Error in qiime 2021.08 Found conflicts! Looking for incompatible packages

Technical Support
1

Hello everyone!

I am trying to install the latest version of QIIME2 (qiime2-2021.08) on Ubuntu, but some conflicts appear:

conda env create -n qiime2-2021.8 --file qiime2-2021.8-py38-linux-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort. \ failed

CondaError: KeyboardInterrupt

I realized that same error have happened on 2020.11, Instalation qiime 2020.11 Found conflicts! Looking for incompatible packages so I assume that this might be a problem with this yml file? Cause I've installed 2020.11 version again and it works just fine.

Does anybody have any suggestions?
Thank you very much in advance!

2

Hey there @zikaishao!

I just performed a clean linux-based install in a new virtual machine, all good here. Let's try to figure out what might be different between our two computational environments.

Can you run the following and share the results here - this'll help give us an idea about your system:

env
conda info -a

:qiime2:

3

Hi @thermokarst , thanks for your reply!

The results of env are:

MANPATH=/gss2/lsf/9.1/man:
HOSTNAME=login
TERM=xterm
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=10.21.225.253 6810 22
LSF_SERVERDIR=/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/etc
SSH_TTY=/dev/pts/4
LSF_LIBDIR=/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
USER=szk20200608
LD_LIBRARY_PATH=/gss1/home/szk20200608/soft/beagle-lib/lib:/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
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:
MAIL=/var/spool/mail/szk20200608
PATH=/gss1/home/szk20200608/soft/miniconda2/bin:/usr/local/mvapich/bin:/usr/lpp/mmfs/bin:/opt/intel//impi/5.0.1.035/intel64/bin:/opt/intel/composer_xe_2015.0.090/bin/intel64:/opt/intel/composer_xe_2015.0.090/mpirt/bin/intel64:/opt/intel/composer_xe_2015.0.090/debugger/gdb/intel64_mic/bin:/gss2/home/galaxy/galaxy/database/dependencies/bowtie/1.1.2/iuc/package_bowtie_1_1_2/a1c1a92e13a6/:/usr/local/mvapich/bin:/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/etc:/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/ibutils/bin:/root/bin:/gss1/home/szk20200608/soft/FastQC/:/gss1/home/szk20200608/soft/miniconda2/config/:/gss1/home/szk20200608/soft/miniconda2/:/gss1/home/szk20200608/soft/miniconda2/bin/:/gss1/home/szk20200608/soft/miniconda2/lib/:/gss1/home/szk20200608/soft/miniconda2/lib/python2.7/:/gss1/home/szk20200608/soft/miniconda2/scripts/:/gss1/home/szk20200608/soft/bbmap/:/gss1/home/szk20200608/soft/redundans/:/gss1/home/szk20200608/soft/stampy-1.0.32/:/gss1/home/szk20200608/soft/ncbi-blast-2.2.30+/bin:/gss1/home/szk20200608/soft/FLASH-1.2.11:/gss1/home/szk20200608/soft/beast/bin:/gss1/home/szk20200608/soft/sratoolkit/sratoolkit.2.11.0-centos_linux64/bin:/gss1/home/szk20200608/bin
PWD=/gss1/home/szk20200608
LANG=en_US.UTF-8
LSF_BINDIR=/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/bin
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
HISTCONTROL=ignoredups
SHLVL=1
HOME=/gss1/home/szk20200608
BINARY_TYPE_HPC=
AUGUSTUS_CONFIG_PATH=/gss1/home/szk20200608/soft/miniconda2/config
LOGNAME=szk20200608
SSH_CONNECTION=10.21.225.253 6810 172.30.2.2 22
LESSOPEN=||/usr/bin/lesspipe.sh %s
LSF_ENVDIR=/gss2/lsf/conf
G_BROKEN_FILENAMES=1
_=/bin/env

and for conda info -a

     active environment : None
       user config file : /gss1/home/szk20200608/.condarc
 populated config files : /gss1/home/szk20200608/.condarc
          conda version : 4.7.12
    conda-build version : not installed
         python version : 2.7.17.final.0
       virtual packages :
       base environment : /gss1/home/szk20200608/soft/miniconda2  (writable)
           channel URLs : https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
                          https://conda.anaconda.org/qiime2/label/r2021.8/linux-64
                          https://conda.anaconda.org/qiime2/label/r2021.8/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /gss1/home/szk20200608/soft/miniconda2/pkgs
                          /gss1/home/szk20200608/.conda/pkgs
       envs directories : /gss1/home/szk20200608/soft/miniconda2/envs
                          /gss1/home/szk20200608/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.12 requests/2.22.0 CPython/2.7.17 Linux/2.6.32-642.el6.x86_64 rhel/6.8 glibc/2.12
                UID:GID : 65788:65538
             netrc file : None
           offline mode : False

# conda environments:
#
base                  *  /gss1/home/szk20200608/soft/miniconda2
qiime2                   /gss1/home/szk20200608/soft/miniconda2/envs/qiime2
qiime2-2020.11           /gss1/home/szk20200608/soft/miniconda2/envs/qiime2-2020.11

sys.version: 2.7.17 |Anaconda, Inc.| (default, Oct 21...
sys.prefix: /gss1/home/szk20200608/soft/miniconda2
sys.executable: /gss1/home/szk20200608/soft/miniconda2/bin/python
conda location: /gss1/home/szk20200608/soft/miniconda2/lib/python2.7/site-packages/conda
conda-build: None
conda-env: /gss1/home/szk20200608/soft/miniconda2/bin/conda-env
user site dirs:

AUGUSTUS_CONFIG_PATH: /gss1/home/szk20200608/soft/miniconda2/config
CIO_TEST: <not set>
CONDA_ROOT: /gss1/home/szk20200608/soft/miniconda2
LD_LIBRARY_PATH: /gss1/home/szk20200608/soft/beagle-lib/lib:/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
MANPATH: /gss2/lsf/9.1/man:
PATH: /gss1/home/szk20200608/soft/miniconda2/bin:/usr/local/mvapich/bin:/usr/lpp/mmfs/bin:/opt/intel//impi/5.0.1.035/intel64/bin:/opt/intel/composer_xe_2015.0.090/bin/intel64:/opt/intel/composer_xe_2015.0.090/mpirt/bin/intel64:/opt/intel/composer_xe_2015.0.090/debugger/gdb/intel64_mic/bin:/gss2/home/galaxy/galaxy/database/dependencies/bowtie/1.1.2/iuc/package_bowtie_1_1_2/a1c1a92e13a6/:/usr/local/mvapich/bin:/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/etc:/gss2/lsf/9.1/linux2.6-glibc2.3-x86_64/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/ibutils/bin:/root/bin:/gss1/home/szk20200608/soft/FastQC/:/gss1/home/szk20200608/soft/miniconda2/config/:/gss1/home/szk20200608/soft/miniconda2/:/gss1/home/szk20200608/soft/miniconda2/bin/:/gss1/home/szk20200608/soft/miniconda2/lib/:/gss1/home/szk20200608/soft/miniconda2/lib/python2.7/:/gss1/home/szk20200608/soft/miniconda2/scripts/:/gss1/home/szk20200608/soft/bbmap/:/gss1/home/szk20200608/soft/redundans/:/gss1/home/szk20200608/soft/stampy-1.0.32/:/gss1/home/szk20200608/soft/ncbi-blast-2.2.30+/bin:/gss1/home/szk20200608/soft/FLASH-1.2.11:/gss1/home/szk20200608/soft/beast/bin:/gss1/home/szk20200608/soft/sratoolkit/sratoolkit.2.11.0-centos_linux64/bin:/gss1/home/szk20200608/bin
REQUESTS_CA_BUNDLE: <not set>
SSL_CERT_FILE: <not set>
5

Hi @zikaishao, thanks for the info!

Nothing immediately jumps out at me, except that it looks like you're using a few channel mirrors. Are you operating behind a national firewall? If so, we've seen problems related to that in the past, unfortunately I don't know if there is much we can do about that. Can you try one of our Docker images or Virtualbox VMs?

7

Hi @thermokarst , thanks for your advice!

I do have a firewall issue here, however, by reinstalling version 2020.11, I managed to proceed with my analysis now. But I will try the other ways you mentioned later.

8

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