Snakemake issue with asyncio / python3.11

[abel-betraoui]

Hi all,

Snakemake is encountering this issue snakemake/snakemake#1952 which leads to this error when running pangolin:

****
Pangolin running in usher mode.
****
Maximum ambiguity allowed is 0.3.
****
Query file:     /pangolin/data/SRR14855875.consensus.fa
****
Data files found:
usher_pb:       /opt/conda/envs/pangolin/lib/python3.11/site-packages/pangolin_data/data/lineageTree.pb
****
Traceback (most recent call last):
  File "/opt/conda/envs/pangolin/lib/python3.11/site-packages/snakemake/__init__.py", line 699, in snakemake
    success = workflow.execute(
              ^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/pangolin/lib/python3.11/site-packages/snakemake/workflow.py", line 960, in execute
    self.scheduler = JobScheduler(
                     ^^^^^^^^^^^^^
  File "/opt/conda/envs/pangolin/lib/python3.11/site-packages/snakemake/scheduler.py", line 98, in __init__
    from ratelimiter import RateLimiter
  File "/opt/conda/envs/pangolin/lib/python3.11/site-packages/ratelimiter.py", line 36, in <module>
    class RateLimiter(object):
  File "/opt/conda/envs/pangolin/lib/python3.11/site-packages/ratelimiter.py", line 127, in RateLimiter
    __aexit__ = asyncio.coroutine(__exit__)
                ^^^^^^^^^^^^^^^^^
AttributeError: module 'asyncio' has no attribute 'coroutine'

The problem is only encountered with python3.11 but this can be a problem when using the pangolin docker image as there is no constraint on the python version when using base image continuumio/miniconda3:4.9.2-alpine.

Cheers

[kapsakcj]

I maintain a separate pangolin docker image here if you'd like to use it. It contains python 3.8.13 in the conda/micromamba environment

https://github.com/StaPH-B/docker-builds/tree/master/pangolin/4.1.3

https://hub.docker.com/r/staphb/pangolin/tags

[wm75]

Thanks for the heads-up @abel-betraoui. With the pangolin docker image you mean the biocontainers ones at https://quay.io/repository/biocontainers/pangolin?tab=history? These are built from bioconda package builds of https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pangolin and should currently use Python 3.8, too.

[abel-betraoui]

I was thinking of the Dockerhub ones, built using the Dockerfile in this very repo.
It starts with :

FROM continuumio/miniconda3:4.9.2-alpine

And even though I couln't find how the base image continuumio/miniconda3:4.9.2-alpine is being built, I noticed a python version upgrade recently in it from 3.10.6 on the 2nd of november to 3.11.0 on the 7th of november

[wm75]

Ah, I see. The biocontainers images have a rather big community and user-base so, personally, I would always prefer these.
But I agree that if the repo here has a Dockerfile it should also produce a working image.