FLAG: 1
refSeqFile = ../data/Cvirginica_v300/Cvirginica_v300.fa.
bamFileName = ../output/02.10-bismark-deduplication/CF06-CM02-Larvae_dedup.sorted.bam.
snpFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF06-CM02-Larvae.candidates.txt.
methCgFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF06-CM02-Larvae.CpG.tab.
methChgFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF06-CM02-Larvae.CHG.tab.
methChhFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF06-CM02-Larvae.CHH.tab.
vQualMin = 15.
nLayerMax = 1000.
vSnpRate = 0.100000.
vSnpPerBase = 0.020000.
mapqThr = 20.
Init chrome name-len array completed, total 684741128 bp of 11 chromosomes.
11 chromes loaded.
Init chrome name-idx hash table completed.
Init chrome seq array completed.
Meth process begins...
Chrome updated to NC_035780.1!
500000 records have been dealed.
1000000 records have been dealed.
1500000 records have been dealed.
2000000 records have been dealed.
Chrome updated to NC_035781.1!
2500000 records have been dealed.
3000000 records have been dealed.
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4000000 records have been dealed.
Chrome updated to NC_035782.1!
4500000 records have been dealed.
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5500000 records have been dealed.
6000000 records have been dealed.
Chrome updated to NC_035783.1!
6500000 records have been dealed.
7000000 records have been dealed.
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8000000 records have been dealed.
8500000 records have been dealed.
Chrome updated to NC_035784.1!
9000000 records have been dealed.
9500000 records have been dealed.
10000000 records have been dealed.
10500000 records have been dealed.
11000000 records have been dealed.
11500000 records have been dealed.
12000000 records have been dealed.
Chrome updated to NC_035785.1!
12500000 records have been dealed.
13000000 records have been dealed.
Chrome updated to NC_035786.1!
13500000 records have been dealed.
14000000 records have been dealed.
Chrome updated to NC_035787.1!
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15000000 records have been dealed.
Chrome updated to NC_035788.1!
15500000 records have been dealed.
16000000 records have been dealed.
16500000 records have been dealed.
Chrome updated to NC_035789.1!
17000000 records have been dealed.
Chrome updated to NC_007175.2!
Meth process ends...
SNP process begins...
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SNP process ends...
SNP process completed.