30 lines
620 B
Bash
Executable File
30 lines
620 B
Bash
Executable File
thread=64
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make clean; make -j 32
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n1=~/data/dataset/D2/n1.fq.gz
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n2=~/data/dataset/D2/n2.fq.gz
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#n1=~/data/dataset/D2/d1.fq
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#n2=~/data/dataset/D2/d2.fq
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#n1=~/data/SRR25735656_1.fastq.gz
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#n2=~/data/SRR25735656_2.fastq.gz
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#n1=/file-data/zzh/dataset/D1/45mr1.fq.gz
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#n2=/file-data/zzh/dataset/D1/45mr2.fq.gz
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reference=~/data/reference/fmt/human_g1k_v37_decoy.fasta
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out=/dev/null
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#out=./oldsam-D2-out.sam
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#out=./D2-1.sam
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#out=./d.sam
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prog=./fastalign
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#prog=/home/zzh/fastbwa
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time $prog mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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$reference \
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$n1 \
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$n2 \
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-o $out
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