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nioo-knaw / epiGBS2

This is the epiGBS2 snakemake pipeline as published in a preprint version.
MIT License
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Dry-Run failed #8

Closed JGPunier closed 3 years ago

JGPunier commented 3 years ago

Hello

I am trying to run epiGBS2 on my working station, using a specific conda environment ("snake") based on Python 3.7 and Snakemake 6.1.1 (as suggested). The dry-run works fine in "denovo" mode (all green), but it fails in "reference" mode, indicating (in red) :

KeyError in line 179 of /home/test/epiGBS2/src/rules/reference.rules: 'mapping_quality' File "/home/test/epiGBS2/Snakefile", line 21, in File "/home/test/epiGBS2/src/rules/reference.rules", line 179, in

I cannot figure out the origin of this issue. I suppose it does not have to do with python/snakemake versions since everything is working fine in denovo mode. Similarly, I doubt that it stems from the config.yaml (zipped file attached, just in case), since the only change I made is a switch from "denovo" to "reference"... I hope you can help me on that. Best regards Jérôme

config.zip

MaartenPostuma commented 3 years ago

Hello Jerome, This issue is known and has since been fixed in the development branch. Unfortunately I've not been able to merge this branch with the default epiGBS2v2 branch yet. But this should be fixed before the end of the week. If you want to run the script before this time you could use git checkout origin/master to switch to the development branch Kind regards, Maarten Postuma

JGPunier commented 3 years ago

Great ! all green now ! Thank you very much ! Jérôme