/usr/bin/qiime: 52: exec: /usr/lib/qiime/bin/tools.py: not found; No functions working in 2019.1 after new installation

After following the installation instructions here, I tried to run qiime2-2019.1. I received no errors during the installation process but for some reason I get the same error even with other commands (ex: quality-filter.py).
source activate qiime2-2019.1
(qiime2-2019.1) [email protected]:~$ qiime tools import \

–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path ~/Documents/Mock_Spike_In/MANIFEST.csv
–output-path ~/Documents/Mock_Spike_In/QIIME2/paired-end-demux.qza
–input-format PairedEndFastqManifestPhred33
/usr/bin/qiime: 52: exec: /usr/lib/qiime/bin/tools.py: not found

I saw a previous forum post with this error that said they were running it in a QIIME1 environment and, although the error only says “qiime” in the filepath, I’m not sure how this might be happening since, after running source activate, it specifies that it is in the (qiime2-2019.1) environment.

I tried removing, cleaning the environment, and re-installing but still get the same error.

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Which version of Conda are you using? If it is lower than 4.6.X, can you update it and try again?

These are QIIME 1 files, looks like you have some environment issues. Can you run the command env and share the results?

I did update conda after the first install because I received a message that it was running a previous version. But the update was installed for the second attempt and qiime2 installation
~$ env
XDG_VTNR=8
XDG_SESSION_ID=c5
CLUTTER_IM_MODULE=xim
SELINUX_INIT=YES
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/riley
SESSION=ubuntu
GPG_AGENT_INFO=/run/user/1002/keyring-I3Aqin/gpg:0:1
TERM=xterm
SHELL=/bin/bash
XDG_MENU_PREFIX=gnome-
VTE_VERSION=3409
WINDOWID=54531246
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1002/11149
GNOME_KEYRING_CONTROL=/run/user/1002/keyring-I3Aqin
GTK_MODULES=overlay-scrollbar:unity-gtk-module
USER=riley
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arj=01;31:.taz=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lz=01;31:.xz=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.jpg=01;35:.jpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.axv=01;35:.anx=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.axa=00;36:.oga=00;36:.spx=00;36:.xspf=00;36:
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session2
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
SSH_AUTH_SOCK=/run/user/1002/keyring-I3Aqin/ssh
SESSION_MANAGER=local/kable-PowerEdge-T630:@/tmp/.ICE-unix/11372,unix/kable-PowerEdge-T630:/tmp/.ICE-unix/11372
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg
PATH=/home/riley/ENTER/bin:/home/riley/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
DESKTOP_SESSION=ubuntu
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
JOB=dbus
PWD=/home/riley
[email protected]=ibus
GNOME_KEYRING_PID=11147
LANG=en_US.UTF-8
GDM_LANG=en_US
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
IM_CONFIG_PHASE=1
COMPIZ_CONFIG_PROFILE=ubuntu
GDMSESSION=ubuntu
SESSIONTYPE=gnome-session
XDG_SEAT=seat0
HOME=/home/riley
SHLVL=1
LANGUAGE=en_US
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
LOGNAME=riley
COMPIZ_BIN_PATH=/usr/bin/
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share/:/usr/share/
QT4_IM_MODULE=xim
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-2vqrJ36rLv
LESSOPEN=| /usr/bin/lesspipe %s
INSTANCE=
TEXTDOMAIN=im-config
XDG_RUNTIME_DIR=/run/user/1002
DISPLAY=:1
XDG_CURRENT_DESKTOP=Unity
GTK_IM_MODULE=ibus
LESSCLOSE=/usr/bin/lesspipe %s %s
TEXTDOMAINDIR=/usr/share/locale/
COLORTERM=gnome-terminal
XAUTHORITY=/home/riley/.Xauthority
_=/usr/bin/env

Can you rerun the command from within your 2019.1 conda env?

Sorry, here is command run from within 2019.1 env
(qiime2-2019.1) [email protected]:~$ command env
XDG_VTNR=8
XDG_SESSION_ID=c5
CLUTTER_IM_MODULE=xim
SELINUX_INIT=YES
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/riley
SESSION=ubuntu
GPG_AGENT_INFO=/run/user/1002/keyring-I3Aqin/gpg:0:1
TERM=xterm
SHELL=/bin/bash
XDG_MENU_PREFIX=gnome-
VTE_VERSION=3409
CONDA_SHLVL=1
CONDA_PROMPT_MODIFIER=(qiime2-2019.1)
WINDOWID=54526269
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1002/11149
GNOME_KEYRING_CONTROL=/run/user/1002/keyring-I3Aqin
GTK_MODULES=overlay-scrollbar:unity-gtk-module
USER=riley
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arj=01;31:.taz=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lz=01;31:.xz=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.jpg=01;35:.jpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.axv=01;35:.anx=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.axa=00;36:.oga=00;36:.spx=00;36:.xspf=00;36:
CONDA_EXE=/home/riley/ENTER/bin/conda
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session2
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
SSH_AUTH_SOCK=/run/user/1002/keyring-I3Aqin/ssh
SESSION_MANAGER=local/kable-PowerEdge-T630:@/tmp/.ICE-unix/11372,unix/kable-PowerEdge-T630:/tmp/.ICE-unix/11372
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg
PATH=/home/riley/ENTER/envs/qiime2-2019.1/bin:/home/riley/ENTER/condabin:/home/riley/ENTER/bin:/home/riley/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
DESKTOP_SESSION=ubuntu
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
CONDA_PREFIX=/home/riley/ENTER/envs/qiime2-2019.1
JOB=dbus
PWD=/home/riley
[email protected]=ibus
GNOME_KEYRING_PID=11147
LANG=en_US.UTF-8
GDM_LANG=en_US
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
IM_CONFIG_PHASE=1
COMPIZ_CONFIG_PROFILE=ubuntu
GDMSESSION=ubuntu
SESSIONTYPE=gnome-session
XDG_SEAT=seat0
HOME=/home/riley
SHLVL=1
LANGUAGE=en_US
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
CONDA_PYTHON_EXE=/home/riley/ENTER/bin/python
LOGNAME=riley
COMPIZ_BIN_PATH=/usr/bin/
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share/:/usr/share/
QT4_IM_MODULE=xim
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-2vqrJ36rLv
CONDA_DEFAULT_ENV=qiime2-2019.1
LESSOPEN=| /usr/bin/lesspipe %s
INSTANCE=
TEXTDOMAIN=im-config
XDG_RUNTIME_DIR=/run/user/1002
DISPLAY=:1
XDG_CURRENT_DESKTOP=Unity
GTK_IM_MODULE=ibus
LESSCLOSE=/usr/bin/lesspipe %s %s
TEXTDOMAINDIR=/usr/share/locale/
COLORTERM=gnome-terminal
XAUTHORITY=/home/riley/.Xauthority
_=/usr/bin/env

Perfect, thanks! Now, within that env, can you also run conda list? Thanks!

That’s strange. I get the following:
EnvironmentLocationNotFound: Not a conda environment: /home/riley/ENTER/envs/qiime2-2019.1

Not sure why it seems to be installed but isn’t?

Looks like your env is corrupt — not sure how or why, but my suggestion is to delete the env and try to install again. You can remove with:

conda deactivate  # if still in 2019.1 env
conda remove -n qiime2-2019.1 --all

I did as instructed and then tried re-installing using the instructions online but now it won’t even install. I get a long list of the following errors for different packages/paths:
CondaVerificationError: The package for r-base located at /home/riley/ENTER/pkgs/r-base-3.4.1-h4fe35fd_8
appears to be corrupted. The path ‘lib/R/share/texmf/tex/latex/omsaer.fd’
specified in the package manifest cannot be found.
ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge::libgfortran-3.0.0-1, conda-forge::libgcc-7.2.0-h69d50b8_2
path: ‘lib/libgfortran.so.3.0.0’

Yikes, looks like you conda/miniconda deployment might be corrupted. You could try cleaning your package cache:

conda clean --all

Then, try reinstalling the QIIME 2 environment.

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It was working at first!..It showed the different packages loading for a minute or so but then it just quit gave the same errors shown above (“CondaVerificationError” and “ClobberError”)

That does sounds quite bad, it might be easiest to uninstall miniconda and reinstall miniconda. It sounds like your conda cache is having a rough time and conda clean wasn’t able to fix it.

After reinstalling, make sure to run conda update conda.

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