2026-01-18 00:40:44 +08:00
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thread=64
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2025-01-14 14:34:09 +08:00
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2026-01-16 02:54:10 +08:00
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make clean; make -j 32
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2025-01-14 14:34:09 +08:00
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2026-01-18 00:40:44 +08:00
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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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2026-01-17 22:54:03 +08:00
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#n1=~/data/SRR25735656_1.fastq.gz
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#n2=~/data/SRR25735656_2.fastq.gz
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2025-01-14 14:34:09 +08:00
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2026-01-15 23:04:02 +08:00
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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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2026-01-11 12:55:11 +08:00
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reference=~/data/reference/fmt/human_g1k_v37_decoy.fasta
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2025-01-14 14:34:09 +08:00
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2026-01-16 22:16:16 +08:00
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#out=/dev/null
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2026-01-16 02:54:10 +08:00
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#out=./oldsam-D2-out.sam
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2026-01-18 00:40:44 +08:00
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out=./D2-1.sam
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#out=./d.sam
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2026-01-11 12:55:11 +08:00
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prog=./fastalign
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#prog=/home/zzh/fastbwa
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time $prog mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
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2025-01-14 14:34:09 +08:00
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$reference \
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$n1 \
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$n2 \
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-o $out -2
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