BSMAP v2.74 Start at: Fri Feb 13 04:30:12 2015 Input reference file: /Users/sr320/git-repos/nb-2015/Cv/data/cvir.v1.fa (format: FASTA) Load in 356237 db seqs, total size 156920694 bp. 3 secs passed total_kmers: 43046721 Create seed table. 8 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand: ++,-+ Single-end alignment(8 threads) Input read file: /Users/sr320/data-genomic/tentacle/2112_Cv_LSU.fastq (format: FASTQ) Output file: /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapoutcvir.v1.sam (format: SAM) Thread #2: 250000 reads finished. 10672 secs passed Thread #0: 50000 reads finished. 10674 secs passed Thread #7: 150000 reads finished. 10674 secs passed Thread #6: 100000 reads finished. 10675 secs passed Thread #3: 400000 reads finished. 10676 secs passed Thread #5: 200000 reads finished. 10676 secs passed Thread #4: 350000 reads finished. 10676 secs passed Thread #1: 300000 reads finished. 10678 secs passed Thread #2: 450000 reads finished. 12041 secs passed Thread #3: 650000 reads finished. 12046 secs passed Thread #7: 550000 reads finished. 12046 secs passed Thread #0: 500000 reads finished. 12047 secs passed Thread #5: 700000 reads finished. 12047 secs passed Thread #6: 600000 reads finished. 12048 secs passed Thread #1: 800000 reads finished. 12049 secs passed Thread #4: 750000 reads finished. 12050 secs passed Thread #2: 850000 reads finished. 13436 secs passed Thread #3: 900000 reads finished. 13444 secs passed Thread #7: 950000 reads finished. 13444 secs passed Thread #6: 1100000 reads finished. 13446 secs passed Thread #0: 1000000 reads finished. 13446 secs passed Thread #1: 1150000 reads finished. 13447 secs passed Thread #5: 1050000 reads finished. 13448 secs passed Thread #4: 1200000 reads finished. 13448 secs passed Thread #2: 1250000 reads finished. 14851 secs passed Thread #1: 1500000 reads finished. 14863 secs passed Thread #3: 1300000 reads finished. 14863 secs passed Thread #0: 1450000 reads finished. 14864 secs passed Thread #7: 1350000 reads finished. 14864 secs passed Thread #6: 1400000 reads finished. 14867 secs passed Thread #5: 1550000 reads finished. 14867 secs passed Thread #4: 1600000 reads finished. 14868 secs passed Thread #2: 1650000 reads finished. 16262 secs passed Thread #4: 2000000 reads finished. 16275 secs passed Thread #7: 1850000 reads finished. 16277 secs passed Thread #3: 1750000 reads finished. 16280 secs passed Thread #1: 1700000 reads finished. 16280 secs passed Thread #0: 1800000 reads finished. 16286 secs passed Thread #5: 1950000 reads finished. 16288 secs passed Thread #6: 1900000 reads finished. 16288 secs passed Thread #2: 2050000 reads finished. 17674 secs passed Thread #4: 2100000 reads finished. 17691 secs passed Thread #7: 2150000 reads finished. 17692 secs passed Thread #1: 2250000 reads finished. 17695 secs passed Thread #3: 2200000 reads finished. 17698 secs passed Thread #0: 2300000 reads finished. 17703 secs passed Thread #5: 2350000 reads finished. 17704 secs passed Thread #6: 2400000 reads finished. 17708 secs passed Thread #2: 2450000 reads finished. 19084 secs passed Thread #4: 2500000 reads finished. 19103 secs passed Thread #7: 2550000 reads finished. 19106 secs passed Thread #1: 2600000 reads finished. 19107 secs passed Thread #3: 2650000 reads finished. 19109 secs passed Thread #5: 2750000 reads finished. 19117 secs passed Thread #0: 2700000 reads finished. 19117 secs passed Thread #6: 2800000 reads finished. 19118 secs passed Thread #2: 2850000 reads finished. 21725 secs passed Thread #1: 3000000 reads finished. 21751 secs passed Thread #4: 2900000 reads finished. 21753 secs passed Thread #7: 2950000 reads finished. 21753 secs passed Thread #3: 3050000 reads finished. 21759 secs passed Thread #5: 3100000 reads finished. 21765 secs passed Thread #6: 3200000 reads finished. 21766 secs passed Thread #0: 3150000 reads finished. 21770 secs passed Thread #2: 3250000 reads finished. 23125 secs passed Thread #1: 3300000 reads finished. 23153 secs passed Thread #7: 3400000 reads finished. 23158 secs passed Thread #4: 3350000 reads finished. 23159 secs passed Thread #3: 3450000 reads finished. 23162 secs passed Thread #5: 3500000 reads finished. 23171 secs passed Thread #6: 3550000 reads finished. 23175 secs passed Thread #0: 3600000 reads finished. 23177 secs passed Thread #2: 3650000 reads finished. 24536 secs passed Thread #7: 3750000 reads finished. 24562 secs passed Thread #1: 3700000 reads finished. 24566 secs passed Thread #4: 3800000 reads finished. 24576 secs passed Thread #3: 3850000 reads finished. 24579 secs passed Thread #5: 3900000 reads finished. 24592 secs passed Thread #6: 3950000 reads finished. 24595 secs passed Thread #0: 4000000 reads finished. 24596 secs passed Thread #2: 4050000 reads finished. 25946 secs passed Thread #7: 4100000 reads finished. 25980 secs passed Thread #1: 4150000 reads finished. 25983 secs passed Thread #3: 4250000 reads finished. 25993 secs passed Thread #4: 4200000 reads finished. 25993 secs passed Thread #5: 4300000 reads finished. 26006 secs passed Thread #6: 4350000 reads finished. 26010 secs passed Thread #0: 4400000 reads finished. 26013 secs passed Thread #2: 4450000 reads finished. 27644 secs passed Thread #7: 4500000 reads finished. 27681 secs passed Thread #1: 4550000 reads finished. 27683 secs passed Thread #3: 4600000 reads finished. 27694 secs passed Thread #4: 4650000 reads finished. 27696 secs passed Thread #5: 4700000 reads finished. 27707 secs passed Thread #6: 4750000 reads finished. 27712 secs passed Thread #0: 4800000 reads finished. 27717 secs passed Thread #2: 4850000 reads finished. 29057 secs passed Thread #7: 4900000 reads finished. 29103 secs passed Thread #1: 4950000 reads finished. 29103 secs passed Thread #3: 5000000 reads finished. 29113 secs passed Thread #4: 5050000 reads finished. 29116 secs passed Thread #5: 5100000 reads finished. 29130 secs passed Thread #6: 5150000 reads finished. 29134 secs passed Thread #0: 5200000 reads finished. 29140 secs passed Thread #2: 5250000 reads finished. 30469 secs passed Thread #7: 5300000 reads finished. 30520 secs passed Thread #1: 5350000 reads finished. 30521 secs passed Thread #3: 5400000 reads finished. 30528 secs passed Thread #4: 5450000 reads finished. 30532 secs passed Thread #5: 5500000 reads finished. 30546 secs passed Thread #6: 5550000 reads finished. 30549 secs passed Thread #0: 5600000 reads finished. 30557 secs passed Thread #2: 5650000 reads finished. 31884 secs passed Thread #1: 5750000 reads finished. 31940 secs passed Thread #3: 5800000 reads finished. 31943 secs passed Thread #7: 5700000 reads finished. 31945 secs passed Thread #4: 5850000 reads finished. 31955 secs passed Thread #5: 5900000 reads finished. 31976 secs passed Thread #6: 5950000 reads finished. 31978 secs passed Thread #0: 6000000 reads finished. 31986 secs passed