I want to remove human contaminants from gut metagenomes. For this I am using BBMap. The first step is to index the contaminant genome (human genome). I am following the exact procedure as described here, which I cross validated by finding the same commands described on other pages (biostars, github).
bbmap.sh -Xmx24G ref=hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz
is simply not working. My script outputs an output and error files. The output file is empty, the error files simply writes the command
java -Djava.library.path=/exports/csce/eddie/biology/groups/mcnally/camille/programs/bbmap/jni/ -ea -Xmx24G -cp /exports/csce/eddie/biology/groups/mcnally/camille/programs/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 -Xmx24G ref=hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz
and I have no other output.
I can't figure out the problem. Am I using the command wrong? Or is it an issue with my java? I am using my university cluster.