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WorkflowError: Failed to solve the job scheduling problem with pulp while trying to run the snakemake pipeline #9

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Aditya-Upa opened this issue Mar 20, 2024 · 1 comment
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@Aditya-Upa
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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 Aditya-Upa added the bug Something isn't working label Mar 20, 2024
@Aditya-Upa
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I tried doing the same in an ubuntu 22.04 (jammy) server as well and was facing similar problems.

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