MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data

References:

• Kang et al. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ, 2015.

• metabat Main Site

• Module Name: metabat (see the modules page for more information)
• Multithreaded app
• Environment variables set
  • METABAT_TESTDATA=/usr/local/apps/metabat/TEST_DATA
• Example files in /usr/local/apps/metabat/TEST_DATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive -c 4 --mem 10g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load metabat

[user@cn3144 ~]$ cp $METABAT_TESTDATA/* .

[user@cn3144 ~]$ runMetaBat.sh -t $SLURM_CPUS_PER_TASK assembly.fa *.bam
Executing: 'jgi_summarize_bam_contig_depths --outputDepth assembly.fa.depth.txt --pairedContigs assembly.fa.paired.txt --minContigLength 1000 --minContigDepth 1  library1.sorted.bam library2.sorted.bam' at Fri Jun 21 15:02:54 EDT 2019
Output depth matrix to assembly.fa.depth.txt
Output pairedContigs lower triangle to assembly.fa.paired.txt
minContigLength: 1000
minContigDepth: 1
jgi_summarize_bam_contig_depths v2.13-29-g2e72973 2019-06-12T22:50:43
Output matrix to assembly.fa.depth.txt
0: Opening bam: library1.sorted.bam
1: Opening bam: library2.sorted.bam
Allocating pairedContigs matrix: 0 MB over 2 threads
Processing bam files
[...]
Closing last bam file
Finished
Finished jgi_summarize_bam_contig_depths at Fri Jun 21 15:09:03 EDT 2019
Creating depth file for metabat at Fri Jun 21 15:09:03 EDT 2019
Executing: 'metabat2  --inFile assembly.fa --outFile assembly.fa.metabat-bins/bin --abdFile assembly.fa.depth.txt' at Fri Jun 21 15:09:03 EDT 2019
MetaBAT 2 (v2.13-29-g2e72973) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, and maxEdges 200. 
40 bins (93197986 bases in total) formed.
Finished metabat2 at Fri Jun 21 15:09:04 EDT 2019

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. metabat.sh). For example:

#!/bin/bash
module load metabat
runMetaBat.sh -t $SLURM_CPUS_PER_TASK assembly.fa *.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=20g metabat.sh

Create a swarmfile (e.g. metabat.swarm). For example:

cd dir1; runMetaBat.sh -t $SLURM_CPUS_PER_TASK assembly.fa *.bam
cd dir2; runMetaBat.sh -t $SLURM_CPUS_PER_TASK assembly.fa *.bam
cd dir3; runMetaBat.sh -t $SLURM_CPUS_PER_TASK assembly.fa *.bam

Submit this job using the swarm command.

swarm -f metabat.swarm -g 20 -t 8 --module metabat