Hello,
I have installed qiime2 2019.10 from conda and can activate the qiime environment with
source activate qiime2-2019.10
testing the installation with qiime --help also works
however when I run the following command
(qiime2-2019.10) Daniel-MacBook:P-009V_rerun2 danielcurtis$ qiime feature-table summarize \
--i-table Merged_table.qza
--o-visualization Merged_table.qzv
--m-sample-metadata-file turf_metadata.tsv
I get the following error
Traceback (most recent call last):
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/qiime", line 11, in
sys.exit(qiime())
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 1135, in invoke
sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 641, in make_context
self.parse_args(ctx, args)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/click/command.py", line 60, in parse_args
value, args = param.handle_parse_result(ctx, opts, args)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 1469, in handle_parse_result
value = self.full_process_value(ctx, value)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/click/option.py", line 149, in full_process_value
return super().full_process_value(ctx, value)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 1790, in full_process_value
return Parameter.full_process_value(self, ctx, value)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 1438, in full_process_value
value = self.process_value(ctx, value)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 1428, in process_value
return self.type_cast_value(ctx, value)
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/click/option.py", line 158, in type_cast_value
import qiime2.sdk.util
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/init.py", line 9, in
from qiime2.sdk import Artifact, Visualization
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/init.py", line 10, in
from .action import Action, Method, Visualizer, Pipeline
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 19, in
import qiime2.core.type as qtype
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/type/init.py", line 10, in
from .semantic import SemanticType, Properties
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/type/semantic.py", line 15, in
from qiime2.core.type.util import is_semantic_type, is_qiime_type
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/type/util.py", line 13, in
from qiime2.core.type.primitive import Int, Float, Bool, Str
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/type/primitive.py", line 13, in
import qiime2.metadata as metadata
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/metadata/init.py", line 9, in
from .metadata import (Metadata, MetadataColumn, NumericMetadataColumn,
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/metadata/metadata.py", line 16, in
import pandas as pd
File "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/init.py", line 17, in
"Unable to import required dependencies:\n" + "\n".join(missing_dependencies)
ImportError: Unable to import required dependencies:
numpy:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy c-extensions failed.
-
Try uninstalling and reinstalling numpy.
-
If you have already done that, then:
- Check that you expected to use Python3.6 from "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/python",
and that you have no directories in your PATH or PYTHONPATH that can
interfere with the Python and numpy version "1.17.3" you're trying to use. - If (1) looks fine, you can open a new issue at
Issues · numpy/numpy · GitHub. Please include details on:- how you installed Python
- how you installed numpy
- your operating system
- whether or not you have multiple versions of Python installed
- if you built from source, your compiler versions and ideally a build log
- Check that you expected to use Python3.6 from "/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/python",
-
If you're working with a numpy git repository, try
git clean -xdf
(removes all files not under version control) and rebuild numpy.
Note: this error has many possible causes, so please don't comment on
an existing issue about this - open a new one instead.
Original error was: dlopen(/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/numpy/core/_multiarray_umath.cpython-36m-darwin.so, 2): Library not loaded: /usr/local/gfortran/lib/libquadmath.0.dylib
Referenced from: /Users/danielcurtis/tcoffee/Version_11.00.8cbe486/gfortran/libgfortran.3.dylib
Reason: image not found
Other details as requested-
I am running qiime2 on macOS Mojave(v10.14.6)
numpy details
version: 1.17.13
build: py36hde6bac1_0
Channel: conda_forge
I believe numpy was installed from conda during the qiime2 installation
I have python 2.7.16 installed on my system but ensure python3 is running before I activate the qiime environment.
which python
/Users/danielcurtis/miniconda3/bin/python
python --version
Python 3.7.4
Appreciate your help troubleshooting the issue.
Thank you,
Daniel
