Getting 0 bins

[Quincy Faber]

I generated a depth file from my data and tried to run Metabat but it will not form any bins.

Here is my code:

jgi_summarize_bam_contig_depths --outputDepth 971-1_S1.depth.txt *.bam
metabat2 -i 972-1_S1.scaffolds.fasta -a 972-1_S1.depth.txt -o metabat/bin

Here’s the output:

MetaBAT 2 (v2.12.1) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, and maxEdges 200.
0 bins (0 bases in total) formed.

My depth.txt file looks correct, I attached it.

[Quincy Faber]

turned out to be an issue with my sample

[Rob Egan]

HI Quincy,

It looks like you don't have any contigs >2500 bases in your assembly. MetaBAT requires a decent assembly before any bins can be made.

If you use the -v option and a more recent version of MetaBAT (like 2.15) it might tell you more information.

-Rob

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