instrain微多樣性

conda activate dRep
time dRep dereplicate dRep_file -g bins_all/* -p 40 --S_algorithm ANImf -comp 90 -con 5
cat dRep_file/dereplicated_genomes/* > all_bin.fna
conda deactivate
parse_stb.py --reverse -f dRep_file/dereplicated_genomes/*  -o genomes.stb
mkdir bt2
bowtie2-build all_bin.fna bt2/all_bin.fna
prodigal -i all_bin.fna -d all_bin.fna.genes.fna -a all_bin.fna.genes.faa

mkdir result
source activate samtools
#p 50 大约一个小时一个样
#p 20,一个样品将近1.5h
for file in seq_L/*_R1.fq.gz; do
    base=$(basename "$file" _R1.fq.gz)
    bowtie2 -p 12 -x bt2/all_bin.fna -1 "$file" -2 "seq_L/${base}_R2.fq.gz" > "${base}-vs-bins_90_5.sam"
    inStrain profile "${base}-vs-bins_90_5.sam" all_bin.fna -o "result/${base}-vs-bins_90_5.IS" -p 12 -s genomes.stb -g all_bin.fna.genes.fna
    rm -f "${base}-vs-bins_90_5.sam"
    rm -f "${base}-vs-bins_90_5.bam"
    rm -f "${base}-vs-bins_90_5.sorted.bam"
    rm -f "${base}-vs-bins_90_5.sorted.bam.bai"
done