Mapping with bbmap.sh

Question

[Hayler Edu]

Hello everyone

Todat I'm trying to do a mapping with bbmap but I have a problem because in the results I have NaN% in everything, this is normal?

I'm using Ictalurus punctatus genome reference but my sample is pimelodus grosskopfii.

In the picture you can see the result.

[GenoMax]

Please post your bbmap.sh command line.

Answer 1

[Mensur Dlakic]

Definitely not normal.

It doesn't seem that BBmap is taking any reads in. That's why your num reads and num bases are all zeros, which results in division by zero and outputs NaN.

You also have two notes on top that might be worth checking out.

[GenoMax]

Those Notes are simply indicating that the BBMap index has been pre-created separately and will be used as is.