I have just started using MetaBat and have tried follow the tutorial found hear https://bitbucket.org/berkeleylab/metabat/wiki/Home . I have supplied it with my assembled contigs file using megahit. I also have a bam file but am not aware of how to use it as input for metabat.
Here are the parameters used, note I did both --sensitive and --specific although I am only putting one command:
metabat -i contigs.fa -o bin1 --sensitive -v --saveDistance saved.gprob
The result I get is one bin file of contig sequences that contains almost exactly what the contig.fa file holds. I have used this same contigs.fa file in Anvio using its default clustering algorithm and can find at least Wolbachia (the most abundant bacteria in my sample) and few other bacteria at low abundance. Please let me know if I am missing something obvious I would love to use metabat since it seems pretty fast and efficent. Thanks in advance