FLAG: 1
refSeqFile = Olurida_v081_100000.fa.
bamFileName = bgdata/v082/zr1394_all_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = ../analyses/20-bs-snp/all.SNP-candidates.txt.
methCgFileName = ../analyses/20-bs-snp/all.CpG-meth-info.tab.
methChgFileName = ../analyses/20-bs-snp/all.CHG-meth-info.tab.
methChhFileName = ../analyses/20-bs-snp/all.CHH-meth-info.tab.
vQualMin = 15.
nLayerMax = 1000.
vSnpRate = 0.100000.
vSnpPerBase = 0.020000.
mapqThr = 20.
Init chrome name-len array completed, total 3816038 bp of 32 chromosomes.
32 chromes loaded.
Init chrome name-idx hash table completed.
Init chrome seq array completed.
Meth process begins...
Chrome updated to Contig0!
Chrome updated to Contig2!
Chrome updated to Contig3!
Chrome updated to Contig5!
Chrome updated to Contig7!
Chrome updated to Contig9!
Chrome updated to Contig65!
Chrome updated to Contig84!
Chrome updated to Contig89!
Chrome updated to Contig468!
Chrome updated to Contig15326!
Chrome updated to Contig16524!
Chrome updated to Contig16668!
Chrome updated to Contig16915!
Chrome updated to Contig17050!
Chrome updated to Contig17624!
Chrome updated to Contig17876!
Chrome updated to Contig18024!
Chrome updated to Contig18052!
Chrome updated to Contig18174!
Chrome updated to Contig18571!
Chrome updated to Contig19267!
Chrome updated to Contig19330!
Chrome updated to Contig19646!
Chrome updated to Contig19826!
Chrome updated to Contig20140!
Chrome updated to Contig20625!
Chrome updated to Contig22814!
500000 records have been dealed.
Chrome updated to Contig23978!
Chrome updated to Contig23979!
Chrome updated to Contig26138!
Chrome updated to Contig34578!
Meth process ends...
SNP process begins...
100000 records have been dealed.
200000 records have been dealed.
300000 records have been dealed.
400000 records have been dealed.
500000 records have been dealed.
SNP process ends...
SNP process completed.