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execute_script.sh
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execute_script.sh
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#step1 单独运行
#=================================
#查看数据库中Malus分类的family数目
#singularity exec /data/Erick_Tong/02Data_analysis_project/09Genome_assembly/03geneke/TETools202309.sif famdb.py lineage -ad Malus
#统计Malus families数目
#singularity exec /data/Erick_Tong/02Data_analysis_project/09Genome_assembly/03geneke/TETools202309.sif famdb.py lineage -ad --format totals Malus
#================================
#================================global variable
threads=8
pa=2 #1pa=4threads
TEsingularity=/data/Erick_Tong/02Data_analysis_project/09Genome_assembly/03geneke/TETools202309.sif
genome_file=Fuji_Ral.fasta #这里结尾必须是.fasta
genome_prefix=Fuji_Ral
timesj=$(date +"%Y_%m_%d")
#Malus(基于已有数据库RepBase+Dfam 运行repeatmasker)
#===============================global variable
#step2 RepeatModeler
#=====================================================================
# 建库
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
BuildDatabase -name ${genome_prefix}_BuildDatabase_${timesj} ${genome_file}
# 运行 RepeatModeler
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
RepeatModeler \
-database ${genome_prefix}_BuildDatabase_${timesj} \
-threads ${threads} \
-LTRStruct 1>repeatmodeler.log 2>&1
mkdir 00_${genome_prefix}_BuildDatabase_${timesj}
mv ${genome_prefix}_BuildDatabase_${timesj}.* 00_${genome_prefix}_BuildDatabase_${timesj}
mkdir 00_${genome_prefix}_denovo_repeatlibrary_${timesj}
mv ${genome_prefix}_BuildDatabase_${timesj}-* 00_${genome_prefix}_denovo_repeatlibrary_${timesj}
# 如果运行终止可以设置recoverDir自动检查运行
# singularity exec ../container/TETools202309.sif RepeatModeler -database Bra \
# -threads 20 -LTRStruct -recoverDir RM_xxxx 1>repeatmodeler.log 2>&1
#=====================================================================
#step3 RepeatMasker
#=====================================================================
## 基于已有数据库RepBase+Dfam 运行repeatmasker
## -e 比对软件；-pa 并行任务数，实际占用线程为pa*4；-gff,输出gff；-s,缓慢模式；-a,输出align文件；-species,物种范围；-dir,结果目录；
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
RepeatMasker \
-e rmblast \
-pa ${pa} \
-gff \
-s \
-a \
-species Malus \
-dir ./01_${genome_prefix}_repeatmasker_result1_RepBaseDfam_${timesj} \
${genome_file} \
> ${genome_prefix}_repeatmasker_result1_RepBaseDfam.log 2>&1
# 基于denovo lib 运行repeatmasker
#-pa 5 5个并行（32线程）-s 慢速* -q 快速 -qq 高速 -gff/-a 生成.gff/.align文件 .tbl结果汇总 -nolow 不包括低复杂重复序列（后面基因结构注释）
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
RepeatMasker \
-e rmblast \
-pa ${pa} \
-gff \
-s \
-a \
-lib 00_${genome_prefix}_denovo_repeatlibrary_${timesj}/${genome_prefix}_BuildDatabase_${timesj}-families.fa \
-dir 02_${genome_prefix}_repeatmasker_result2_denovolib_${timesj} \
01_${genome_prefix}_repeatmasker_result1_RepBaseDfam_${timesj}/${genome_prefix}.fasta.masked \
> ${genome_prefix}_repeatmasker_result2_denovolib.log 2>&1
# 合并结果repeatmasker_result1、repeatmasker_result2----------------------------(全部重复)
mkdir 03_${genome_prefix}_combine_repeatmasker_result12_${timesj}
#合并
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
perl /opt/RepeatMasker/util/combineRMFiles.pl \
01_${genome_prefix}_repeatmasker_result1_RepBaseDfam_${timesj}/${genome_prefix}.fasta \
02_${genome_prefix}_repeatmasker_result2_denovolib_${timesj}/${genome_prefix}.fasta.masked \
03_${genome_prefix}_combine_repeatmasker_result12_${timesj}/${genome_prefix}
# 根据.out文件生成生成.gff文件
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
rmOutToGFF3.pl \
03_${genome_prefix}_combine_repeatmasker_result12_${timesj}/${genome_prefix}.out \
> 03_${genome_prefix}_combine_repeatmasker_result12_${timesj}/${genome_prefix}.out.gff
#软屏蔽
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
maskFile.pl \
-fasta ${genome_file} \
-annotations 03_${genome_prefix}_combine_repeatmasker_result12_${timesj}/${genome_prefix}.out \
-softmask
mv ${genome_file}.masked 03_${genome_prefix}_combine_repeatmasker_result12_${timesj}/${genome_prefix}.soft_masked.fasta
#硬屏蔽
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
maskFile.pl \
-fasta ${genome_file} \
-annotations 03_${genome_prefix}_combine_repeatmasker_result12_${timesj}/${genome_prefix}.out
mv ${genome_file}.masked 03_${genome_prefix}_combine_repeatmasker_result12_${timesj}/${genome_prefix}.hard_masked.fasta
# 绘图
#calcDivergenceFromAlign.pl -s hap02-repeat.div rmout_combine02/hap02.align
#createRepeatLandscape.pl -div hap02-repeat.div -g 660000000 > hap02-repeat.div.html
#-g 基因组大小
# 合并结果repeatmasker_result1、repeatmasker_result2----------------------------(全部重复)
####################################################
####################################################
# 合并结果repeatmasker_result1、repeatmasker_result2----------------------------(去除低复杂重复重复)
mkdir 04_delete03_Simple_repeat.Low_complexity_masked_${timesj}
##01去除低复杂重复
grep -v "Simple_repeat" 03_${genome_prefix}_combine_repeatmasker_result12_${timesj}/${genome_prefix}.out | grep -v "Low_complexity" > 04_delete03_Simple_repeat.Low_complexity_masked_${timesj}/${genome_prefix}_delete_sample_repeat_masked.out
# 根据.out文件生成生成.gff文件
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
rmOutToGFF3.pl \
04_delete03_Simple_repeat.Low_complexity_masked_${timesj}/${genome_prefix}_delete_sample_repeat_masked.out \
> 04_delete03_Simple_repeat.Low_complexity_masked_${timesj}/${genome_prefix}_delete_sample_repeat_masked.out.gff
#软屏蔽
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
maskFile.pl \
-fasta ${genome_file} \
-annotations 04_delete03_Simple_repeat.Low_complexity_masked_${timesj}/${genome_prefix}_delete_sample_repeat_masked.out \
-softmask
mv ${genome_file}.masked 04_delete03_Simple_repeat.Low_complexity_masked_${timesj}/${genome_prefix}.soft_masked.fasta
#硬屏蔽
singularity exec -B $PWD:$PWD -B /data:/data -B /biodata:/biodata ${TEsingularity} \
maskFile.pl \
-fasta ${genome_file} \
-annotations 04_delete03_Simple_repeat.Low_complexity_masked_${timesj}/${genome_prefix}_delete_sample_repeat_masked.out
mv ${genome_file}.masked 04_delete03_Simple_repeat.Low_complexity_masked_${timesj}/${genome_prefix}.hard_masked.fasta
# 合并结果repeatmasker_result1、repeatmasker_result2----------------------------(去除低复杂重复重复)
# 绘图
#calcDivergenceFromAlign.pl -s hap02-repeat.div rmout_combine02/hap02.align
#createRepeatLandscape.pl -div hap02-repeat.div -g 660000000 > hap02-repeat.div.html
#-g 基因组大小
###################################################