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Prokka isn't running if Kraken fails #173

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thorellk opened this issue May 19, 2022 · 0 comments
Open

Prokka isn't running if Kraken fails #173

thorellk opened this issue May 19, 2022 · 0 comments

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@thorellk
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thorellk commented May 19, 2022 •
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I just ran BACTpipe over ~70 samples and for some Kraken failed due to out of memory problems. Unfortunately this means prokka didn't run either. I think we should change so that prokka runs if there is an assembly output from Shovill and if there is no Kraken output to use into prokka then we just call it Unknown unknown as species classification. What do you think?
@thorellk thorellk changed the title Prokka isn't running if Kraken faoö Prokka isn't running if Kraken fails May 19, 2022
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