# 新建文件夹并进入
mkdir Pilon && cd Pilon
# 得到genome00.fasta
perl -e 'while (<>) { if (m/^>/) { print; } else { tr/atcg/ATCG/; print; } }' /media/aa/DATA/SZQ2/bj/my/genome/5.1210/02hifiasm_primary/assembly.p_ctg.fa > genome00.fasta
round1
/media/aa/DATA/JJH/software/bowtie2-2.4.1-linux-x86_64/bowtie2-build --threads 8 genome00.fasta genome00
/media/aa/DATA/JJH/software/bowtie2-2.4.1-linux-x86_64/bowtie2 -x genome00 -1 /media/aa/DATA/SZQ2/bj/my/genome/5.1210/01cleandata/A5.1210.L350_FDSW22H000294-3r_1.fq.clean -2 /media/aa/DATA/SZQ2/bj/my/genome/5.1210/01cleandata/A5.1210.L350_FDSW22H000294-3r_2.fq.clean --score-min L,-0.3,-0.3 -p 8 -I 0 -X 1000 --fr -S bowtie2.00.sam 2> bowtie2.00.log
# real 3m18.445s
# user 25m37.612s
# sys 0m13.719s
samtools sort -@ 8 -o bowtie2.00.bam -O BAM bowtie2.00.sam
java -jar /media/aa/DATA/JJH/software/picard-tools/picard.jar MarkDuplicates I=bowtie2.00.bam O=bowtie2_RD.00.bam M=bowtie2_RD.00.metrics
/media/aa/DATA/SZQ2/samtools-0.1.19/samtools index bowtie2_RD.00.bam
/media/aa/DATA/SZQ2/samtools-0.1.19/samtools faidx genome00.fasta
java -Xmx100G -jar /media/aa/DATA/JJH/software/pilon/pilon-1.23.jar --genome genome00.fasta --frags bowtie2_RD.00.bam --fix all --changes --output pilon01
# real 2m19.524s
# user 2m44.993s
# sys 0m4.779s
/media/aa/DATA1/bin/pilon_stats.pl --arrow-genome /media/aa/DATA/SZQ2/bj/my/genome/5.1210/02hifiasm_primary/assembly.p_ctg.fa pilon01.changes > pilon01.changes.stats
round2
ln -s pilon01.fasta genome01.fasta
/media/aa/DATA/JJH/software/bowtie2-2.4.1-linux-x86_64/bowtie2-build --threads 8 genome01.fasta genome01
/media/aa/DATA/JJH/software/bowtie2-2.4.1-linux-x86_64/bowtie2 -x genome01 -1 /media/aa/DATA/SZQ2/bj/my/genome/5.1210/01cleandata/A5.1210.L350_FDSW22H000294-3r_1.fq.clean -2 /media/aa/DATA/SZQ2/bj/my/genome/5.1210/01cleandata/A5.1210.L350_FDSW22H000294-3r_2.fq.clean --score-min L,-0.3,-0.3 -p 8 -I 0 -X 1000 --fr -S bowtie2.01.sam 2> bowtie2.01.log
samtools sort -@ 8 -o bowtie2.01.bam -O BAM bowtie2.01.sam
java -jar /media/aa/DATA/JJH/software/picard-tools/picard.jar MarkDuplicates I=bowtie2.01.bam O=bowtie2_RD.01.bam M=bowtie2_RD.01.metrics
samtools index bowtie2_RD.01.bam
samtools faidx genome01.fasta
java -Xmx101G -jar /media/aa/DATA/JJH/software/pilon/pilon-1.23.jar --genome genome01.fasta --frags bowtie2_RD.01.bam --fix all --changes --output pilon02
/media/aa/DATA1/bin/pilon_stats.pl pilon02.changes > pilon02.changes.stats
得到 pilon02.fasta