FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_all_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
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 Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.