Run fails on Antismash "pip is looking at multiple versions of antismash to determine which version is compatible with other requirements."

[artfet]

While the dry-run works perfectly fine, once I do the normal run to perfom on the example dataset, I receive the following error:

Building DAG of jobs... Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'. Creating conda environment workflow/envs/antismash.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /home/artemfetter/bgcflow/workflow/rules/../envs/antismash.yaml: Command: mamba env create --quiet --file "/home/artemfetter/bgcflow/.snakemake/conda/d14246e7f492284418d37b3bc4074a88_.yaml" --prefix "/home/artemfetter/bgcflow/.snakemake/conda/d14246e7f492284418d37b3bc4074a88_" Output: Channels: - conda-forge - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Installing pip dependencies: ...working... Pip subprocess error: Running command git clone --filter=blob:none --quiet https://github.com/antismash/antismash.git /tmp/pip-req-build-dbve5cx2 Running command git checkout -q 25d2d74e011079d443f60beeb9b45becd0ff609d WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fb1aa047df0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/brawn/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fb1aa068160>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/brawn/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fb1aa0684c0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/brawn/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fb1aa068670>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/brawn/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fb1aa068820>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/brawn/ ERROR: Could not find a version that satisfies the requirement brawn==1.0.1 (from antismash) (from versions: none) ERROR: No matching distribution found for brawn==1.0.1 Ran pip subprocess with arguments: ['/home/artemfetter/bgcflow/.snakemake/conda/d14246e7f492284418d37b3bc4074a88_/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/artemfetter/bgcflow/.snakemake/conda/condaenv.ol3bi07y.requirements.txt', '--exists-action=b'] Pip subprocess output: Collecting git+https://github.com/antismash/antismash.git@7-1-0-1 (from -r /home/artemfetter/bgcflow/.snakemake/conda/condaenv.ol3bi07y.requirements.txt (line 1)) Cloning https://github.com/antismash/antismash.git (to revision 7-1-0-1) to /tmp/pip-req-build-dbve5cx2 Resolved https://github.com/antismash/antismash.git to commit 25d2d74e011079d443f60beeb9b45becd0ff609d Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' INFO: pip is looking at multiple versions of antismash to determine which version is compatible with other requirements. This could take a while. failed CondaEnvException: Pip failed

Is it something I did wrong during the installation process or might it have to do with the latest Antismash version?

Best regards

[matinnuhamunada]

Hi @artfet , thanks for using BGCFlow :)

From your message, the error suggested that either the brawn package does not exist on the PyPI server, or there might be network issues preventing access to PyPI. As brawn v1.0.1 is there on the server (https://pypi.org/project/brawn/), I'm guessing that the internet connection is a problem?

Can you try again on a stable connection and see if it helps?

Let us know if you still encounter the problem, at least from our test, the environment can be build:
https://github.com/NBChub/bgcflow/actions/runs/8827142528/job/24233935142