Unable to execute qiime2 commands

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:

    1. 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.
    2. If (1) looks fine, you can open a new issue at
      https://github.com/numpy/numpy/issues. 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
  • 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

Hey @dancurtis87!

This jumped out at me:

In particular, this bit:

Referenced from: /Users/danielcurtis/tcoffee/Version_11.00.8cbe486/gfortran/libgfortran.3.dylib

This looks like you have some kind of fortran installation (maybe related to tcoffee?) that is impacting your QIIME 2 environment. How about you run the following, and post the results here:

env

Hi @thermokarst

Thanks for getting back to me. Here is the output as requested

(qiime2-2019.10) Daniel-MacBook:P-009V_rerun2 danielcurtis$ env
AS=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-as
LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib -L/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib
AR=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-ar
RSTUDIO_WHICH_R=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/R
MANPATH=/opt/local/share/man:/usr/local/share/man:/usr/share/man:/opt/X11/share/man:/usr/local/git/share/man:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/share/man:/Applications/Xcode.app/Contents/Developer/usr/share/man:/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/share/man
CODESIGN_ALLOCATE=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-codesign_allocate
JAVA_LD_LIBRARY_PATH=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/server
TERM_PROGRAM=Apple_Terminal
HOST=x86_64-apple-darwin13.4.0
SHELL=/bin/bash
TERM=xterm-256color
NM=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-nm
PYTHONNOUSERSITE=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/python*/site-packages/
CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/danielcurtis/miniconda3/envs/qiime2-2019.10/include
TMPDIR=/var/folders/d4/hgdxgj450ms0qzwggyjtql1h0000gn/T/
PAGESTUFF=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-pagestuff
CONDA_SHLVL=2
PERL5LIB=:/Users/danielcurtis/tcoffee/Version_11.00.8cbe486/perl/lib/perl5
Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.rXGc8DHmuR/Render
LIPO=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-lipo
CONDA_PROMPT_MODIFIER=(qiime2-2019.10)
TERM_PROGRAM_VERSION=421.2
SIZE=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-size
NMEDIT=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-nmedit
RSTUDIO_WHICH_R_PREV=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/R
OLDPWD=/Users/danielcurtis/Desktop/QIIME2/DataAnalysis/Year4_Resequencing
TERM_SESSION_ID=C7F3EB45-5384-46E2-8AA4-A1611280A61A
INSTALL_NAME_TOOL=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-install_name_tool
SEGEDIT=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-segedit
GFORTRAN=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-gfortran
ARBHOME=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/arb
SEG_HACK=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-seg_hack
USER=danielcurtis
CLANGXX=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-clang++
LIBTOOL=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-libtool
CONDA_BACKUP_HOST=x86_64-apple-darwin13.4.0
CONDA_EXE=/Users/danielcurtis/miniconda3/bin/conda
PERLBREW_BASHRC_VERSION=0.76
OTOOL=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-otool
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.ZKiWx8suMx/Listeners
DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem /Users/danielcurtis/miniconda3/envs/qiime2-2019.10/include
CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
STRINGS=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-strings
PERLBREW_ROOT=/Users/danielcurtis/perl5/perlbrew
_CE_CONDA=
CHECKSYMS=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-checksyms
CONDA_PREFIX_1=/Users/danielcurtis/miniconda3
ARBHOME_BACKUP=
PATH=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin:/Users/danielcurtis/miniconda3/bin:/Users/danielcurtis/miniconda3/condabin:/Users/danielcurtis/.pyenv/shims:/Users/danielcurtis/tcoffee/Version_11.00.8cbe486/bin:/Users/danielcurtis/perl5/perlbrew/bin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/opt/X11/bin:/usr/local/git/bin
DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra -isystem /Users/danielcurtis/miniconda3/envs/qiime2-2019.10/include
LD=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-ld
CONDA_PREFIX=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10
F90=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-gfortran
DIR_4_TCOFFEE=/Users/danielcurtis/tcoffee/Version_11.00.8cbe486
PWD=/Users/danielcurtis/Desktop/QIIME2/DataAnalysis/Year4_Resequencing/P-009V_rerun2
JAVA_HOME=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10
STRIP=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-strip
CACHE_4_TCOFFEE=/Users/danielcurtis/.t_coffee/cache/
MPLBACKEND=Agg
F95=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-gfortran
LANG=en_US.UTF-8
DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
PERLBREW_HOME=/Users/danielcurtis/.perlbrew
XPC_FLAGS=0x0
F77=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-gfortran
REDO_PREBINDING=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-redo_prebinding
CXX=x86_64-apple-darwin13.4.0-clang++
CLANG=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-clang
_CE_M=
XPC_SERVICE_NAME=0
PYENV_SHELL=bash
SHLVL=1
HOME=/Users/danielcurtis
FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe
CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/danielcurtis/miniconda3/envs/qiime2-2019.10/include
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
FC=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-gfortran
MAFFT_BINARIES=/Users/danielcurtis/tcoffee/Version_11.00.8cbe486/plugins/macosx/
INDR=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-indr
CONDA_PYTHON_EXE=/Users/danielcurtis/miniconda3/bin/python
LOGNAME=danielcurtis
[email protected]
JAVA_HOME_CONDA_BACKUP=
CONDA_DEFAULT_ENV=qiime2-2019.10
DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem /Users/danielcurtis/miniconda3/envs/qiime2-2019.10/include
RANLIB=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-ranlib
CMAKE_PREFIX_PATH=:/Users/danielcurtis/miniconda3/envs/qiime2-2019.10
CC=x86_64-apple-darwin13.4.0-clang
SEG_ADDR_TABLE=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/bin/x86_64-apple-darwin13.4.0-seg_addr_table
JAVA_LD_LIBRARY_PATH_BACKUP=
LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath /Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib -L/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib
R_LIBS_USER=/Users/danielcurtis/miniconda3/envs/qiime2-2019.10/lib/R/library/
LOCKDIR_4_TCOFFEE=/Users/danielcurtis/tcoffee/Version_11.00.8cbe486/lck/
FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe
TMP_4_TCOFFEE=/Users/danielcurtis/tcoffee/Version_11.00.8cbe486/tmp/
_=/usr/bin/env

Hello again,

Deleting the t-coffee installation worked and qiime2 is now executing the command. So far things look good.

Is this kind of interference from a fortran installation something that warrants looking into? Are conflicts due to other software dependencies something to be aware of when using qiime2? Just so I know what to look for if I plan on installing other software.

Appreciate your help! :beers:

Woohoo!

In general - nope! I don’t know what the standard install procedure is for t-coffee - but it looks like your environment was configured in such a way that it gave priority to t-coffee’s environment, over anything else. This falls into the general category of “environment issues” - a significant number of installation issues I see on this forum are related to environments with dubious configurations. This happens - copying and pasting install commands from software, or snippets from stack overflow (not saying you did that here), but, such is life.

Happy QIIMEing! :qiime2: