Errors when installing qiime2-2019.10

Hank_Leo · November 12, 2019, 5:58pm

Hi, I tried to install the QIIME2-2019.10 within a miniconda2 environment in the Linux centos x64 system. I have updated conda. however, I got the following errors when I run qiime --help,

(qiime2-2019.10) [biofilm@localhost qiime]$ qiime --help
Traceback (most recent call last):
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 716, in main
    with self.make_context(prog_name, args, **extra) as ctx:
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 641, in make_context
    self.parse_args(ctx, args)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/click/command.py", line 43, in parse_args
    return super().parse_args(ctx, args)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 1089, in parse_args
    rest = Command.parse_args(self, ctx, args)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 940, in parse_args
    value, args = param.handle_parse_result(ctx, opts, args)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 1477, in handle_parse_result
    self.callback, ctx, self, value)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 96, in invoke_param_callback
    return callback(ctx, param, value)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 860, in show_help
    echo(ctx.get_help(), color=ctx.color)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 516, in get_help
    return self.command.get_help(self)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 879, in get_help
    self.format_help(ctx, formatter)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 898, in format_help
    self.format_options(ctx, formatter)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/click/command.py", line 157, in format_options
    for subcommand in self.list_commands(ctx):
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 92, in list_commands
    plugins = sorted(self._plugin_lookup)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
    import q2cli.core.cache
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/core/cache.py", line 404, in <module>
    CACHE = DeploymentCache()
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/core/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/core/cache.py", line 93, in _get_cached_state
    current_requirements = self._get_current_requirements()
  File "/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/core/cache.py", line 131, in _get_current_requirements
    import pkg_resources
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 951, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 894, in _find_spec
  File "<frozen importlib._bootstrap_external>", line 1157, in find_spec
  File "<frozen importlib._bootstrap_external>", line 1131, in _get_spec
  File "<frozen importlib._bootstrap_external>", line 1112, in _legacy_get_spec
  File "<frozen importlib._bootstrap>", line 441, in spec_from_loader
  File "<frozen importlib._bootstrap_external>", line 544, in spec_from_file_location
  File "/opt/qiime/setuptools-0.6c11-release/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 29
    def _bypass_ensure_directory(name, mode=0777):
                                               ^
SyntaxError: invalid token

It seems an environment-related issue, [Qiime2- 2018.11 doesn't work on](http://Qiime2- 2018.11 doesn’t work on). So I checked the env. I didn’t set the PYTHONPATH before, how can fix it ?

(qiime2-2019.10) [biofilm@localhost qiime]$ env
AS=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-as
RSTUDIO_WHICH_R=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/R
LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib -Wl,-rpath-link,/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib -L/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib
AR=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-ar
JAVA_LD_LIBRARY_PATH=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/server
GCC_NM=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
HOSTNAME=localhost.localdomain
SELINUX_ROLE_REQUESTED=
PYENV_ROOT=/home/biofilm/.pyenv
HOST=x86_64-conda_cos6-linux-gnu
TERM=xterm-256color
SHELL=/bin/bash
NM=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-nm
PYTHONNOUSERSITE=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/python*/site-packages/
HISTSIZE=1000
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include
SSH_CLIENT=131.114.147.18 50732 22
CONDA_SHLVL=2
PERL5LIB=/usr/share/perl5:/usr/share/perl5:/opt/PfamScan:/usr/local/lib/mireap
CONDA_PROMPT_MODIFIER=(qiime2-2019.10)
SGE_CELL=default
SELINUX_USE_CURRENT_RANGE=
SIZE=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-size
QTDIR=/usr/lib64/qt-3.3
OLDPWD=/home/biofilm/hank/soft
QTINC=/usr/lib64/qt-3.3/include
ATLAS=None
SSH_TTY=/dev/pts/3
GFORTRAN=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gfortran
ARBHOME=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/arb
PYCOGENT=/opt/qiime/pycogent-1.5.3-release/./
USER=biofilm
LD_LIBRARY_PATH=/opt/qiime/python-2.7.3-release/lib
PYRO_LOOKUP_FILE=/opt/qiime/ampliconnoise-1.27-release/Data/LookUp_E123.dat
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lz=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.bz=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.rar=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
CONDA_EXE=/home/biofilm/hank/soft/miniconda2/bin/conda
DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include
LD_GOLD=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-ld.gold
CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib -Wl,-rpath-link,/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib -L/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib
STRINGS=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-strings
CPP=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-cpp
_CE_CONDA=
CXXFILT=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-c++filt
CONDA_PREFIX_1=/home/biofilm/hank/soft/miniconda2
ARBHOME_BACKUP=
TEST_DB=1
MAIL=/var/spool/mail/biofilm
PATH=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin:/home/biofilm/.pyenv/shims:/home/biofilm/.pyenv/bin:/home/biofilm/hank/soft/miniconda3/bin:/home/biofilm/hank/soft/miniconda3/condabin:/usr/local/bin/velvet:/usr/local/bin/sra_toolkit:/opt/spades/bin:/usr/local/bin/soap3_gpu:/usr/local/bin/soap2:/opt/RepeatMasker/RepeatMasker:/usr/lib64/qt-3.3/bin:/opt/qiime/pprospector-1.0.1-release/bin:/opt/qiime/tax2tree-1.0-release/bin:/opt/qiime/pynast-1.2.2-release/bin:/opt/qiime/emperor-0.9.3-release/bin:/opt/qiime/biom-format-1.3.1-release/bin:/opt/qiime/ipython-latest-repository-f68be49d/bin:/opt/qiime/pyqi-0.3.1-release/bin:/opt/qiime/pyzmq-2.1.11-release/bin:/opt/qiime/qcli-0.1.0-release/bin:/opt/qiime/tornado-3.1.1-release/bin:/opt/qiime/python-2.7.3-release/bin:/opt/qiime/cytoscape-2.7.0-release:/opt/qiime/cdhit-3.1-release:/opt/qiime/uclust-1.2.22-release:/opt/qiime/rdpclassifier-2.2-release:/opt/qiime/muscle-3.8.31-release:/opt/qiime/blast-2.2.22-release/bin:/opt/qiime/parsinsert-1.0.4-release:/opt/qiime/infernal-1.0.2-release/bin:/opt/qiime/bwa-0.6.2-release:/opt/qiime/fasttree-2.1.3-release:/opt/qiime/mothur-1.25.0-release:/opt/qiime/vienna-1.8.4-release:/opt/qiime/ea-utils-1.1.2-537-release:/opt/qiime/SeqPrep-latest-repository-85e2389e:/opt/qiime/chimeraslayer-4.29.2010-release/ChimeraSlayer:/opt/qiime/chimeraslayer-4.29.2010-release/NAST-iEr:/opt/qiime/drisee-1.2-release:/opt/qiime/cdbtools-10.11.2010-release:/opt/qiime/ampliconnoise-1.27-release/Scripts:/opt/qiime/ampliconnoise-1.27-release/bin:/opt/qiime/raxml-7.3.0-release:/opt/qiime/sourcetracker-0.9.5-release:/opt/qiime/rtax-0.984-release:/opt/qiime/blat-35-release:/opt/qiime/clearcut-1.0.9-release:/opt/qiime/python-2.7.3-release/bin/python:/usr/local/bin/oases:/usr/local/bin/mireap:/usr/local/bin/lshat:/usr/local/bin/fastx:/opt/circos/current/bin:/usr/local/bin/bowtie2:/usr/local/bin/bowtie:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/home/biofilm/bin
BLAS=None
LAPACK=None
DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include
LD=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-ld
CONDA_PREFIX=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10
F90=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gfortran
PWD=/home/biofilm/hank/soft/qiime
JAVA_HOME=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10
STRIP=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-strip
ELFEDIT=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-elfedit
MPLBACKEND=Agg
F95=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-f95
GCC_RANLIB=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
LANG=en_US.UTF-8
KDE_IS_PRELINKED=1
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
SGE_ROOT=/usr/share/gridengine
LOADEDMODULES=
KDEDIRS=/usr
DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
QIIME_CONFIG_FP=/opt/qiime/qiime_config
F77=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gfortran
SELINUX_LEVEL_REQUESTED=
CXX=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-c++
_CE_M=
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
HISTCONTROL=ignoredups
OBJCOPY=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-objcopy
PYENV_SHELL=bash
SHLVL=1
HOME=/home/biofilm
FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include
FC=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gfortran
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
GCC=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gcc
ADDR2LINE=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-addr2line
CONDA_PYTHON_EXE=/home/biofilm/hank/soft/miniconda2/bin/python
**PYTHONPATH**=/opt/qiime/pprospector-1.0.1-release/lib/python2.7/site-packages:/opt/qiime/tax2tree-1.0-release/lib/python2.7/site-packages:/opt/qiime/pynast-1.2.2-release/lib/python2.7/site-packages:/opt/qiime/matplotlib-1.3.1-release/lib/python2.7/site-packages:/opt/qiime/pycogent-1.5.3-release/lib/python2.7/site-packages:/opt/qiime/emperor-0.9.3-release/lib/python2.7/site-packages:/opt/qiime/biom-format-1.3.1-release/lib/python2.7/site-packages:/opt/qiime/ipython-latest-repository-f68be49d/lib/python2.7/site-packages:/opt/qiime/sphinx-1.0.4-release/lib/python2.7/site-packages:/opt/qiime/pyqi-0.3.1-release/lib/python2.7/site-packages:/opt/qiime/MySQL-python-1.2.3-release/lib/python2.7/site-packages:/opt/qiime/mpi4py-1.2.2-release/lib/python2.7/site-packages:/opt/qiime/pysqlite-2.6.3-release/lib/python2.7/site-packages:/opt/qiime/setuptools-0.6c11-release/lib/python2.7/site-packages:/opt/qiime/gdata-2.0.17-release/lib/python2.7/site-packages:/opt/qiime/qcli-0.1.0-release/lib/python2.7/site-packages:/opt/qiime/numpy-1.7.1-release/lib/python2.7/site-packages:/opt/qiime/tornado-3.1.1-release/lib/python2.7/site-packages:/opt/qiime/pyzmq-2.1.11-release/lib/python2.7/site-packages:
LOGNAME=biofilm
QTLIB=/usr/lib64/qt-3.3/lib
CVS_RSH=ssh
SSH_CONNECTION=131.114.147.18 50732 193.205.83.138 22
MODULESHOME=/usr/share/Modules
JAVA_HOME_CONDA_BACKUP=
CONDA_DEFAULT_ENV=qiime2-2019.10
SEQ_LOOKUP_FILE=/opt/qiime/ampliconnoise-1.27-release/Data/Tran.dat
LESSOPEN=|/usr/bin/lesspipe.sh %s
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include
RANLIB=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-ranlib
BLASTMAT=/opt/qiime/blast-2.2.22-release/data
SOURCETRACKER_PATH=/opt/qiime/sourcetracker-0.9.5-release/.
CMAKE_PREFIX_PATH=:/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10:/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/x86_64-conda_cos6-linux-gnu/sysroot/usr
CC=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-cc
RDP_JAR_PATH=/opt/qiime/rdpclassifier-2.2-release/rdp_classifier-2.2.jar
READELF=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-readelf
JAVA_LD_LIBRARY_PATH_BACKUP=
GCC_AR=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
OBJDUMP=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-objdump
R_LIBS_USER=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/lib/R/library/
GPROF=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-gprof
G_BROKEN_FILENAMES=1
GXX=/home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/bin/x86_64-conda_cos6-linux-gnu-g++
FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/biofilm/hank/soft/miniconda2/envs/qiime2-2019.10/include
BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
}
_=/bin/env

thermokarst · November 13, 2019, 2:51pm

Hey there @Hank_Leo! Looks like the smoking gun is right here:

Python 2.7 shouldn't be showing up in your QIIME 2 env at all, and is likely leaking in from somewhere else (as you mentioned, this seems to be an environment-related issue - I agree).

The $PYTHONPATH that is currently set appears to be full of QIIME 1 related stuff... does that bring back any memories?

Fixing it will likely require you to update the PYTHONPATH env var (and maybe others, too). This is moving outside of our ability to help though - is there a sysadmin for this machine that you can work with? The environment seems to be very heavily customized (and some of those customizations don't look like they will play well with other tools) - I am worried that if you start changing things you might bring this whole thing crashing down.

Keep us posted...

Hank_Leo · November 13, 2019, 5:41pm

I am not sure for qiime1 memories, cause I use this server for the first time.
Can I delete the file /opt/qiime to fix ?

thermokarst · November 18, 2019, 11:47pm

I would check with whoever administers this server, first.