FLAG: 1
refSeqFile = ../data/Cvirginica_v300/Cvirginica_v300.fa.
bamFileName = ../output/02.10-bismark-deduplication/CF01-CM02-Larvae_dedup.sorted.bam.
snpFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF01-CM02-Larvae.candidates.txt.
methCgFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF01-CM02-Larvae.CpG.tab.
methChgFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF01-CM02-Larvae.CHG.tab.
methChhFileName = ../output/12-snp-calling-BS-Snper/per-sample/CF01-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.
2500000 records have been dealed.
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4500000 records have been dealed.
Chrome updated to NC_035781.1!
5000000 records have been dealed.
5500000 records have been dealed.
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Chrome updated to NC_035782.1!
9500000 records have been dealed.
10000000 records have been dealed.
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Chrome updated to NC_035783.1!
15000000 records have been dealed.
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19000000 records have been dealed.
Chrome updated to NC_035784.1!
19500000 records have been dealed.
20000000 records have been dealed.
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27500000 records have been dealed.
Chrome updated to NC_035785.1!
28000000 records have been dealed.
28500000 records have been dealed.
29000000 records have been dealed.
Chrome updated to NC_035786.1!
29500000 records have been dealed.
30000000 records have been dealed.
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31000000 records have been dealed.
Chrome updated to NC_035787.1!
31500000 records have been dealed.
32000000 records have been dealed.
32500000 records have been dealed.
33000000 records have been dealed.
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34000000 records have been dealed.
Chrome updated to NC_035788.1!
34500000 records have been dealed.
35000000 records have been dealed.
35500000 records have been dealed.
36000000 records have been dealed.
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37000000 records have been dealed.
37500000 records have been dealed.
Chrome updated to NC_035789.1!
38000000 records have been dealed.
38500000 records have been dealed.
Chrome updated to NC_007175.2!
Meth process ends...
SNP process begins...
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38900000 records have been dealed.
SNP process ends...
SNP process completed.