METABOLIC菌群代谢分析

文章
标题：METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks
期刊：Microbiome
时间：2022

MAG map到宏基因组测序数据计算功能通路的丰度信息

主页：https://github.com/AnantharamanLab/METABOLIC
wiki：https://github.com/AnantharamanLab/METABOLIC/wiki
manual: https://github.com/AnantharamanLab/METABOLIC/wiki/METABOLIC-Usage

安装

conda env create -f ./METABOLIC_v4.0_env.yml
conda env config vars set GTDBTK_DATA_PATH="/public/home/zzumgg03/huty/databases/gtdb_v207/release207_v2/"
conda activate METABOLIC_v4.0
mkdir METABOLIC_running_folder
cd METABOLIC_running_folder
git clone https://github.com/AnantharamanLab/METABOLIC.git
# 或者手动下载zip解压
cd METABOLIC-master/
bash run_to_setup.sh

Full installation debug

# Can't exec "diamond": No such file or directory at ../Accessory_scripts/make_pepunit_db.pl line 33
conda install -c bioconda diamond
# Can't locate Statistics/Descriptive.pm in @INC
conda install -c bioconda perl-statistics-descriptive
# Can't locate Parallel/ForkManager.pm in @INC
perl -MCPAN -e shell
install Parallel::ForkManager
# Can't locate Bio/Perl.pm in @INC
perl -MCPAN -e shell
install Bio::Perl

perl METABOLIC-G.pl -help
perl METABOLIC-C.pl -help

使用测试数据

#!/bin/bash
#SBATCH -p normal
#SBATCH --nodes=1
#SBATCH --ntasks=30
#SBATCH --ntasks-per-node=30
#SBATCH --mem=100G

source /public/home/zzumgg03/huty/softwares/miniconda3/etc/profile.d/conda.sh
conda activate METABOLIC_v4.0

route="/public/home/zzumgg03/huty/metabolic/METABOLIC_running_folder/METABOLIC-master"
perl $route/METABOLIC-C.pl -in-gn METABOLIC-master/METABOLIC_test_files/Guaymas_Basin_genome_files/ \
-r METABOLIC-master/METABOLIC_test_files/Reads_address.txt \
-o out_test -t 30