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ktmeaton / plague-phylogeography

Phylogeography of Yersinia pestis.
https://ktmeaton.github.io/plague-phylogeography/
MIT License
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WorkflowError: Failed to solve the job scheduling problem with pulp while trying to run the snakemake pipeline #9

Open Aditya-Upa opened 7 months ago

Aditya-Upa commented 7 months ago

About the Server : Description: Ubuntu 16.04.7 LTS Release: 16.04 Codename: xenial

I installed the ktmeaton plague phylogeography snakemake pipeline in an environment using mamba (as it has been specified in the documentation).
mamba env create -f workflow/envs/merge/environment.yaml I even installed the lsd2 file and moved it to the bin directory of the environment I just created as was specified. snakemake --version 5.27.4 But when I tried to run the following : snakemake --profile profiles/laptop help I got the following error : WorkflowError: Failed to solve the job scheduling problem with pulp. Please report a bug and use --scheduler greedy as a workaround: Pulp: Error while trying to execute, use msg=True for more detailscbc

While it is a workaround to use --scheduler greedy tag and the job is getting completed; while running the next command in your list : snakemake --profile profiles/laptop all --scheduler greedy

The code is getting stuck at the following step : Job 21: Running the nf-core/eager pipeline for local Biosample testlocal1. and exiting.

Can you please tell me how to fix this issue ?

Aditya-Upa commented 7 months ago

I tried doing the same in an ubuntu 22.04 (jammy) server as well and was facing similar problems.