SqueezeMeta
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jtamames
Conda stuck solving environment when installing v1.5
If this happens, just use mamba instead of conda to create the environment (I use it for everything nowadays, so I didn't notice the problems with the original conda command). Mamba is much faster replacement for conda, and should solve the environment in less than a minute.
# Install mamba in your base conda environment
conda install -c conda-forge mamba
# Then use the mamba command as you would use the conda command
mamba create -n SqueezeMeta -c conda-forge -c bioconda -c fpusan squeezemeta
I will make a post-release with updated installation instructions sometime this weekend.
Hi,
thanks for putting that info out upfront. I have the problem you are mentioning, that conda gets stuck while solving the environment. I then tried using mamba as you suggested but then I am getting the following error:
mamba create -n SqueezeMeta_1.5.0 -c conda-forge -c bioconda -c fpusan squeezemeta
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
Supported by @QuantStack
GitHub: https://github.com/QuantStack/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Getting conda-forge linux-64
Getting conda-forge noarch
Getting bioconda linux-64
Getting bioconda noarch
Getting fpusan Getting fpusanlinux-64
noarch
Getting Getting pkgs/main linux-64pkgs/main
noarch
Getting pkgs/r linux-64
Getting pkgs/r noarch
Looking for: [u'squeezemeta']
78855 packages in https://conda.anaconda.org/conda-forge/noarch
234422 packages in https://conda.anaconda.org/conda-forge/linux-64
40153 packages in https://conda.anaconda.org/bioconda/linux-64
33963 packages in https://conda.anaconda.org/bioconda/noarch
23775 packages in https://repo.anaconda.com/pkgs/main/linux-64
5025 packages in https://repo.anaconda.com/pkgs/r/noarch
4550 packages in https://repo.anaconda.com/pkgs/main/noarch
6637 packages in https://repo.anaconda.com/pkgs/r/linux-64
6 packages in https://conda.anaconda.org/fpusan/linux-64
17 packages in https://conda.anaconda.org/fpusan/noarch
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/btschits/miniconda3/lib/python2.7/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/home/btschits/miniconda3/lib/python2.7/site-packages/mamba/mamba.py", line 522, in exception_converter
raise e
RuntimeError: Did not find key as expected!
`$ /home/btschits/miniconda3/condabin/mamba create -n SqueezeMeta_1.5.0 -c conda-forge -c bioconda -c fpusan squeezemeta`
environment variables:
ALL_PROXY=<set>
CIO_TEST=<not set>
CONDA_EXE=/home/btschits/miniconda3/bin/conda
CONDA_PYTHON_EXE=/home/btschits/miniconda3/bin/python
CONDA_ROOT=/home/btschits/miniconda3
CONDA_SHLVL=0
FTP_PROXY=<set>
HTTPS_PROXY=<set>
HTTP_PROXY=<set>
LD_LIRARY_PATH=/home/btschits/lib/
MANPATH=:/opt/puppetlabs/puppet/share/man:/home/btschits/bin
PATH=/home/btschits/apps:/home/btschits/apps/Prodigal-2.6.3:/home/btschits/
usr/bin:/home/btschits/apps/perl-5.30.1:/home/btschits/bin:/home/btsch
its/apps/MUMmer3.23:/home/btschits/perl5/bin:/home/btschits/.local/bin
:/home/btschits/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/
local/games:/usr/games:/opt/puppetlabs/bin:/home/btschits/bin:/home/bt
schits/apps/ncbi-blast-2.9.0+/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
all_proxy=<set>
ftp_proxy=<set>
http_proxy=<set>
https_proxy=<set>
no_proxy=<set>
active environment : None
shell level : 0
user config file : /home/btschits/.condarc
populated config files : /home/btschits/.condarc
conda version : 4.8.3
conda-build version : not installed
python version : 2.7.16.final.0
virtual packages : __glibc=2.24
base environment : /home/btschits/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://conda.anaconda.org/fpusan/linux-64
https://conda.anaconda.org/fpusan/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 : /home/btschits/miniconda3/pkgs
/home/btschits/.conda/pkgs
envs directories : /home/btschits/miniconda3/envs
/home/btschits/.conda/envs
platform : linux-64
user-agent : conda/4.8.3 requests/2.24.0 CPython/2.7.16 Linux/4.9.0-13-amd64 debian/9.13 glibc/2.24
UID:GID : 60785:1120
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Do you have any idea about what might go wrong here?
Thanks again and of course also thanks for making the new release available. Having concoct integrated as additional binning tool is fantastic.
cheers
By any chance are you using miniconda2 instead of miniconda3?
https://github.com/mamba-org/mamba/issues/640
File "/home/btschits/miniconda3/lib/python2.7/site-packages/conda/exceptions.py", line 1079, in __call__
Ok apparently you are using miniconda3 BUT somehow it is using python 2 instead of 3, so I still believe it might be related. Can you try again in a fresh miniconda3 install?
thanks for your response. I will give it a try with a fresh miniconda3 installation and let you know how it goes.
Hello I have the same problem
`-bash-4.2$ mamba create -n SqueezeMeta_v1.5.0-post.2 -c conda-forge -c bioconda -c fpusan squeezemeta
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ ____ / / _/ _/ _/ \ o _, / / ___/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.19.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['squeezemeta']
conda-forge/linux-64 Using cache conda-forge/noarch Using cache bioconda/linux-64 Using cache bioconda/noarch Using cache pkgs/main/linux-64 Using cache pkgs/main/noarch Using cache pkgs/r/linux-64 Using cache pkgs/r/noarch Using cache fpusan/linux-64 [====================] (00m:00s) No change fpusan/noarch [====================] (00m:00s) No change
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/kassammo/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1080, in __call__
return func(*args, **kwargs)
File "/home/kassammo/miniconda3/lib/python3.7/site-packages/mamba/mamba.py", line 917, in exception_converter
raise e
File "/home/kassammo/miniconda3/lib/python3.7/site-packages/mamba/mamba.py", line 911, in exception_converter
exit_code = _wrapped_main(*args, **kwargs)
File "/home/kassammo/miniconda3/lib/python3.7/site-packages/mamba/mamba.py", line 869, in _wrapped_main
result = do_call(args, p)
File "/home/kassammo/miniconda3/lib/python3.7/site-packages/mamba/mamba.py", line 738, in do_call
exit_code = create(args, parser)
File "/home/kassammo/miniconda3/lib/python3.7/site-packages/mamba/mamba.py", line 614, in create
return install(args, parser, "create")
File "/home/kassammo/miniconda3/lib/python3.7/site-packages/mamba/mamba.py", line 486, in install
index = load_channels(pool, channels, repos)
File "/home/kassammo/miniconda3/lib/python3.7/site-packages/mamba/utils.py", line 171, in load_channels
repo = subdir.create_repo(pool)
RuntimeError: Could not read JSON repodata file (/home/kassammo/miniconda3/pkgs/cache/b556ea5a.json) parse error line 1312536
$ /home/kassammo/miniconda3/bin/mamba create -n SqueezeMeta_v1.5.0-post.2 -c conda-forge -c bioconda -c fpusan squeezemeta
environment variables:
CIO_TEST=
active environment : None
user config file : /home/kassammo/.condarc
populated config files : conda version : 4.11.0 conda-build version : not installed python version : 3.7.10.final.0 virtual packages : __linux=3.10.0=0 __glibc=2.17=0 __unix=0=0 __archspec=1=x86_64 base environment : /home/kassammo/miniconda3 (writable) conda av data dir : /home/kassammo/miniconda3/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/fpusan/linux-64 https://conda.anaconda.org/fpusan/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 : /home/kassammo/miniconda3/pkgs /home/kassammo/.conda/pkgs envs directories : /home/kassammo/miniconda3/envs /home/kassammo/.conda/envs platform : linux-64 user-agent : conda/4.11.0 requests/2.27.1 CPython/3.7.10 Linux/3.10.0-1160.42.2.el7.x86_64 centos/7.9.2009 glibc/2.17 UID:GID : 916994788:100 netrc file : None offline mode : False
An unexpected error has occurred. Conda has prepared the above report.`
There is a problem with your conda/mamba installation.
https://github.com/mamba-org/mamba/issues/512
https://github.com/mamba-org/mamba/issues/947
According to the devs some causes might be mamba being installed in an environment different from the base environment, or /tmp being full.
It's probably better if check this and try again in a clean miniconda3 + mamba install.
Hi,
sorry for getting back to you so late on that issue I noticed that I screwed up my conda base env a while back when I made the mistake and installed a package into base requiring python 2.7. So I did a fresh miniconda3 installation as you suggested and then installed SqueezeMeta_1.5.0 using Mamba and everything worked fine. One thing I noticed was that the first fresh miniconda3 installation I did was using the latest version available, which had python 3.9. However, using that version I always ended up with error messages when trying to install mamba (or any package for that matter) in the base env. Only when I installed miniconda3 with python 3.7 I was able to install Mamba.
Thanks again for your help.
cheers
Hm, the problem with the latest version of miniconda seems weird, but if it happens with all the packages I'll let the conda guys figure it out :P. Glad that it's working for you!