宏基因组单样品分箱-metabinner-CSDN博客

本文链接：https://blog.csdn.net/youfeng_xjy/article/details/140528124

source activate metabinner_env

cd ~/.conda/envs/metabinner_env/bin
cd scripts

# 1.前期准备
mkdir /home/xujiayang/PAH/output_of_coveragefile_Cu_3
bash gen_coverage_file.sh -a /home/xujiayang/PAH/ASSEMBLY_Spades/VS-Cu-3_D58.fasta -o /home/xujiayang/PAH/output_of_coveragefile_Cu_3 /home/xujiayang/PAH/qc2/Cu/VS-Cu-3_D58_1.fastq /home/xujiayang/PAH/qc2/Cu/VS-Cu-3_D58_2.fastq
python gen_kmer.py /home/xujiayang/PAH/ASSEMBLY_Spades/VS-Cu-3_D58.fasta 1000 4 


# 2.设置路径
mkdir /home/xujiayang/PAH/output_metabinner_Cu_3

metabinner_path=~/.conda/envs/metabinner_env/bin
contig_file=/home/xujiayang/PAH/ASSEMBLY_Spades/VS-Cu-3_D58.fasta
output_dir=/home/xujiayang/PAH/output_metabinner_Cu_3
coverage_profiles=/home/xujiayang/PAH/output_of_coveragefile_Cu_3/coverage_profile_f1k.tsv
kmer_profile=/home/xujiayang/PAH/ASSEMBLY_Spades/VS-Cu-3_D58_kmer_4_f1000.csv


# 3.正式运行
bash run_metabinner.sh -a ${contig_file} -o ${output_dir} -d ${coverage_profiles} -k ${kmer_profile} -p ${metabinner_path} -t 12
# 输出的路径在下面这行
#${output_dir}/metabinner_res/ensemble_res/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins/ensemble_3logtrans/addrefined2and3comps/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins



# 4. 把结果Bin拷贝到bins/output_bins_Cu_3文件夹
cp -r /home/xujiayang/PAH/output_metabinner_Cu_3/metabinner_res/ensemble_res/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins/ensemble_3logtrans/addrefined2and3comps/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins bins/output_bins_Cu_3