.4 0 lockfile 0.12.2 py35_0 mafft 7.221 0 bioconda markupsafe 0.23 py35_2 matplotlib 2.0.0 np112py35_0 mistune 0.7.4 py35_0 mkl 2017.0.1 0 natsort 5.0.2 py35_0 nbconvert 5.1.1 py35_0 nbformat 4.3.0 py35_0 ncurses 5.9 10 nose 1.3.7 py35_1 notebook 5.0.0 py35_0 numpy 1.12.1 py35_0 openssl 1.0.2k 1 pandas 0.19.2 np112py35_1 pandocfilters 1.4.1 py35_0 pango 1.40.3 1 path.py 10.3.1 py35_0 patsy 0.4.1 py35_0 pcre 8.39 1 pexpect 4.2.1 py35_0 pickleshare 0.7.4 py35_0 pip 9.0.1 py35_1 pixman 0.34.0 0 poyo 0.4.0 py35_0 qiime2 prompt_toolkit 1.0.14 py35_0 psutil 5.2.2 py35_0 ptyprocess 0.5.1 py35_0 pygments 2.2.0 py35_0 pyparsing 2.1.4 py35_0 pyqt 5.6.0 py35_2 python 3.5.3 1 python-dateutil 2.6.0 py35_0 python-frontmatter 0.2.1 py35_0 qiime2 pytz 2017.2 py35_0 pyyaml 3.12 py35_0 pyzmq 16.0.2 py35_0 q2-alignment 2017.4.0 py35_0 qiime2/label/2017.4 q2-composition 2017.4.0 py35_0 qiime2/label/2017.4 q2-dada2 2017.4.0 py35_0 qiime2/label/2017.4 q2-deblur 2017.4.0 py35_0 qiime2/label/2017.4 q2-demux 2017.4.0 py35_0 qiime2/label/2017.4 q2-diversity 2017.4.0 py35_0 qiime2/label/2017.4 q2-emperor 2017.4.0 py35_0 qiime2/label/2017.4 q2-feature-classifier 2017.4.0 py35_0 qiime2/label/2017.4 q2-feature-table 2017.4.0 py35_0 qiime2/label/2017.4 q2-phylogeny 0.0.6 py35_0 qiime2 q2-quality-filter 2017.4.0 py35_0 qiime2/label/2017.4 q2-taxa 2017.4.0 py35_0 qiime2/label/2017.4 q2-types 2017.4.0 py35_0 qiime2/label/2017.4 q2cli 2017.4.0 py35_0 qiime2/label/2017.4 q2templates 2017.4.0 py35_0 qiime2/label/2017.4 qiime 2.0.6 py35_0 qiime2 qiime2 2017.4.0 py35_0 qiime2/label/2017.4 qt 5.6.2 3 qtconsole 4.3.0 py35_0 r 3.3.1 r3.3.1_1 r-assertthat 0.1 r3.3.1_4 r-base 3.3.1 6 r-bh 1.62.0_1 r3.3.1_0 r-bitops 1.0_6 r3.3.1_2 r-boot 1.3_18 r3.3.1_0 r-class 7.3_14 r3.3.1_0 r-cluster 2.0.5 r3.3.1_0 r-codetools 0.2_15 r3.3.1_0 r-colorspace 1.3_1 r3.3.1_0 r-data.table 1.10.0 r3.3.1_0 r-dichromat 2.0_0 r3.3.1_2 r-digest 0.6.10 r3.3.1_0 r-foreign 0.8_67 r3.3.1_0 r-futile.logger 1.4.1 r3.3.1_0 bioconda r-futile.options 1.0.0 r3.3.1_0 bioconda r-ggplot2 2.2.0 r3.3.1_0 r-gtable 0.2.0 r3.3.1_0 r-hwriter 1.3.2 r3.3.1_0 bioconda r-kernsmooth 2.23_15 r3.3.1_0 r-labeling 0.3 r3.3.1_2 r-lambda.r 1.1.7 r3.3.1_0 bioconda r-lattice 0.20_34 r3.3.1_0 r-latticeextra 0.6_28 r3.3.1_0 r-lazyeval 0.2.0 r3.3.1_0 r-magrittr 1.5 r3.3.1_2 r-mass 7.3_45 r3.3.1_0 r-matrix 1.2_7.1 r3.3.1_0 r-mgcv 1.8_12 r3.3.1_0 r-munsell 0.4.3 r3.3.1_0 r-nlme 3.1_128 r3.3.1_0 r-nnet 7.3_12 r3.3.1_0 r-plyr 1.8.4 r3.3.1_0 r-rcolorbrewer 1.1_2 r3.3.1_3 r-rcpp 0.12.8 r3.3.1_0 r-rcppparallel 4.3.20 r3.3.1_1 bioconda r-recommended 3.3.1 r3.3.1_0 r-reshape2 1.4.2 r3.3.1_0 r-rpart 4.1_10 r3.3.1_0 r-scales 0.4.1 r3.3.1_0 r-snow 0.4_1 r3.3.1_0 bioconda r-spatial 7.3_11 r3.3.1_0 r-stringi 1.1.2 r3.3.1_0 r-stringr 1.1.0 r3.3.1_0 r-survival 2.39_4 r3.3.1_0 r-tibble 1.2 r3.3.1_0 readline 6.2 2 requests 2.13.0 py35_0 scikit-bio 0.5.1 py35_0 biocore scikit-learn 0.18.1 np112py35_1 scipy 0.19.0 np112py35_0 seaborn 0.7.1 py35_0 setuptools 27.2.0 py35_0 simplegeneric 0.8.1 py35_1 sip 4.18 py35_0 six 1.10.0 py35_0 sortmerna 2.0 0 biocore sqlite 3.13.0 0 statsmodels 0.8.0 np112py35_0 terminado 0.6 py35_0 testpath 0.3 py35_0 tk 8.5.18 0 tornado 4.4.2 py35_0 traitlets 4.3.2 py35_0 tzlocal 1.3 py35_0 qiime2 vsearch 2.0.3 0 bioconda wcwidth 0.1.7 py35_0 wheel 0.29.0 py35_0 whichcraft 0.4.0 py35_0 qiime2 widgetsnbextension 2.0.0 py35_0 xz 5.2.2 1 yaml 0.1.6 0 zeromq 4.1.5 0 zlib 1.2.8 3
Okay, thanks for that info! Somehow you wound up with multiple versions of QIIME 2 installed in your conda environment. You need to remove that environment, reinstall QIIME 2, then if you are still having the fasttree issue, you can reinstall fasttree.
conda env remove -n qiime2-2017.4
conda create -n qiime2-2017.4 --file https://data.qiime2.org/distro/core/qiime2-2017.4-conda-linux-64.txt
conda install -c bioconda fasttree
Please note, you don’t need to uninstall and reinstall q2-phylogeny, that step in @gregcaporaso’s post doesn’t apply here.
Removing the environment and updating fasttree to the bioconda version solved the problem.
Thank you!
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