KeyError in main_workflow.smk


I’m attempting to set up a Kansas Nextstrain build, but recently I have been running into a KeyError at the very start of the program, and I haven’t been able to find a similar question on the forums.
I have a local installation, which I have just updated today. I started running into this error soon after, and downloaded a fresh copy of the main_workflow.smk file in case that was somehow the issue. It still won’t work.

Here’s the error:

Thanks for your help!

Hmm, it appears that your local profile, khel_build, isn’t picking up the recently added “emerging lineages” file that’s configured in defaults/parameters.yaml.

This could be because your my_profiles/khel_build/config.yaml doesn’t include defaults/parameters.yaml under the configfile key (see example).

If you can post your my_profiles/khel_build/config.yaml file, we may be able to help troubleshoot further.

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Thanks so much for your help!

I actually just fixed the issue by updating my parameters.yaml file… I suppose I somehow updated one file, but not the other. My defaults/parameters.yaml file included subclades, but not emerging lineages. I replaced it with the defaults/parameters.yaml from Git, and it seems to have solved the issue!

I am now receiving another error, partway through the job 17 execution:

"unrecognized arguments: --ignore-seqs Wuhan/Hu-1/2019 Wuhan/WHO1/2019.

In case this is a result of a similar issue to above, I will go through my ncov folder, updating files to the latest versions, and report back.

Updating all files resolved the issues.

Thanks so much for your timely help!

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