MetaBat only produce one bin

Question

[erikras1223]

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

Answer 1

[jlfroula]

Yes...you need to run runMetaBat.sh unless you already have a "depth.txt" file. There are two ways to run metabat. The easiest is
runMetaBat.sh <assembly.fa> < *.bam >

The other way is generate the depth.txt file by doing . jgi_summarize_bam_contig_depths --outputDepth depth.txt Bams/*.bam
then
metabat -i assembly.fasta -a depth.txt -o bin

The "depth.txt" file shows the average read depths per contig for each sample. So if you had 5 samples, you'd have hopefully aligned each of the 5 read samples to the one assembly and get 5 bam files. These 5 bam files are input to either runMetaBat.sh or jgi_summarize_bam_contig_depths.

[h.l.wong]

Thanks jlfroula, do you need to sort the bam files first?

Answer 2

[scarborough.matthew]

Hello! I am having the same problem as you. Did you ever find a fix?

[erikras1223]

I believe i had to run metabat.sh not metabat.

[scarborough.matthew]

Alright-- thanks for responding!

Answer 3

[donkang34]

We recommend you to try MetaBAT 2 which performs better with a few samples. And you don't need to tune parameters any more.