Hi Qiime experts,
I am using my school cluster to run qiime and so far v2017.9 works but then I installed 2018.2 and I get the following error:
[samd1993@login1 ~]$ source activate qiime2-2018.2
(qiime2-2018.2) [samd1993@login1 ~]$ qiime --help
-bash: qiime: command not found
As you can see, 2018.2 activates but then any commands wont work and return " -bash: qiime: command not found"
ANy help would be much appreciated. Thanks!
It seems qiime isn’t installed in that environment.
If you installed it yourself I would say try again as it hasn’t been installed.
If someone else did, then ask them or an admin what is wrong… it looks to me like it isn’t installed.
Hi @Sam_Degregori,
A couple more things you can try:
When you activate your environment, what does the following say?
env
and
which python
That should give us something to get started with.
Thanks!
Hi Evan,
When I do which python I get this:
(qiime2-2018.2) [samd1993@n2195 ~]$ which python
/u/local/apps/anaconda/python2-4.2.0/bin/python
When I do env I get this crazy output:
(qiime2-2018.2) [samd1993@n2195 ~]$ env
MKLROOT=/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl
MODULE_VERSION_STACK=3.2.6
MANPATH=/u/local/compilers/intel-cs/2013.0.028/mpi/man:/u/local/compilers/intel-cs/2013.0.028/itac/man:/u/local/compilers/intel-cs/2013.0.028/composer_xe/man/en_US:/u/systems/UGE8.0.1vm/man:/u/local/Modules/3.2.6/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man/en:/usr/share/man:/usr/local/man:/u/local/man:/u/local/compilers/intel-cs/2013.0.028/inspector_xe/man:/u/local/compilers/intel-cs/2013.0.028/vtune_amplifier_xe/man:/u/local/compilers/intel-cs/2013.0.028/advisor_xe/man
VT_MPI=impi4
HOSTNAME=n2195
IPPROOT=/u/local/compilers/intel-cs/2013.0.028/composer_xe/ipp
INTEL_LICENSE_FILE=/u/local/compilers/intel/cs/licenses/license.dat
TERM=xterm
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=172.16.96.80 38130 41729
LIBRARY_PATH=/u/local/compilers/intel-cs/2013.0.028/composer_xe/compiler/lib/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/ipp/lib/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl/lib/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/tbb/lib/intel64
SGE_CELL=hoffman2
QTDIR=/usr/lib64/qt-3.3
LANGUAGE_TERRITORY=en_US
QTINC=/usr/lib64/qt-3.3/include
MIC_LD_LIBRARY_PATH=/u/local/compilers/intel-cs/2013.0.028/composer_xe/compiler/lib/mic:/opt/intel/mic/coi/device-linux-release/lib:/opt/intel/mic/myo/lib:/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl/lib/mic:/u/local/compilers/intel-cs/2013.0.028/composer_xe/tbb/lib/mic
SSH_TTY=/dev/pts/3
USER=samd1993
LD_LIBRARY_PATH=/u/local/compilers/intel-cs/2013.0.028/mpi/intel64/lib:/u/local/compilers/intel-cs/2013.0.028/itac/intel64/itac/slib_impi4:/u/local/compilers/intel-cs/2013.0.028/composer_xe/compiler/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/u/local/compilers/intel-cs/2013.0.028/composer_xe/mpirt/bin/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/ipp/lib/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl/lib/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/tbb/lib/intel64
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:mi=01;05;37;41: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:.tbz=01;31:.tbz2=01;31:.bz=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=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:.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=01;36:.au=01;36:.flac=01;36:.mid=01;36:.midi=01;36:.mka=01;36:.mp3=01;36:.mpc=01;36:.ogg=01;36:.ra=01;36:.wav=01;36:.axa=01;36:.oga=01;36:.spx=01;36:.xspf=01;36:
BIN_DIR=bin64
MKL_LIB=/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl/lib/intel64
CPATH=/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl/include:/u/local/compilers/intel-cs/2013.0.028/composer_xe/tbb/include
OLDSCRATCH=/u/scratch/s/samd1993
NLSPATH=/u/local/compilers/intel-cs/2013.0.028/composer_xe/compiler/lib/intel64/locale/en_US:/u/local/compilers/intel-cs/2013.0.028/composer_xe/ipp/lib/intel64/locale/en_US:/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl/lib/intel64/locale/en_US:/u/local/compilers/intel-cs/2013.0.028/composer_xe/debugger/intel64/locale/en_US
VT_ADD_LIBS=-ldwarf -lelf -lvtunwind -lnsl -lm -ldl -lpthread
LIBGL_ALWAYS_INDIRECT=1
MODULE_VERSION=3.2.6
MAIL=/var/spool/mail/samd1993
PATH=/u/home/s/samd1993/.conda/envs/qiime2-2018.2/bin:/u/local/apps/anaconda/python2-4.2.0/bin:/u/local/compilers/intel-cs/2013.0.028/bin:/u/local/compilers/intel-cs/2013.0.028/advisor_xe/bin64:/u/local/compilers/intel-cs/2013.0.028/vtune_amplifier_xe/bin64:/u/local/compilers/intel-cs/2013.0.028/inspector_xe/bin64:/u/local/compilers/intel-cs/2013.0.028/mpi/intel64/bin:/u/local/compilers/intel-cs/2013.0.028/itac/intel64/bin:/u/local/compilers/intel-cs/2013.0.028/composer_xe/bin/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/mpirt/bin/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/bin/intel64_mic:/u/local/compilers/intel-cs/2013.0.028/composer_xe/debugger/gui/intel64:/u/systems/UGE8.0.1vm/bin/lx-amd64:/u/local/bin:/u/local/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/u/home/s/samd1993/bin
CONDA_PATH_BACKUP=/u/local/apps/anaconda/python2-4.2.0/bin:/u/local/compilers/intel-cs/2013.0.028/bin:/u/local/compilers/intel-cs/2013.0.028/advisor_xe/bin64:/u/local/compilers/intel-cs/2013.0.028/vtune_amplifier_xe/bin64:/u/local/compilers/intel-cs/2013.0.028/inspector_xe/bin64:/u/local/compilers/intel-cs/2013.0.028/mpi/intel64/bin:/u/local/compilers/intel-cs/2013.0.028/itac/intel64/bin:/u/local/compilers/intel-cs/2013.0.028/composer_xe/bin/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/mpirt/bin/intel64:/u/local/compilers/intel-cs/2013.0.028/composer_xe/bin/intel64_mic:/u/local/compilers/intel-cs/2013.0.028/composer_xe/debugger/gui/intel64:/u/systems/UGE8.0.1vm/bin/lx-amd64:/u/local/bin:/u/local/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/u/home/s/samd1993/bin
CONDA_PREFIX=/u/home/s/samd1993/.conda/envs/qiime2-2018.2
TBBROOT=/u/local/compilers/intel-cs/2013.0.028/composer_xe/tbb
PWD=/u/home/s/samd1993
LMFILES=/u/local/Modules/modulefiles/ATS:/u/local/Modules/modulefiles/intel/13.cs:/u/local/Modules/modulefiles/anaconda/python2-4.2
IDB_HOME=/u/local/compilers/intel-cs/2013.0.028/composer_xe/bin/intel64
SGE_EXECD_PORT=6449
LANG=en_US.UTF-8
SGE_QMASTER_PORT=6448
MODULEPATH=/u/local/Modules/modulefiles:
VT_LIB_DIR=/u/local/compilers/intel-cs/2013.0.028/itac/intel64/itac/lib_impi4
SGE_ROOT=/u/systems/UGE8.0.1vm
LOADEDMODULES=ATS:intel/13.cs:anaconda/python2-4.2
PS1=(qiime2-2018.2) [\u@\h \W]$
VT_ROOT=/u/local/compilers/intel-cs/2013.0.028/itac
VTUNE_AMPLIFIER_XE_2013_DIR=/u/local/compilers/intel-cs/2013.0.028/vtune_amplifier_xe
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
HISTCONTROL=ignoredups
MKL_DIR=/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl
MKL_INC=/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl/include
SHLVL=1
HOME=/u/home/s/samd1993
CONDA_PS1_BACKUP=[\u@\h \W]$
VT_SLIB_DIR=/u/local/compilers/intel-cs/2013.0.028/itac/intel64/itac/slib_impi4
VT_ARCH=intel64
LOGNAME=samd1993
QTLIB=/usr/lib64/qt-3.3/lib
CVS_RSH=ssh
CLASSPATH=/u/local/compilers/intel-cs/2013.0.028/itac/intel64/itac/lib_impi4
SSH_CONNECTION=172.16.96.80 38130 172.16.104.244 41729
MODULESHOME=/u/local/Modules/3.2.6
CONDA_DEFAULT_ENV=qiime2-2018.2
LESSOPEN=||/usr/bin/lesspipe.sh %s
SGE_CLUSTER_NAME=h2
ADVISOR_XE_2013_DIR=/u/local/compilers/intel-cs/2013.0.028/advisor_xe
INCLUDE=/u/local/compilers/intel-cs/2013.0.028/composer_xe/compiler/include:/u/local/compilers/intel-cs/2013.0.028/composer_xe/mkl/include
NEWSCRATCH=/u/flashscratch/s/samd1993
SCRATCH=/u/flashscratch/s/samd1993
G_BROKEN_FILENAMES=1
I_MPI_ROOT=/u/local/compilers/intel-cs/2013.0.028/mpi
_=/bin/env
Hope this gives more info. Thanks for putting on that workshop in Bethesda btw it helped a lot.
Sam
Hi @Sam_Degregori,
I think we've got the problem here, this is your system's module's Python for the anaconda module (or whatever is set up as the equivalent). We need to see your conda environment's Python which would look like this:
/u/home/s/samd1993/.conda/envs/qiime2-2018.2/bin/python
Interestingly, that is set correctly in your $PATH (thanks for the env output!). Could you run the following:
ls /u/home/s/samd1993/.conda/envs/qiime2-2018.2/bin
I'm kind of expecting that to be more or less empty, since I think you have a broken install. But maybe something else is happening.
Thanks!
Hi Evan,
I get this output:
[samd1993@login3 ~]$ ls /u/home/s/samd1993/.conda/envs/qiime2-2018.2/bin
activate conda deactivate
Thoughts?
Sam
Hi @Sam_Degregori, @ebolyen might have something more to add to this still, but that bin directory you provided the listing to above is missing all sorts of tools and packages that should be there. It sounds like maybe your deployment of QIIME 2 is incomplete, so maybe it makes sense to remove and start over:
source deactivate
conda env remove -n qiime2-2018.2
conda clean --all
Then, try the Native Install commands again from the beginning, make sure to follow all the steps (including updating your installation of conda. Keep us posted and let us know how it goes! 
Hi Matthew,
Looks like you are correct and I ran out of space in my server account. After contacting our university’s cluster support they actually installed the new version on the cluster for everyone to use. Thanks to this thread all of UCLA has qiime2-2018.2 now 
Thanks for the help
Sam
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