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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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Freyja 1.4.5 depthcutoff #211

Closed whottel closed 11 months ago

whottel commented 1 year ago

Hello,

I am using Cecret v.3.7.20230725, which looks to now be using the updated freyja container 1.4.5-20230808. With this new version for some wastewater SC2 samples I am getting the following freyja demix error: "demix: Solver error encountered, most likely due to insufficient sequencing depth. Try increasing the --depthcutoff parameter."

These samples do produce a demix file with freyja version 1.4.4-20230718.

It looks like 1.4.5-20230808 added the --depthcutoff parameter to freyja demix with defauly value set to 0. In a shell session of the freyja image I was able to produce a demix file for the impacted samples by setting --depthcutoff to 10 when running freyja demix. Can --depthcutoff be set to a value other than 0 in a cecret config file, or can this be value be set to the same value as params.minimum_depth? Also, attached are the depths and variants files of an example impacted sample generated using Cecret v.3.7.20230725.

2312877-SC2WW-IA-VH01284-230809_S82_depths.tsv.xlsx 2312877-SC2WW-IA-VH01284-230809_S82_variants.tsv.xlsx

Thanks, Wes

erinyoung commented 1 year ago

Yes! You can adjust params.freyja_demix_options.

In a config file it looks like

params.freyja_demix_options = '--depthcutoff 10'

On the command line it would look like

<your typical command> --freyja_demix_options '--depthcutoff 10'

I'll look into setting the default for freyja demix to align better with the minimum_depth parameter.

whottel commented 1 year ago

Great, thanks for the quick response! I will update my config and run again.

-Wes