testing classifiers.
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ref_seqs.qza --i-reference-taxonomy ref_taxa.qza --o-classifier nb_classifier.qza
long error…
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/bin/qiime”, line 11, in
sys.exit(qiime())
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 697, in main
rv = self.invoke(ctx)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 535, in invoke
return callback(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 244, in call
arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 326, in handle_in_params
kwargs, fallback=cmd_fallback)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/handlers.py”, line 375, in get_value
artifact = qiime2.sdk.Result.load(path)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 65, in load
archiver = archive.Archiver.load(filepath)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py”, line 301, in load
return cls(path, Format(rec))
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/format/v1.py”, line 29, in init
super().init(archive_record)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/format/v0.py”, line 72, in init
self.type = sdk.parse_type(type)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/util.py”, line 57, in parse_type
pm = qiime2.sdk.PluginManager()
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py”, line 44, in new
self._init()
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py”, line 59, in _init
plugin = entry_point.load()
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/pkg_resources/init.py”, line 2325, in load
return self.resolve()
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/pkg_resources/init.py”, line 2331, in resolve
module = import(self.module_name, fromlist=[‘name’], level=0)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_vsearch/plugin_setup.py”, line 12, in
import q2_vsearch._cluster_features
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py”, line 15, in
import skbio
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/init.py”, line 13, in
import skbio.io # noqa
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/io/init.py”, line 248, in
import_module(‘skbio.io.format.lsmat’)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/importlib/init.py”, line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/io/format/lsmat.py”, line 77, in
from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/stats/distance/init.py”, line 193, in
from ._base import (DissimilarityMatrixError, DistanceMatrixError,
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/stats/distance/_base.py”, line 12, in
from IPython.core.pylabtools import print_figure
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/IPython/init.py”, line 55, in
from .terminal.embed import embed
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/IPython/terminal/embed.py”, line 16, in
from IPython.terminal.interactiveshell import TerminalInteractiveShell
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/IPython/terminal/interactiveshell.py”, line 22, in
from prompt_toolkit.shortcuts import create_prompt_application, create_eventloop, create_prompt_layout, create_output
ImportError: cannot import name ‘create_prompt_application’
Any ideas?
Thanks Denise