---
name: "runMetaBat.sh"
section: "1"
platform: "linux"
package: "metabat"
version: "2.15-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/runMetaBat.sh"
---

# runMetaBat.sh(1)

Wrapper for MetaBAT

## NAME

runMetaBat.sh - Wrapper for MetaBAT

## DESCRIPTION

**runMetaBat.sh**  *\<select metabat options\> assembly.fa sample1.bam \[ sample2.bam ...\]*

## OPTIONS

You can specify any metabat options EXCEPT:

**-i** **--inFile**

**-o** **--outFile**

**-a** **--abdFile**

Also for depth calculations stage only, you can set the following environmental variables:

- PCTID=97

  **--** reads below this threshold will be discarded

- BADMAP=0

  **--** output the discarded reads to a sub directory

- MINDEPTH=1.0

  **--** require contigs to have this minimum depth to be output

For full metabat options: metabat2 **-h**

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.