roberta-davidson

Actually I didn't really consider competitive mapping, although it may also work well but I haven't tried it myself. At this stage I'm simply performing two mappings and being stringent...

What we see when mapping to the whole reference genome is that for whatever reason, bwa preferentially maps reads to NUMTs instead of the MT, so there are always gaps...

Great, thanks!! :)

Hey @anugos @jfy133 ! Found a bit of a workaround. I downloaded [this](https://quay.io/repository/biocontainers/prokka?tab=info) container for Prokka and then modified my config to use this container. Also would not work via...

The original command in error from running mag was: ``` [17:36:49] Could not run command: cat MEGAHIT\-MetaBAT2\-Bushfire_A24936\.15\/MEGAHIT\-MetaBAT2\-Bushfire_A24936\.15\.IS\.tmp\.44\.faa | parallel --gnu --plain -j 2 --block 43333 --recstart '>' --pipe blastp -query...