where is the "feature-classifier" plugin?

when I tried to use the “feature-classifier”, it said
“(qiime2-2019.4) [email protected]:~/qiime2/humanbody$ qiime feature-classifier
Error: QIIME 2 has no plugin/command named 'feature-classifier’.”
I also used the command “qiime --help” to list all the plugins, indeed, there is no “feature classifier”.
I am using the qiime2-2019.4, and I also found the qiime2docs said the plugin exists
Also, “types” is missing.

Blockquote
https://docs.qiime2.org/2019.4/plugins/available/feature-classifier/
. but for me, it hides itself, who would like to help tell me why? Thanks a lot!

Hello @Decen!

Hmm, looks like it was uninstalled somehow. Can you run the following and include the entire output here?

conda list --revisions

This only shows commands that can be run. To list all plugins, please run qiime info.

Hi Thermokarst,

I run conda list --revisions, I can see

2019-06-14 14:02:39  (rev 0)
    +_r-mutex-1.0.0
    +arb-bio-tools-6.0.6 (bioconda)
    +asn1crypto-0.24.0 (conda-forge)
    +atomicwrites-1.3.0 (conda-forge)
    +attrs-19.1.0 (conda-forge)
    +backcall-0.1.0 (conda-forge)
    +bibtexparser-1.1.0 (conda-forge)
    +binutils_impl_linux-64-2.31.1
    +binutils_linux-64-2.31.1
    +bioconductor-biobase-2.42.0 (bioconda)
    +bioconductor-biocgenerics-0.28.0 (bioconda)
    +bioconductor-biocparallel-1.16.6 (bioconda)
    +bioconductor-biostrings-2.50.2 (bioconda)
    +bioconductor-dada2-1.10.0 (bioconda)
    +bioconductor-delayedarray-0.8.0 (bioconda)
    +bioconductor-genomeinfodb-1.18.1 (bioconda)
    +bioconductor-genomeinfodbdata-1.2.0 (bioconda)
    +bioconductor-genomicalignments-1.18.1 (bioconda)
    +bioconductor-genomicranges-1.34.0 (bioconda)
    +bioconductor-iranges-2.16.0 (bioconda)
    +bioconductor-rsamtools-1.34.0 (bioconda)
    +bioconductor-s4vectors-0.20.1 (bioconda)
    +bioconductor-shortread-1.40.0 (bioconda)
    +bioconductor-summarizedexperiment-1.12.0 (bioconda)
    +bioconductor-xvector-0.22.0 (bioconda)
    +bioconductor-zlibbioc-1.28.0 (bioconda)
    +biom-format-2.1.7 (conda-forge)
    +blas-1.1 (conda-forge)
    +blast-2.7.1 (bioconda)
    +bleach-3.1.0 (conda-forge)
    +bokeh-1.1.0 (conda-forge)
    +boost-1.67.0 (conda-forge)
    +boost-cpp-1.67.0 (conda-forge)
    +bwidget-1.9.11
    +bz2file-0.98 (conda-forge)
    +bzip2-1.0.6 (conda-forge)
    +ca-certificates-2019.3.9 (conda-forge)
    +cachecontrol-0.12.5 (conda-forge)
    +cairo-1.16.0 (conda-forge)
    +certifi-2019.3.9 (conda-forge)
    +cffi-1.12.3 (conda-forge)
    +chardet-3.0.4 (conda-forge)
    +click-7.0 (conda-forge)
    +cryptography-2.6.1 (conda-forge)
    +curl-7.64.1 (conda-forge)
    +cutadapt-2.3 (bioconda)
    +cycler-0.10.0 (conda-forge)
    +dbus-1.13.6 (conda-forge)
    +deblur-1.1.0 (bioconda)
    +decorator-4.4.0 (conda-forge)
    +defusedxml-0.5.0 (conda-forge)
    +dnaio-0.3 (bioconda)
    +emperor-1.0.0b19 (conda-forge)
    +entrypoints-0.3 (conda-forge)
    +expat-2.2.5 (conda-forge)
    +fastcluster-1.1.25 (conda-forge)
    +fasttree-2.1.10 (bioconda)
    +fontconfig-2.13.1 (conda-forge)
    +freetype-2.10.0 (conda-forge)
    +future-0.17.1 (conda-forge)
    +gcc_impl_linux-64-7.3.0 (conda-forge)
    +gcc_linux-64-7.3.0 (conda-forge)
    +gettext-0.19.8.1 (conda-forge)
    +gfortran_impl_linux-64-7.3.0
    +gfortran_linux-64-7.3.0
    +glib-2.58.3 (conda-forge)
    +gmp-6.1.2 (conda-forge)
    +gneiss-0.4.4 (bioconda)
    +gnutls-3.5.19 (conda-forge)
    +graphite2-1.3.13 (conda-forge)
    +gsl-2.4 (conda-forge)
    +gst-plugins-base-1.14.4 (conda-forge)
    +gstreamer-1.14.4 (conda-forge)
    +gxx_impl_linux-64-7.3.0 (conda-forge)
    +gxx_linux-64-7.3.0 (conda-forge)
    +h5py-2.9.0 (conda-forge)
    +harfbuzz-2.4.0 (conda-forge)
    +hdf5-1.10.4 (conda-forge)
    +hdmedians-0.13 (conda-forge)
    +icu-58.2 (conda-forge)
    +idna-2.8 (conda-forge)
    +ijson-2.3 (conda-forge)
    +ipykernel-5.1.0 (conda-forge)
    +ipython-7.5.0 (conda-forge)
    +ipython_genutils-0.2.0 (conda-forge)
    +ipywidgets-7.4.2 (conda-forge)
    +iqtree-1.6.10 (bioconda)
    +jedi-0.13.3 (conda-forge)
    +jinja2-2.10.1 (conda-forge)
    +jpeg-9c (conda-forge)
    +jsonschema-3.0.1 (conda-forge)
    +jupyter_client-5.2.4 (conda-forge)
    +jupyter_core-4.4.0 (conda-forge)
    +kiwisolver-1.1.0 (conda-forge)
    +krb5-1.16.3 (conda-forge)
    +libarbdb-6.0.6 (bioconda)
    +libcurl-7.64.1 (conda-forge)
    +libedit-3.1.20170329 (conda-forge)
    +libffi-3.2.1 (conda-forge)
    +libgcc-7.2.0 (conda-forge)
    +libgcc-ng-8.2.0
    +libgfortran-ng-7.3.0
    +libiconv-1.15 (conda-forge)
    +libidn2-2.1.1 (conda-forge)
    +libpng-1.6.37 (conda-forge)
    +libsodium-1.0.16 (conda-forge)
    +libssh2-1.8.2 (conda-forge)
    +libstdcxx-ng-8.2.0
    +libtiff-4.0.10 (conda-forge)
    +libunistring-0.9.10 (conda-forge)
    +libuuid-2.32.1 (conda-forge)
    +libxcb-1.13 (conda-forge)
    +libxml2-2.9.9 (conda-forge)
    +lockfile-0.12.2 (conda-forge)
    +lz4-c-1.8.3 (conda-forge)
    +mafft-7.310 (bioconda)
    +make-4.2.1 (conda-forge)
    +markupsafe-1.1.1 (conda-forge)
    +matplotlib-3.0.3 (conda-forge)
    +matplotlib-base-3.0.3 (conda-forge)
    +mistune-0.8.4 (conda-forge)
    +more-itertools-4.3.0 (conda-forge)
    +msgpack-python-0.6.1 (conda-forge)
    +natsort-6.0.0 (conda-forge)
    +nbconvert-5.5.0 (conda-forge)
    +nbformat-4.4.0 (conda-forge)
    +ncurses-6.1 (conda-forge)
    +nettle-3.3 (conda-forge)
    +networkx-2.3 (conda-forge)
    +nose-1.3.7 (conda-forge)
    +notebook-5.7.8 (conda-forge)
    +numpy-1.16.2 (conda-forge)
    +olefile-0.46 (conda-forge)
    +openblas-0.3.3 (conda-forge)
    +openjdk-11.0.1 (conda-forge)
    +openssl-1.1.1b (conda-forge)
    +packaging-19.0 (conda-forge)
    +pandas-0.24.2 (conda-forge)
    +pandoc-2.7.2 (conda-forge)
    +pandocfilters-1.4.2 (conda-forge)
    +pango-1.40.14 (conda-forge)
    +parso-0.4.0 (conda-forge)
    +patsy-0.5.1 (conda-forge)
    +pcre-8.41 (conda-forge)
    +perl-5.26.2 (conda-forge)
    +perl-archive-tar-2.32 (bioconda)
    +perl-carp-1.38 (bioconda)
    +perl-compress-raw-bzip2-2.086 (bioconda)
    +perl-compress-raw-zlib-2.086 (bioconda)
    +perl-exporter-5.72 (bioconda)
    +perl-exporter-tiny-1.002001 (bioconda)
    +perl-extutils-makemaker-7.36 (bioconda)
    +perl-io-compress-2.086 (bioconda)
    +perl-io-zlib-1.10 (bioconda)
    +perl-list-moreutils-0.428 (bioconda)
    +perl-list-moreutils-xs-0.428 (bioconda)
    +perl-pathtools-3.75 (bioconda)
    +perl-scalar-list-utils-1.45 (bioconda)
    +perl-xsloader-0.24 (bioconda)
    +pexpect-4.7.0 (conda-forge)
    +pickleshare-0.7.5 (conda-forge)
    +pigz-2.3.4 (conda-forge)
    +pillow-6.0.0 (conda-forge)
    +pip-19.1.1 (conda-forge)
    +pixman-0.34.0 (conda-forge)
    +pluggy-0.11.0 (conda-forge)
    +prometheus_client-0.6.0 (conda-forge)
    +prompt_toolkit-2.0.9 (conda-forge)
    +psutil-5.6.2 (conda-forge)
    +pthread-stubs-0.4 (conda-forge)
    +ptyprocess-0.6.0 (conda-forge)
    +py-1.8.0 (conda-forge)
    +pycparser-2.19 (conda-forge)
    +pygments-2.4.0 (conda-forge)
    +pyopenssl-19.0.0 (conda-forge)
    +pyparsing-2.3.0 (conda-forge)
    +pyqt-5.9.2 (conda-forge)
    +pyrsistent-0.15.1 (conda-forge)
    +pysocks-1.6.8 (conda-forge)
    +pytest-4.4.2 (conda-forge)
    +python-3.6.7 (conda-forge)
    +python-dateutil-2.8.0 (conda-forge)
    +pytz-2019.1 (conda-forge)
    +pyyaml-5.1.1 (conda-forge)
    +pyzmq-18.0.1 (conda-forge)
    *+q2-alignment-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-composition-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-cutadapt-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-dada2-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-deblur-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-demux-2019.4.1 (qiime2/label/r2019.4)*
*    +q2-diversity-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-emperor-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-feature-classifier-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-feature-table-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-fragment-insertion-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-gneiss-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-longitudinal-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-metadata-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-phylogeny-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-quality-control-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-quality-filter-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-sample-classifier-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-taxa-2019.4.0 (qiime2/label/r2019.4)*
*    +q2-types-2019.4.1 (qiime2/label/r2019.4)*
*    +q2-vsearch-2019.4.0 (qiime2/label/r2019.4)*
*    +q2cli-2019.4.0 (qiime2/label/r2019.4)*
*    +q2templates-2019.4.0 (qiime2/label/r2019.4)*
*    +qiime2-2019.4.0 (qiime2/label/r2019.4)*
    +qt-5.9.7 (conda-forge)
    +r-assertthat-0.2.1 (conda-forge)
    +r-base-3.5.1 (conda-forge)
    +r-bh-1.69.0_1 (conda-forge)
    +r-bitops-1.0_6 (conda-forge)
    +r-cli-1.1.0 (conda-forge)
    +r-cluster-2.0.9 (conda-forge)
    +r-colorspace-1.4_1 (conda-forge)
    +r-crayon-1.3.4 (conda-forge)
    +r-data.table-1.12.2 (conda-forge)
    +r-digest-0.6.18 (conda-forge)
    +r-fansi-0.4.0 (conda-forge)
    +r-formatr-1.6 (conda-forge)
    +r-futile.logger-1.4.3 (conda-forge)
    +r-futile.options-1.0.1 (conda-forge)
    +r-ggplot2-3.1.1 (conda-forge)
    +r-glue-1.3.1 (conda-forge)
    +r-gtable-0.3.0 (conda-forge)
    +r-hwriter-1.3.2 (conda-forge)
    +r-labeling-0.3 (conda-forge)
    +r-lambda.r-1.2.3 (conda-forge)
    +r-lattice-0.20_38 (conda-forge)
    +r-latticeextra-0.6_28 (conda-forge)
    +r-lazyeval-0.2.2 (conda-forge)
    +r-magrittr-1.5 (conda-forge)
    +r-mass-7.3_51.4 (conda-forge)
    +r-matrix-1.2_17 (conda-forge)
    +r-matrixstats-0.54.0 (conda-forge)
    +r-mgcv-1.8_28 (conda-forge)
    +r-munsell-0.5.0 (conda-forge)
    +r-nlme-3.1_139 (conda-forge)
    +r-permute-0.9_5 (conda-forge)
    +r-pillar-1.3.1 (conda-forge/label/gcc7)
    +r-pkgconfig-2.0.2 (conda-forge)
    +r-plyr-1.8.4 (conda-forge)
    +r-r6-2.4.0 (conda-forge)
    +r-rcolorbrewer-1.1_2 (conda-forge)
    +r-rcpp-1.0.1 (conda-forge)
    +r-rcppparallel-4.4.2 (conda-forge)
    +r-rcurl-1.95_4.12 (conda-forge)
    +r-reshape2-1.4.3 (conda-forge)
    +r-rlang-0.3.4 (conda-forge)
    +r-scales-1.0.0 (conda-forge)
    +r-snow-0.4_3 (conda-forge)
    +r-stringi-1.4.3 (conda-forge)
    +r-stringr-1.4.0 (conda-forge)
    +r-tibble-2.1.1 (conda-forge)
    +r-utf8-1.1.4 (conda-forge)
    +r-vegan-2.5_4 (conda-forge)
    +r-viridislite-0.3.0 (conda-forge)
    +r-withr-2.1.2 (conda-forge)
    +raxml-8.2.12 (bioconda)
    +readline-7.0 (conda-forge)
    +requests-2.21.0 (conda-forge)
    +scikit-bio-0.5.5 (conda-forge)
    +scikit-learn-0.20.2 (conda-forge)
    +scipy-1.2.1 (conda-forge)
    +seaborn-0.9.0 (conda-forge)
    +send2trash-1.5.0 (conda-forge)
    +setuptools-41.0.1 (conda-forge)
    +sina-1.4.0 (bioconda)
    +sip-4.19.8 (conda-forge)
    +six-1.12.0 (conda-forge)
    +sortmerna-2.0 (bioconda)
    +sqlite-3.28.0 (conda-forge)
    +statsmodels-0.9.0 (conda-forge)
    +tbb-2019.6 (conda-forge)
    +terminado-0.8.2 (conda-forge)
    +testpath-0.4.2 (conda-forge)
    +tk-8.6.9 (conda-forge)
    +tktable-2.10
    +tornado-6.0.2 (conda-forge)
    +traitlets-4.3.2 (conda-forge)
    +tzlocal-1.5.1 (conda-forge)
    +unifrac-0.9.3 (bioconda)
    +urllib3-1.24.2 (conda-forge)
    +vsearch-2.7.0 (bioconda)
    +wcwidth-0.1.7 (conda-forge)
    +webencodings-0.5.1 (conda-forge)
    +wget-1.20.1 (conda-forge)
    +wheel-0.33.1 (conda-forge)
    +widgetsnbextension-3.4.2 (conda-forge)
    +xopen-0.5.1 (bioconda)
    +xorg-kbproto-1.0.7 (conda-forge)
    +xorg-libice-1.0.9 (conda-forge)
    +xorg-libsm-1.2.3 (conda-forge)
    +xorg-libx11-1.6.7 (conda-forge)
    +xorg-libxau-1.0.9 (conda-forge)
    +xorg-libxdmcp-1.1.3 (conda-forge)
    +xorg-libxext-1.3.4 (conda-forge)
    +xorg-libxrender-0.9.10 (conda-forge)
    +xorg-renderproto-0.11.1 (conda-forge)
    +xorg-xextproto-7.3.0 (conda-forge)
    +xorg-xproto-7.0.31 (conda-forge)
    +xz-5.2.4 (conda-forge)
    +yaml-0.1.7 (conda-forge)
    +zeromq-4.3.1 (conda-forge)
    +zlib-1.2.11 (conda-forge)
    +zstd-1.4.0 (conda-forge)

**2019-06-21 18:38:23  (rev 1)**
**     ca-certificates  {2019.3.9 (conda-forge) -> 2019.5.15}**
**     certifi  {2019.3.9 (conda-forge) -> 2019.6.16}**
**     openssl  {1.1.1b (conda-forge) -> 1.1.1c}**
**     scikit-learn  {0.20.2 (conda-forge) -> 0.19.1}**
**    -q2-feature-classifier-2019.4.0 (qiime2/label/r2019.4)**
**    +libopenblas-0.2.20**

and if I run qiime info, I can see

**System versions**
**Python version: 3.6.7**
**QIIME 2 release: 2019.4**
**QIIME 2 version: 2019.4.0**
**q2cli version: 2019.4.0**

**Installed plugins**
**alignment: 2019.4.0**
**composition: 2019.4.0**
**cutadapt: 2019.4.0**
**dada2: 2019.4.0**
**deblur: 2019.4.0**
**demux: 2019.4.1**
**diversity: 2019.4.0**
**emperor: 2019.4.0**
**feature-table: 2019.4.0**
**fragment-insertion: 2019.4.0**
**gneiss: 2019.4.0**
**longitudinal: 2019.4.0**
**metadata: 2019.4.0**
**phylogeny: 2019.4.0**
**quality-control: 2019.4.0**
**quality-filter: 2019.4.0**
**sample-classifier: 2019.4.0**
**taxa: 2019.4.0**
**types: 2019.4.1**
**vsearch: 2019.4.0**

Anyway, I do not find what’s wrong? Could you please help out?

Cheers,

Decen

Here is the problem right here — you appear to have upgraded scikit-learn (from 0.19.1 to 0.20.2), which uninstalled q2-feature-classifier. You should be able to reinstall by running:

conda install \
  -c qiime2-staging/label/r2019.4 \
  -c conda-forge \
  -c bioconda \
  -c defaults \
  --override-channels \
  q2-feature-classifier

Keep us posted!

1 Like

Hi ThermoKarst,

Thanks a lot! for the first time, I tried your command, but failed, then I tried the qiime2 command “conda install --override-channels -c defaults scikit-learn=0.20.2”, also failed, finally, I tried your command again, Pass. when I run “qiime info”, here it is.
Many many many thanks! but I also wanna know, if I use your command, will the newest vesion of “scikit-learn=XXXX” be installed? or the qiime 2 command “nda install --override-channels -c defaults scikit-learn=XXXX” can do the same thing?

Best,

Decen

Not necessarily, but the supported version of scikit-learn will be installed (for QIIME 2 2019.4, that version is 0.20.2 — no need for you to install separately).

My recommendation is to just stick to the official install directions, hope that helps!