Abricate stuck at solving environment

[hassantarabai]

Hello,

I am gettting stuck at "solving environment" when am trying to install abricate on the server. installation works fine on my laptop.

Any reason you might think causing that ?

Regards.

[mars188]

Yes, same issue here. I'm trying to install abricate on cluster and it's stuck at "solving environment" step whereas it was working fine few months ago. I have no choice but to install it on the server/cluster.

Any/all help will be appreciated!

[DrJoshPhD]

Same issue here trying to install it on a personal machine.

EDIT: creating a python 3.7 environment solved this for me, this may require manually installing perl-list-moreutils ( conda install perl-list-moreutils).

[bede]

This issue appears to be preventing installation of flanker either locally or using GitHub actions. https://github.com/wtmatlock/flanker/issues/51

[rpetit3]

Hello!

I was able to create an abricate environment today without any issues.

conda create -n abricate -c conda-forge -c bioconda abricate

I would suggest up check out your base environment. It should be pretty empty with not much installed on it.

conda env export -n base

If your base environment is nice and clean maybe give Mamba a try, since its much faster at solving environments.

mamba create -n abricate -c conda-forge -c bioconda abricate

Cheers

[bede]

Hi all! I'm still seeing this issue today on a new machine also with a pretty clean base environment.

Both conda create -n abricate -c conda-forge -c bioconda abricate

and mamba create -n abricate -c conda-forge -c bioconda abricate

install Abricate 0.3. If I specify 1.0.1 I get UnsatisfiableError.

I can hack together a works-on-my-machine Mamba solution but for bioconda packages depending on abricate this is a problem.

Perhaps this issue should be reopened?

[rpetit3]

What versions of mamba and conda do you have? I was able to successfully build a new environment today for abricate 1.0.1 using mamba

mamba --version
mamba 1.1.0
conda 22.9.0

[bede]

Thanks @rpetit3, my conda is slightly newer than yours

% mamba --version                                                   
mamba 1.1.0
conda 22.11.1

% mamba create -n abricate -c conda-forge -c bioconda abricate=1.0.1
…
Looking for: ['abricate=1.0.1']

conda-forge/osx-64                                          Using cache
conda-forge/noarch                                          Using cache
bioconda/osx-64                                             Using cache
bioconda/noarch                                             Using cache
pkgs/r/osx-64                                                 No change
pkgs/main/osx-64                                              No change
pkgs/r/noarch                                                 No change
pkgs/main/noarch                                              No change
Could not solve for environment specs
Encountered problems while solving:
  - nothing provides t_coffee needed by perl-bio-tools-run-alignment-tcoffee-1.7.4-pl5262hdfd78af_3

The environment can't be solved, aborting the operation

% conda create -n abricate -c conda-forge -c bioconda abricate=1.0.1
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
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                                                                                                                                        

UnsatisfiableError: 
Note that strict channel priority may have removed packages required for satisfiability.

My base env is small but not empty, do you think it's to blame?

% conda env export     
name: base
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - brotlipy=0.7.0=py311h5547dcb_1005
  - bzip2=1.0.8=h0d85af4_4
  - c-ares=1.18.1=h0d85af4_0
  - ca-certificates=2022.12.7=h033912b_0
  - certifi=2022.12.7=pyhd8ed1ab_0
  - cffi=1.15.1=py311ha86e640_2
  - charset-normalizer=2.1.1=pyhd8ed1ab_0
  - colorama=0.4.6=pyhd8ed1ab_0
  - conda=22.11.1=py311h6eed73b_1
  - conda-package-handling=1.9.0=py311h5547dcb_1
  - cryptography=38.0.4=py311h61927ef_0
  - fmt=9.1.0=hb8565cd_0
  - gettext=0.21.1=h8a4c099_0
  - icu=70.1=h96cf925_0
  - idna=3.4=pyhd8ed1ab_0
  - krb5=1.19.3=hb98e516_0
  - libarchive=3.5.2=hbf7dfe4_3
  - libcurl=7.86.0=h581aaea_1
  - libcxx=14.0.6=hccf4f1f_0
  - libedit=3.1.20191231=h0678c8f_2
  - libev=4.33=haf1e3a3_1
  - libffi=3.4.2=h0d85af4_5
  - libiconv=1.17=hac89ed1_0
  - libidn2=2.3.4=hb7f2c08_0
  - libmamba=1.1.0=h8b63968_2
  - libmambapy=1.1.0=py311hcc19a12_2
  - libnghttp2=1.47.0=h5aae05b_1
  - libsolv=0.7.22=hd9580d2_0
  - libsqlite=3.40.0=ha978bb4_0
  - libssh2=1.10.0=h47af595_3
  - libunistring=0.9.10=h0d85af4_0
  - libxml2=2.10.3=hb9e07b5_0
  - libzlib=1.2.13=hfd90126_4
  - lz4-c=1.9.3=he49afe7_1
  - lzo=2.10=haf1e3a3_1000
  - mamba=1.1.0=py311h8082e30_2
  - ncurses=6.3=h96cf925_1
  - openssl=3.0.7=hfd90126_1
  - pigz=2.6=h5dbffcc_0
  - pip=22.3.1=pyhd8ed1ab_0
  - pluggy=1.0.0=pyhd8ed1ab_5
  - pybind11-abi=4=hd8ed1ab_3
  - pycosat=0.6.4=py311h5547dcb_1
  - pycparser=2.21=pyhd8ed1ab_0
  - pyopenssl=22.1.0=pyhd8ed1ab_0
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.11.0=h559f36b_0_cpython
  - python.app=1.4=py311h5547dcb_1
  - python_abi=3.11=3_cp311
  - readline=8.1.2=h3899abd_0
  - reproc=14.2.3=h0d85af4_0
  - reproc-cpp=14.2.3=he49afe7_0
  - requests=2.28.1=pyhd8ed1ab_1
  - ruamel.yaml=0.17.21=py311h5547dcb_2
  - ruamel.yaml.clib=0.2.7=py311h5547dcb_1
  - setuptools=65.5.1=pyhd8ed1ab_0
  - tk=8.6.12=h5dbffcc_0
  - toolz=0.12.0=pyhd8ed1ab_0
  - tqdm=4.64.1=pyhd8ed1ab_0
  - tzdata=2022g=h191b570_0
  - urllib3=1.26.13=pyhd8ed1ab_0
  - wget=1.20.3=hd3787cc_1
  - wheel=0.38.4=pyhd8ed1ab_0
  - xz=5.2.6=h775f41a_0
  - yaml-cpp=0.7.0=hf0c8a7f_2
  - zlib=1.2.13=hfd90126_4
  - zstd=1.5.2=hfa58983_4
prefix: /Users/bede/miniconda3

[bede]

Changing my channel priority to flexible allows me to install 1.0.1, but IIRC this isn't considered good practice? I've noticed that conda install abricate=1.0.1 has also started failing in GitHub Actions at some stage, suggesting that this install is broken even in a fresh conda installation.