Questions on the Meganizing step

User Questions
2

I should add, I also tested the ‘contaminants’ marking/removal you mention here with our original DIAMOND runs, these do get annotated with taxa and functions, but the contaminants are still present. I’m using this via daa-meganizer option --conFile as follows:

daa-meganizer -i $DAA \
    -a2t $MEGAN_DATA/$ACC2TAX \
    -a2interpro2go $MEGAN_DATA/$ACC2IP \
    -a2seed $MEGAN_DATA/$ACC2SEED \
    -a2kegg $MEGAN_DATA/$ACC2KEGG \
    -a2eggnog $MEGAN_DATA/$ACC2EGGNOG \
    --conFile contaminants.txt \
    -v > $NAME.meganize.log

contaminants.txt is:

Chordata

Am I missing a crucial step?

Thanks @Daniel !