RUNMETABAT.SH(1)

🎀 NAME 🎀

okay bestie, welcome to the runMetaBat.sh page — section 1 of the User Commands manual, no cap. It's a wrapper for MetaBAT. That's the whole vibe. 💅

✨ DESCRIPTION ✨

so like, runMetaBat.sh is the lil script that runs MetaBAT for you and handles the boring bits, and you call it like this:

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

you feed it your <select metabat options>, then your assembly.fa, then one or more BAM files — sample1.bam and then [ sample2.bam ...] however many you got. it's giving pipeline energy. 🦋

🌸 OPTIONS 🌸

you can pass any metabat options you want, literally any of them — EXCEPT these three, bestie, they're off-limits because the wrapper handles them itself:

• -i, --inFile — nope, not yours to set 🙈
• -o, --outFile — also no 🚫
• -a, --abdFile — nope nope nope 💀

not me gatekeeping these flags but fr fr, the script owns them. don't fight the script.

🧚 environment variables (depth calculations stage only)

okay so only for the depth calculations stage, you can also set these environmental variables — and yes they have defaults, slay:

• PCTID=97 — reads below this threshold will be discarded. like if your read's identity % is under 97, it's out. bye 👋
• BADMAP=0 — output the discarded reads to a sub directory. set this and the rejected reads get their own lil folder to vibe in. 📁
• MINDEPTH=1.0 — require contigs to have this minimum depth to be output. under 1.0 depth? not making the cut, periodt. ⭐

and if you want the full metabat options menu, run:

metabat2 -h

go off, bestie. 👑

👑 AUTHOR 👑

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. iconic of him honestly. 🫶

and that's the whole page, bestie!! runMetaBat.sh 2.15, May 2020 — go assemble something beautiful 💖✨🌸