BSMAP v2.74 Start at: Wed Mar 7 13:41:51 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly10k.fa (format: FASTA) Load in 35320 db seqs, total size 691523275 bp. 7 secs passed total_kmers: 43046721 Create seed table. 32 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: /Volumes/Serine/wd/18-03-07/WG-BS/1_ATCACG_L001_R1_001.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/Serine/wd/18-03-07/bsmap/1_ATCACG_L001_R1_001-bsmap_out_jelly10k.sam (format: SAM) Thread #1: 50000 reads finished. 177 secs passed Thread #3: 100000 reads finished. 179 secs passed Thread #6: 350000 reads finished. 181 secs passed Thread #5: 400000 reads finished. 181 secs passed Thread #0: 250000 reads finished. 181 secs passed Thread #7: 200000 reads finished. 182 secs passed Thread #4: 300000 reads finished. 182 secs passed Thread #2: 150000 reads finished. 189 secs passed Thread #3: 500000 reads finished. 324 secs passed Thread #1: 450000 reads finished. 325 secs passed Thread #6: 550000 reads finished. 327 secs passed Thread #4: 750000 reads finished. 328 secs passed Thread #0: 650000 reads finished. 328 secs passed Thread #5: 600000 reads finished. 328 secs passed Thread #7: 700000 reads finished. 329 secs passed Thread #2: 800000 reads finished. 345 secs passed Thread #3: 850000 reads finished. 464 secs passed Thread #1: 900000 reads finished. 465 secs passed Thread #5: 1100000 reads finished. 468 secs passed Thread #6: 950000 reads finished. 468 secs passed Thread #4: 1000000 reads finished. 469 secs passed Thread #0: 1050000 reads finished. 472 secs passed Thread #7: 1150000 reads finished. 473 secs passed Thread #2: 1200000 reads finished. 502 secs passed Thread #1: 1300000 reads finished. 610 secs passed Thread #3: 1250000 reads finished. 611 secs passed Thread #5: 1350000 reads finished. 614 secs passed Thread #4: 1450000 reads finished. 615 secs passed Thread #6: 1400000 reads finished. 616 secs passed Thread #0: 1500000 reads finished. 619 secs passed Thread #7: 1550000 reads finished. 620 secs passed Thread #2: 1600000 reads finished. 658 secs passed Thread #1: 1650000 reads finished. 756 secs passed Thread #3: 1700000 reads finished. 757 secs passed Thread #5: 1750000 reads finished. 760 secs passed Thread #6: 1850000 reads finished. 763 secs passed Thread #4: 1800000 reads finished. 763 secs passed Thread #0: 1900000 reads finished. 766 secs passed Thread #7: 1950000 reads finished. 767 secs passed Thread #2: 2000000 reads finished. 814 secs passed Thread #1: 2050000 reads finished. 904 secs passed Thread #3: 2100000 reads finished. 904 secs passed Thread #5: 2150000 reads finished. 909 secs passed Thread #6: 2200000 reads finished. 911 secs passed Thread #4: 2250000 reads finished. 911 secs passed Thread #0: 2300000 reads finished. 915 secs passed Thread #7: 2350000 reads finished. 916 secs passed Thread #2: 2400000 reads finished. 975 secs passed Thread #3: 2500000 reads finished. 1052 secs passed Thread #1: 2450000 reads finished. 1053 secs passed Thread #5: 2550000 reads finished. 1058 secs passed Thread #6: 2600000 reads finished. 1060 secs passed Thread #4: 2650000 reads finished. 1061 secs passed Thread #0: 2700000 reads finished. 1064 secs passed Thread #7: 2750000 reads finished. 1066 secs passed Thread #2: 2800000 reads finished. 1138 secs passed Thread #3: 2850000 reads finished. 1200 secs passed Thread #1: 2900000 reads finished. 1202 secs passed Thread #5: 2950000 reads finished. 1206 secs passed Thread #6: 3000000 reads finished. 1209 secs passed Thread #4: 3050000 reads finished. 1210 secs passed Thread #0: 3100000 reads finished. 1212 secs passed Thread #7: 3150000 reads finished. 1216 secs passed Thread #2: 3200000 reads finished. 1301 secs passed Thread #3: 3250000 reads finished. 1348 secs passed Thread #1: 3300000 reads finished. 1351 secs passed Thread #5: 3350000 reads finished. 1356 secs passed Thread #4: 3450000 reads finished. 1360 secs passed Thread #6: 3400000 reads finished. 1361 secs passed Thread #0: 3500000 reads finished. 1362 secs passed Thread #7: 3550000 reads finished. 1365 secs passed Thread #2: 3600000 reads finished. 1461 secs passed Thread #3: 3650000 reads finished. 1497 secs passed Thread #1: 3700000 reads finished. 1498 secs passed Thread #5: 3750000 reads finished. 1504 secs passed Thread #4: 3800000 reads finished. 1509 secs passed Thread #6: 3850000 reads finished. 1509 secs passed Thread #0: 3900000 reads finished. 1511 secs passed Thread #7: 3950000 reads finished. 1514 secs passed Thread #2: 4000000 reads finished. 1618 secs passed Thread #3: 4050000 reads finished. 1646 secs passed Thread #1: 4100000 reads finished. 1646 secs passed Thread #5: 4150000 reads finished. 1652 secs passed Thread #6: 4250000 reads finished. 1657 secs passed Thread #4: 4200000 reads finished. 1658 secs passed Thread #0: 4300000 reads finished. 1661 secs passed Thread #7: 4350000 reads finished. 1664 secs passed Thread #2: 4400000 reads finished. 1774 secs passed Thread #3: 4450000 reads finished. 1792 secs passed Thread #1: 4500000 reads finished. 1793 secs passed Thread #5: 4550000 reads finished. 1798 secs passed Thread #4: 4650000 reads finished. 1803 secs passed Thread #6: 4600000 reads finished. 1803 secs passed Thread #0: 4700000 reads finished. 1807 secs passed Thread #7: 4750000 reads finished. 1811 secs passed Thread #2: 4800000 reads finished. 1929 secs passed Thread #3: 4850000 reads finished. 1938 secs passed Thread #1: 4900000 reads finished. 1939 secs passed Thread #5: 4950000 reads finished. 1945 secs passed Thread #4: 5000000 reads finished. 1949 secs passed Thread #6: 5050000 reads finished. 1949 secs passed Thread #0: 5100000 reads finished. 1954 secs passed Thread #7: 5150000 reads finished. 1959 secs passed Thread #3: 5250000 reads finished. 2084 secs passed Thread #1: 5300000 reads finished. 2084 secs passed Thread #2: 5200000 reads finished. 2084 secs passed Thread #5: 5350000 reads finished. 2090 secs passed Thread #4: 5400000 reads finished. 2095 secs passed Thread #6: 5450000 reads finished. 2095 secs passed Thread #0: 5500000 reads finished. 2100 secs passed Thread #7: 5550000 reads finished. 2104 secs passed Thread #3: 5600000 reads finished. 2229 secs passed Thread #1: 5650000 reads finished. 2230 secs passed Thread #5: 5750000 reads finished. 2236 secs passed Thread #4: 5800000 reads finished. 2238 secs passed Thread #2: 5700000 reads finished. 2238 secs passed Thread #6: 5850000 reads finished. 2239 secs passed Thread #0: 5900000 reads finished. 2245 secs passed Thread #7: 5950000 reads finished. 2250 secs passed Thread #3: 6000000 reads finished. 2372 secs passed Thread #1: 6050000 reads finished. 2374 secs passed Thread #5: 6100000 reads finished. 2380 secs passed Thread #4: 6150000 reads finished. 2382 secs passed Thread #6: 6250000 reads finished. 2384 secs passed Thread #0: 6300000 reads finished. 2390 secs passed Thread #2: 6200000 reads finished. 2393 secs passed Thread #7: 6350000 reads finished. 2396 secs passed Thread #3: 6400000 reads finished. 2517 secs passed Thread #1: 6450000 reads finished. 2517 secs passed Thread #5: 6500000 reads finished. 2525 secs passed Thread #4: 6550000 reads finished. 2527 secs passed Thread #6: 6600000 reads finished. 2529 secs passed Thread #0: 6650000 reads finished. 2534 secs passed Thread #7: 6750000 reads finished. 2542 secs passed Thread #2: 6700000 reads finished. 2548 secs passed Thread #3: 6800000 reads finished. 2660 secs passed Thread #1: 6850000 reads finished. 2661 secs passed Thread #5: 6900000 reads finished. 2669 secs passed Thread #4: 6950000 reads finished. 2672 secs passed Thread #6: 7000000 reads finished. 2676 secs passed Thread #0: 7050000 reads finished. 2683 secs passed Thread #7: 7100000 reads finished. 2690 secs passed Thread #2: 7150000 reads finished. 2705 secs passed Thread #1: 7250000 reads finished. 2805 secs passed Thread #3: 7200000 reads finished. 2805 secs passed Thread #5: 7300000 reads finished. 2814 secs passed Thread #4: 7350000 reads finished. 2817 secs passed Thread #6: 7400000 reads finished. 2821 secs passed Thread #0: 7450000 reads finished. 2828 secs passed Thread #7: 7500000 reads finished. 2836 secs passed Thread #2: 7550000 reads finished. 2859 secs passed Thread #1: 7600000 reads finished. 2949 secs passed Thread #3: 7650000 reads finished. 2949 secs passed Thread #5: 7700000 reads finished. 2958 secs passed Thread #4: 7750000 reads finished. 2960 secs passed Thread #6: 7800000 reads finished. 2964 secs passed Thread #0: 7850000 reads finished. 2972 secs passed Thread #7: 7900000 reads finished. 2980 secs passed Thread #2: 7950000 reads finished. 3012 secs passed Thread #1: 8000000 reads finished. 3092 secs passed Thread #3: 8050000 reads finished. 3093 secs passed Thread #5: 8100000 reads finished. 3101 secs passed Thread #4: 8150000 reads finished. 3103 secs passed Thread #6: 8200000 reads finished. 3107 secs passed Thread #0: 8250000 reads finished. 3116 secs passed Thread #7: 8300000 reads finished. 3125 secs passed Thread #2: 8350000 reads finished. 3166 secs passed Thread #1: 8400000 reads finished. 3239 secs passed Thread #3: 8450000 reads finished. 3240 secs passed Thread #5: 8500000 reads finished. 3249 secs passed Thread #4: 8550000 reads finished. 3251 secs passed Thread #6: 8600000 reads finished. 3255 secs passed Thread #0: 8650000 reads finished. 3265 secs passed Thread #7: 8700000 reads finished. 3274 secs passed Thread #2: 8750000 reads finished. 3322 secs passed Thread #1: 8800000 reads finished. 3387 secs passed Thread #3: 8850000 reads finished. 3387 secs passed Thread #5: 8900000 reads finished. 3396 secs passed Thread #4: 8950000 reads finished. 3398 secs passed Thread #6: 9000000 reads finished. 3402 secs passed Thread #0: 9050000 reads finished. 3413 secs passed Thread #0: 9402890 reads finished. 3421 secs passed Thread #7: 9100000 reads finished. 3422 secs passed Thread #2: 9150000 reads finished. 3463 secs passed Thread #1: 9200000 reads finished. 3492 secs passed Thread #3: 9250000 reads finished. 3493 secs passed Thread #5: 9300000 reads finished. 3494 secs passed Thread #4: 9350000 reads finished. 3495 secs passed Thread #6: 9400000 reads finished. 3495 secs passed Total number of aligned reads: 1497866 (16%) Done. Finished at Wed Mar 7 14:40:06 2018 Total time consumed: 3495 secs BSMAP v2.74 Start at: Wed Mar 7 14:40:07 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly10k.fa (format: FASTA) Load in 35320 db seqs, total size 691523275 bp. 7 secs passed total_kmers: 43046721 Create seed table. 30 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: /Volumes/Serine/wd/18-03-07/WG-BS/2_CGATGT_L001_R1_001.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/Serine/wd/18-03-07/bsmap/2_CGATGT_L001_R1_001-bsmap_out_jelly10k.sam (format: SAM) Thread #4: 50000 reads finished. 158 secs passed Thread #6: 300000 reads finished. 160 secs passed Thread #3: 100000 reads finished. 160 secs passed Thread #5: 250000 reads finished. 161 secs passed Thread #1: 150000 reads finished. 162 secs passed Thread #7: 350000 reads finished. 171 secs passed Thread #2: 200000 reads finished. 171 secs passed Thread #0: 400000 reads finished. 177 secs passed Thread #4: 450000 reads finished. 288 secs passed Thread #6: 500000 reads finished. 289 secs passed Thread #5: 600000 reads finished. 291 secs passed Thread #3: 550000 reads finished. 292 secs passed Thread #1: 650000 reads finished. 296 secs passed Thread #7: 700000 reads finished. 309 secs passed Thread #2: 750000 reads finished. 312 secs passed Thread #0: 800000 reads finished. 323 secs passed Thread #6: 900000 reads finished. 418 secs passed Thread #4: 850000 reads finished. 418 secs passed Thread #5: 950000 reads finished. 422 secs passed Thread #3: 1000000 reads finished. 423 secs passed Thread #1: 1050000 reads finished. 428 secs passed Thread #7: 1100000 reads finished. 448 secs passed Thread #2: 1150000 reads finished. 454 secs passed Thread #0: 1200000 reads finished. 469 secs passed Thread #4: 1300000 reads finished. 546 secs passed Thread #6: 1250000 reads finished. 546 secs passed Thread #5: 1350000 reads finished. 549 secs passed Thread #3: 1400000 reads finished. 552 secs passed Thread #1: 1450000 reads finished. 559 secs passed Thread #7: 1500000 reads finished. 585 secs passed Thread #2: 1550000 reads finished. 593 secs passed Thread #0: 1600000 reads finished. 613 secs passed Thread #6: 1700000 reads finished. 671 secs passed Thread #4: 1650000 reads finished. 672 secs passed Thread #5: 1750000 reads finished. 675 secs passed Thread #3: 1800000 reads finished. 679 secs passed Thread #1: 1850000 reads finished. 688 secs passed Thread #7: 1900000 reads finished. 722 secs passed Thread #2: 1950000 reads finished. 731 secs passed Thread #0: 2000000 reads finished. 757 secs passed Thread #6: 2050000 reads finished. 799 secs passed Thread #4: 2100000 reads finished. 800 secs passed Thread #5: 2150000 reads finished. 804 secs passed Thread #3: 2200000 reads finished. 809 secs passed Thread #1: 2250000 reads finished. 821 secs passed Thread #7: 2300000 reads finished. 861 secs passed Thread #2: 2350000 reads finished. 873 secs passed Thread #0: 2400000 reads finished. 902 secs passed Thread #6: 2450000 reads finished. 929 secs passed Thread #4: 2500000 reads finished. 930 secs passed Thread #5: 2550000 reads finished. 934 secs passed Thread #3: 2600000 reads finished. 940 secs passed Thread #1: 2650000 reads finished. 954 secs passed Thread #7: 2700000 reads finished. 1001 secs passed Thread #2: 2750000 reads finished. 1014 secs passed Thread #0: 2800000 reads finished. 1049 secs passed Thread #6: 2850000 reads finished. 1059 secs passed Thread #4: 2900000 reads finished. 1062 secs passed Thread #5: 2950000 reads finished. 1065 secs passed Thread #3: 3000000 reads finished. 1071 secs passed Thread #1: 3050000 reads finished. 1087 secs passed Thread #7: 3100000 reads finished. 1140 secs passed Thread #2: 3150000 reads finished. 1156 secs passed Thread #6: 3250000 reads finished. 1188 secs passed Thread #4: 3300000 reads finished. 1192 secs passed Thread #5: 3350000 reads finished. 1194 secs passed Thread #0: 3200000 reads finished. 1195 secs passed Thread #3: 3400000 reads finished. 1201 secs passed Thread #1: 3450000 reads finished. 1219 secs passed Thread #7: 3500000 reads finished. 1279 secs passed Thread #2: 3550000 reads finished. 1297 secs passed Thread #6: 3600000 reads finished. 1318 secs passed Thread #4: 3650000 reads finished. 1323 secs passed Thread #5: 3700000 reads finished. 1326 secs passed Thread #3: 3800000 reads finished. 1333 secs passed Thread #0: 3750000 reads finished. 1341 secs passed Thread #1: 3850000 reads finished. 1352 secs passed Thread #7: 3900000 reads finished. 1419 secs passed Thread #2: 3950000 reads finished. 1438 secs passed Thread #6: 4000000 reads finished. 1448 secs passed Thread #4: 4050000 reads finished. 1453 secs passed Thread #5: 4100000 reads finished. 1456 secs passed Thread #3: 4150000 reads finished. 1465 secs passed Thread #1: 4250000 reads finished. 1487 secs passed Thread #0: 4200000 reads finished. 1487 secs passed Thread #7: 4300000 reads finished. 1559 secs passed Thread #6: 4400000 reads finished. 1577 secs passed Thread #2: 4350000 reads finished. 1580 secs passed Thread #4: 4450000 reads finished. 1582 secs passed Thread #5: 4500000 reads finished. 1586 secs passed Thread #3: 4550000 reads finished. 1596 secs passed Thread #1: 4600000 reads finished. 1620 secs passed Thread #0: 4650000 reads finished. 1633 secs passed Thread #7: 4700000 reads finished. 1699 secs passed Thread #6: 4750000 reads finished. 1706 secs passed Thread #4: 4850000 reads finished. 1713 secs passed Thread #5: 4900000 reads finished. 1717 secs passed Thread #2: 4800000 reads finished. 1721 secs passed Thread #3: 4950000 reads finished. 1729 secs passed Thread #1: 5000000 reads finished. 1753 secs passed Thread #0: 5050000 reads finished. 1779 secs passed Thread #6: 5150000 reads finished. 1838 secs passed Thread #7: 5100000 reads finished. 1839 secs passed Thread #4: 5200000 reads finished. 1843 secs passed Thread #5: 5250000 reads finished. 1847 secs passed Thread #3: 5350000 reads finished. 1860 secs passed Thread #2: 5300000 reads finished. 1862 secs passed Thread #1: 5400000 reads finished. 1887 secs passed Thread #0: 5450000 reads finished. 1925 secs passed Thread #6: 5500000 reads finished. 1968 secs passed Thread #4: 5600000 reads finished. 1975 secs passed Thread #7: 5550000 reads finished. 1978 secs passed Thread #5: 5650000 reads finished. 1979 secs passed Thread #3: 5700000 reads finished. 1992 secs passed Thread #2: 5750000 reads finished. 2003 secs passed Thread #1: 5800000 reads finished. 2020 secs passed Thread #0: 5850000 reads finished. 2071 secs passed Thread #6: 5900000 reads finished. 2099 secs passed Thread #4: 5950000 reads finished. 2105 secs passed Thread #5: 6050000 reads finished. 2108 secs passed Thread #7: 6000000 reads finished. 2117 secs passed Thread #3: 6100000 reads finished. 2123 secs passed Thread #2: 6150000 reads finished. 2143 secs passed Thread #1: 6200000 reads finished. 2153 secs passed Thread #0: 6250000 reads finished. 2218 secs passed Thread #6: 6300000 reads finished. 2228 secs passed Thread #4: 6350000 reads finished. 2235 secs passed Thread #5: 6400000 reads finished. 2237 secs passed Thread #3: 6500000 reads finished. 2254 secs passed Thread #7: 6450000 reads finished. 2257 secs passed Thread #2: 6550000 reads finished. 2283 secs passed Thread #1: 6600000 reads finished. 2286 secs passed Thread #6: 6700000 reads finished. 2357 secs passed Thread #0: 6650000 reads finished. 2363 secs passed Thread #4: 6750000 reads finished. 2365 secs passed Thread #5: 6800000 reads finished. 2368 secs passed Thread #3: 6850000 reads finished. 2388 secs passed Thread #7: 6900000 reads finished. 2397 secs passed Thread #1: 7000000 reads finished. 2418 secs passed Thread #2: 6950000 reads finished. 2424 secs passed Thread #6: 7050000 reads finished. 2485 secs passed Thread #4: 7150000 reads finished. 2498 secs passed Thread #5: 7200000 reads finished. 2498 secs passed Thread #0: 7100000 reads finished. 2509 secs passed Thread #3: 7250000 reads finished. 2521 secs passed Thread #7: 7300000 reads finished. 2536 secs passed Thread #1: 7350000 reads finished. 2550 secs passed Thread #2: 7400000 reads finished. 2565 secs passed Thread #6: 7450000 reads finished. 2615 secs passed Thread #4: 7500000 reads finished. 2628 secs passed Thread #5: 7550000 reads finished. 2628 secs passed Thread #3: 7650000 reads finished. 2652 secs passed Thread #0: 7600000 reads finished. 2655 secs passed Thread #7: 7700000 reads finished. 2675 secs passed Thread #1: 7750000 reads finished. 2683 secs passed Thread #2: 7800000 reads finished. 2708 secs passed Thread #6: 7850000 reads finished. 2746 secs passed Thread #5: 7950000 reads finished. 2758 secs passed Thread #4: 7900000 reads finished. 2759 secs passed Thread #3: 8000000 reads finished. 2785 secs passed Thread #0: 8050000 reads finished. 2802 secs passed Thread #7: 8100000 reads finished. 2814 secs passed Thread #1: 8150000 reads finished. 2815 secs passed Thread #2: 8200000 reads finished. 2848 secs passed Thread #6: 8250000 reads finished. 2875 secs passed Thread #5: 8300000 reads finished. 2887 secs passed Thread #4: 8350000 reads finished. 2890 secs passed Thread #3: 8400000 reads finished. 2915 secs passed Thread #0: 8450000 reads finished. 2948 secs passed Thread #1: 8550000 reads finished. 2948 secs passed Thread #7: 8500000 reads finished. 2953 secs passed Thread #2: 8600000 reads finished. 2989 secs passed Thread #6: 8650000 reads finished. 3005 secs passed Thread #5: 8700000 reads finished. 3017 secs passed Thread #4: 8750000 reads finished. 3020 secs passed Thread #3: 8800000 reads finished. 3047 secs passed Thread #1: 8900000 reads finished. 3084 secs passed Thread #7: 8950000 reads finished. 3095 secs passed Thread #0: 8850000 reads finished. 3096 secs passed Thread #2: 9000000 reads finished. 3132 secs passed Thread #6: 9050000 reads finished. 3133 secs passed Thread #5: 9100000 reads finished. 3146 secs passed Thread #4: 9150000 reads finished. 3149 secs passed Thread #3: 9200000 reads finished. 3176 secs passed Thread #1: 9250000 reads finished. 3218 secs passed Thread #7: 9300000 reads finished. 3234 secs passed Thread #0: 9350000 reads finished. 3242 secs passed Thread #6: 9450000 reads finished. 3263 secs passed Thread #2: 9400000 reads finished. 3273 secs passed Thread #5: 9500000 reads finished. 3277 secs passed Thread #4: 9550000 reads finished. 3281 secs passed Thread #3: 9600000 reads finished. 3307 secs passed Thread #1: 9650000 reads finished. 3351 secs passed Thread #7: 9700000 reads finished. 3373 secs passed Thread #0: 9750000 reads finished. 3388 secs passed Thread #6: 9800000 reads finished. 3392 secs passed Thread #5: 9900000 reads finished. 3406 secs passed Thread #4: 9950000 reads finished. 3411 secs passed Thread #2: 9850000 reads finished. 3414 secs passed Thread #3: 10000000 reads finished. 3438 secs passed Thread #1: 10050000 reads finished. 3484 secs passed Thread #7: 10100000 reads finished. 3513 secs passed Thread #6: 10200000 reads finished. 3522 secs passed Thread #0: 10150000 reads finished. 3535 secs passed Thread #5: 10250000 reads finished. 3537 secs passed Thread #4: 10300000 reads finished. 3541 secs passed Thread #2: 10350000 reads finished. 3554 secs passed Thread #3: 10400000 reads finished. 3570 secs passed Thread #1: 10450000 reads finished. 3616 secs passed Thread #7: 10500000 reads finished. 3652 secs passed Thread #6: 10550000 reads finished. 3653 secs passed Thread #5: 10650000 reads finished. 3666 secs passed Thread #4: 10700000 reads finished. 3670 secs passed Thread #0: 10600000 reads finished. 3681 secs passed Thread #2: 10750000 reads finished. 3695 secs passed Thread #3: 10800000 reads finished. 3702 secs passed Thread #1: 10850000 reads finished. 3748 secs passed Thread #6: 10950000 reads finished. 3783 secs passed Thread #7: 10900000 reads finished. 3792 secs passed Thread #5: 11000000 reads finished. 3798 secs passed Thread #4: 11050000 reads finished. 3801 secs passed Thread #0: 11100000 reads finished. 3829 secs passed Thread #3: 11200000 reads finished. 3834 secs passed Thread #2: 11150000 reads finished. 3837 secs passed Thread #1: 11250000 reads finished. 3882 secs passed Thread #6: 11300000 reads finished. 3912 secs passed Thread #5: 11400000 reads finished. 3926 secs passed Thread #7: 11350000 reads finished. 3930 secs passed Thread #4: 11450000 reads finished. 3930 secs passed Thread #3: 11550000 reads finished. 3963 secs passed Thread #0: 11500000 reads finished. 3974 secs passed Thread #2: 11600000 reads finished. 3976 secs passed Thread #2: 11954873 reads finished. 3990 secs passed Thread #1: 11650000 reads finished. 4010 secs passed Thread #6: 11700000 reads finished. 4028 secs passed Thread #5: 11750000 reads finished. 4035 secs passed Thread #4: 11850000 reads finished. 4037 secs passed Thread #7: 11800000 reads finished. 4039 secs passed Thread #3: 11900000 reads finished. 4042 secs passed Thread #0: 11950000 reads finished. 4044 secs passed Total number of aligned reads: 1865600 (16%) Done. Finished at Wed Mar 7 15:47:31 2018 Total time consumed: 4044 secs BSMAP v2.74 Start at: Wed Mar 7 15:47:31 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly10k.fa (format: FASTA) Load in 35320 db seqs, total size 691523275 bp. 8 secs passed total_kmers: 43046721 Create seed table. 29 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: /Volumes/Serine/wd/18-03-07/WG-BS/3_TTAGGC_L001_R1_001.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/Serine/wd/18-03-07/bsmap/3_TTAGGC_L001_R1_001-bsmap_out_jelly10k.sam (format: SAM) Thread #6: 50000 reads finished. 157 secs passed Thread #3: 100000 reads finished. 159 secs passed Thread #1: 200000 reads finished. 160 secs passed Thread #7: 150000 reads finished. 160 secs passed Thread #5: 250000 reads finished. 160 secs passed Thread #0: 400000 reads finished. 161 secs passed Thread #4: 350000 reads finished. 161 secs passed Thread #2: 300000 reads finished. 174 secs passed Thread #6: 450000 reads finished. 288 secs passed Thread #5: 650000 reads finished. 289 secs passed Thread #1: 550000 reads finished. 289 secs passed Thread #3: 500000 reads finished. 289 secs passed Thread #7: 600000 reads finished. 290 secs passed Thread #0: 700000 reads finished. 290 secs passed Thread #4: 750000 reads finished. 293 secs passed Thread #2: 800000 reads finished. 318 secs passed Thread #6: 850000 reads finished. 417 secs passed Thread #5: 900000 reads finished. 417 secs passed Thread #1: 950000 reads finished. 418 secs passed Thread #3: 1000000 reads finished. 419 secs passed Thread #0: 1100000 reads finished. 420 secs passed Thread #7: 1050000 reads finished. 420 secs passed Thread #4: 1150000 reads finished. 424 secs passed Thread #2: 1200000 reads finished. 462 secs passed Thread #6: 1250000 reads finished. 545 secs passed Thread #5: 1300000 reads finished. 546 secs passed Thread #1: 1350000 reads finished. 547 secs passed Thread #3: 1400000 reads finished. 549 secs passed Thread #0: 1450000 reads finished. 550 secs passed Thread #7: 1500000 reads finished. 551 secs passed Thread #4: 1550000 reads finished. 554 secs passed Thread #2: 1600000 reads finished. 605 secs passed Thread #6: 1650000 reads finished. 673 secs passed Thread #5: 1700000 reads finished. 674 secs passed Thread #1: 1750000 reads finished. 676 secs passed Thread #3: 1800000 reads finished. 679 secs passed Thread #0: 1850000 reads finished. 679 secs passed Thread #7: 1900000 reads finished. 680 secs passed Thread #4: 1950000 reads finished. 684 secs passed Thread #2: 2000000 reads finished. 748 secs passed Thread #5: 2100000 reads finished. 803 secs passed Thread #6: 2050000 reads finished. 803 secs passed Thread #1: 2150000 reads finished. 805 secs passed Thread #7: 2300000 reads finished. 811 secs passed Thread #3: 2200000 reads finished. 811 secs passed Thread #0: 2250000 reads finished. 812 secs passed Thread #4: 2350000 reads finished. 816 secs passed Thread #2: 2400000 reads finished. 895 secs passed Thread #6: 2500000 reads finished. 937 secs passed Thread #5: 2450000 reads finished. 937 secs passed Thread #1: 2550000 reads finished. 938 secs passed Thread #3: 2650000 reads finished. 946 secs passed Thread #7: 2600000 reads finished. 946 secs passed Thread #0: 2700000 reads finished. 947 secs passed Thread #4: 2750000 reads finished. 952 secs passed Thread #2: 2800000 reads finished. 1044 secs passed Thread #6: 2850000 reads finished. 1070 secs passed Thread #5: 2900000 reads finished. 1070 secs passed Thread #1: 2950000 reads finished. 1071 secs passed Thread #7: 3050000 reads finished. 1079 secs passed Thread #3: 3000000 reads finished. 1079 secs passed Thread #0: 3100000 reads finished. 1080 secs passed Thread #4: 3150000 reads finished. 1085 secs passed Thread #2: 3200000 reads finished. 1189 secs passed Thread #6: 3250000 reads finished. 1198 secs passed Thread #5: 3300000 reads finished. 1199 secs passed Thread #1: 3350000 reads finished. 1199 secs passed Thread #7: 3400000 reads finished. 1209 secs passed Thread #3: 3450000 reads finished. 1209 secs passed Thread #0: 3500000 reads finished. 1210 secs passed Thread #4: 3550000 reads finished. 1216 secs passed Thread #6: 3650000 reads finished. 1328 secs passed Thread #5: 3700000 reads finished. 1328 secs passed Thread #1: 3750000 reads finished. 1329 secs passed Thread #2: 3600000 reads finished. 1333 secs passed Thread #7: 3800000 reads finished. 1338 secs passed Thread #3: 3850000 reads finished. 1339 secs passed Thread #0: 3900000 reads finished. 1340 secs passed Thread #4: 3950000 reads finished. 1347 secs passed Thread #6: 4000000 reads finished. 1453 secs passed Thread #1: 4100000 reads finished. 1455 secs passed Thread #5: 4050000 reads finished. 1455 secs passed Thread #7: 4200000 reads finished. 1466 secs passed Thread #3: 4250000 reads finished. 1471 secs passed Thread #0: 4300000 reads finished. 1473 secs passed Thread #2: 4150000 reads finished. 1475 secs passed Thread #4: 4350000 reads finished. 1480 secs passed Thread #6: 4400000 reads finished. 1581 secs passed Thread #5: 4500000 reads finished. 1583 secs passed Thread #1: 4450000 reads finished. 1583 secs passed Thread #7: 4550000 reads finished. 1596 secs passed Thread #3: 4600000 reads finished. 1601 secs passed Thread #0: 4650000 reads finished. 1603 secs passed Thread #4: 4750000 reads finished. 1610 secs passed Thread #2: 4700000 reads finished. 1619 secs passed Thread #6: 4800000 reads finished. 1710 secs passed Thread #5: 4850000 reads finished. 1711 secs passed Thread #1: 4900000 reads finished. 1711 secs passed Thread #7: 4950000 reads finished. 1726 secs passed Thread #3: 5000000 reads finished. 1731 secs passed Thread #0: 5050000 reads finished. 1732 secs passed Thread #4: 5100000 reads finished. 1740 secs passed Thread #2: 5150000 reads finished. 1763 secs passed Thread #6: 5200000 reads finished. 1838 secs passed Thread #1: 5300000 reads finished. 1839 secs passed Thread #5: 5250000 reads finished. 1839 secs passed Thread #7: 5350000 reads finished. 1855 secs passed Thread #3: 5400000 reads finished. 1860 secs passed Thread #0: 5450000 reads finished. 1861 secs passed Thread #4: 5500000 reads finished. 1870 secs passed Thread #2: 5550000 reads finished. 1907 secs passed Thread #6: 5600000 reads finished. 1967 secs passed Thread #1: 5650000 reads finished. 1968 secs passed Thread #5: 5700000 reads finished. 1969 secs passed Thread #7: 5750000 reads finished. 1985 secs passed Thread #3: 5800000 reads finished. 1991 secs passed Thread #0: 5850000 reads finished. 1992 secs passed Thread #4: 5900000 reads finished. 2002 secs passed Thread #2: 5950000 reads finished. 2053 secs passed Thread #6: 6000000 reads finished. 2096 secs passed Thread #1: 6050000 reads finished. 2096 secs passed Thread #5: 6100000 reads finished. 2098 secs passed Thread #7: 6150000 reads finished. 2115 secs passed Thread #3: 6200000 reads finished. 2121 secs passed Thread #0: 6250000 reads finished. 2122 secs passed Thread #4: 6300000 reads finished. 2132 secs passed Thread #2: 6350000 reads finished. 2197 secs passed Thread #6: 6400000 reads finished. 2224 secs passed Thread #1: 6450000 reads finished. 2226 secs passed Thread #5: 6500000 reads finished. 2228 secs passed Thread #7: 6550000 reads finished. 2245 secs passed Thread #3: 6600000 reads finished. 2251 secs passed Thread #0: 6650000 reads finished. 2251 secs passed Thread #4: 6700000 reads finished. 2262 secs passed Thread #2: 6750000 reads finished. 2340 secs passed Thread #6: 6800000 reads finished. 2352 secs passed Thread #1: 6850000 reads finished. 2355 secs passed Thread #5: 6900000 reads finished. 2356 secs passed Thread #7: 6950000 reads finished. 2374 secs passed Thread #0: 7050000 reads finished. 2379 secs passed Thread #3: 7000000 reads finished. 2380 secs passed Thread #4: 7100000 reads finished. 2391 secs passed Thread #6: 7200000 reads finished. 2481 secs passed Thread #1: 7250000 reads finished. 2484 secs passed Thread #2: 7150000 reads finished. 2485 secs passed Thread #5: 7300000 reads finished. 2485 secs passed Thread #7: 7350000 reads finished. 2502 secs passed Thread #0: 7400000 reads finished. 2508 secs passed Thread #3: 7450000 reads finished. 2511 secs passed Thread #4: 7500000 reads finished. 2521 secs passed Thread #6: 7550000 reads finished. 2608 secs passed Thread #1: 7600000 reads finished. 2610 secs passed Thread #5: 7700000 reads finished. 2613 secs passed Thread #2: 7650000 reads finished. 2627 secs passed Thread #7: 7750000 reads finished. 2631 secs passed Thread #0: 7800000 reads finished. 2638 secs passed Thread #3: 7850000 reads finished. 2642 secs passed Thread #4: 7900000 reads finished. 2653 secs passed Thread #6: 7950000 reads finished. 2737 secs passed Thread #1: 8000000 reads finished. 2739 secs passed Thread #5: 8050000 reads finished. 2740 secs passed Thread #7: 8150000 reads finished. 2759 secs passed Thread #0: 8200000 reads finished. 2767 secs passed Thread #2: 8100000 reads finished. 2769 secs passed Thread #3: 8250000 reads finished. 2771 secs passed Thread #4: 8300000 reads finished. 2783 secs passed Thread #6: 8350000 reads finished. 2864 secs passed Thread #1: 8400000 reads finished. 2867 secs passed Thread #5: 8450000 reads finished. 2868 secs passed Thread #7: 8500000 reads finished. 2888 secs passed Thread #0: 8550000 reads finished. 2895 secs passed Thread #3: 8650000 reads finished. 2900 secs passed Thread #2: 8600000 reads finished. 2912 secs passed Thread #4: 8700000 reads finished. 2914 secs passed Thread #6: 8750000 reads finished. 2992 secs passed Thread #1: 8800000 reads finished. 2995 secs passed Thread #5: 8850000 reads finished. 2999 secs passed Thread #7: 8900000 reads finished. 3020 secs passed Thread #0: 8950000 reads finished. 3027 secs passed Thread #3: 9000000 reads finished. 3029 secs passed Thread #4: 9100000 reads finished. 3042 secs passed Thread #2: 9050000 reads finished. 3054 secs passed Thread #6: 9150000 reads finished. 3119 secs passed Thread #1: 9200000 reads finished. 3123 secs passed Thread #5: 9250000 reads finished. 3127 secs passed Thread #7: 9300000 reads finished. 3149 secs passed Thread #0: 9350000 reads finished. 3156 secs passed Thread #3: 9400000 reads finished. 3158 secs passed Thread #4: 9450000 reads finished. 3173 secs passed Thread #2: 9500000 reads finished. 3200 secs passed Thread #6: 9550000 reads finished. 3248 secs passed Thread #1: 9600000 reads finished. 3251 secs passed Thread #5: 9650000 reads finished. 3254 secs passed Thread #7: 9700000 reads finished. 3277 secs passed Thread #0: 9750000 reads finished. 3284 secs passed Thread #3: 9800000 reads finished. 3287 secs passed Thread #4: 9850000 reads finished. 3303 secs passed Thread #2: 9900000 reads finished. 3343 secs passed Thread #6: 9950000 reads finished. 3376 secs passed Thread #1: 10000000 reads finished. 3378 secs passed Thread #5: 10050000 reads finished. 3382 secs passed Thread #7: 10100000 reads finished. 3406 secs passed Thread #0: 10150000 reads finished. 3413 secs passed Thread #3: 10200000 reads finished. 3416 secs passed Thread #4: 10250000 reads finished. 3433 secs passed Thread #2: 10300000 reads finished. 3485 secs passed Thread #6: 10350000 reads finished. 3504 secs passed Thread #1: 10400000 reads finished. 3506 secs passed Thread #5: 10450000 reads finished. 3509 secs passed Thread #7: 10500000 reads finished. 3535 secs passed Thread #0: 10550000 reads finished. 3541 secs passed Thread #3: 10600000 reads finished. 3546 secs passed Thread #4: 10650000 reads finished. 3563 secs passed Thread #2: 10700000 reads finished. 3629 secs passed Thread #6: 10750000 reads finished. 3632 secs passed Thread #1: 10800000 reads finished. 3633 secs passed Thread #5: 10850000 reads finished. 3637 secs passed Thread #7: 10900000 reads finished. 3664 secs passed Thread #0: 10950000 reads finished. 3670 secs passed Thread #3: 11000000 reads finished. 3675 secs passed Thread #4: 11050000 reads finished. 3694 secs passed Thread #6: 11150000 reads finished. 3759 secs passed Thread #1: 11200000 reads finished. 3761 secs passed Thread #5: 11250000 reads finished. 3765 secs passed Thread #2: 11100000 reads finished. 3772 secs passed Thread #7: 11300000 reads finished. 3793 secs passed Thread #0: 11350000 reads finished. 3799 secs passed Thread #3: 11400000 reads finished. 3804 secs passed Thread #4: 11450000 reads finished. 3823 secs passed Thread #4: 11817358 reads finished. 3869 secs passed Thread #6: 11500000 reads finished. 3884 secs passed Thread #1: 11550000 reads finished. 3884 secs passed Thread #5: 11600000 reads finished. 3887 secs passed Thread #2: 11650000 reads finished. 3895 secs passed Thread #7: 11700000 reads finished. 3896 secs passed Thread #0: 11750000 reads finished. 3897 secs passed Thread #3: 11800000 reads finished. 3898 secs passed Total number of aligned reads: 1854633 (16%) Done. Finished at Wed Mar 7 16:52:29 2018 Total time consumed: 3898 secs BSMAP v2.74 Start at: Wed Mar 7 16:52:29 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly10k.fa (format: FASTA) Load in 35320 db seqs, total size 691523275 bp. 8 secs passed total_kmers: 43046721 Create seed table. 27 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: /Volumes/Serine/wd/18-03-07/WG-BS/4_TGACCA_L001_R1_001.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/Serine/wd/18-03-07/bsmap/4_TGACCA_L001_R1_001-bsmap_out_jelly10k.sam (format: SAM) Thread #4: 150000 reads finished. 167 secs passed Thread #6: 250000 reads finished. 168 secs passed Thread #2: 200000 reads finished. 169 secs passed Thread #1: 350000 reads finished. 170 secs passed Thread #5: 400000 reads finished. 172 secs passed Thread #7: 300000 reads finished. 173 secs passed Thread #3: 100000 reads finished. 174 secs passed Thread #0: 50000 reads finished. 175 secs passed Thread #6: 500000 reads finished. 307 secs passed Thread #4: 450000 reads finished. 309 secs passed Thread #2: 550000 reads finished. 310 secs passed Thread #1: 600000 reads finished. 312 secs passed Thread #5: 650000 reads finished. 314 secs passed Thread #7: 700000 reads finished. 318 secs passed Thread #3: 750000 reads finished. 324 secs passed Thread #0: 800000 reads finished. 326 secs passed Thread #6: 850000 reads finished. 448 secs passed Thread #4: 900000 reads finished. 450 secs passed Thread #2: 950000 reads finished. 452 secs passed Thread #1: 1000000 reads finished. 454 secs passed Thread #5: 1050000 reads finished. 456 secs passed Thread #7: 1100000 reads finished. 463 secs passed Thread #3: 1150000 reads finished. 472 secs passed Thread #0: 1200000 reads finished. 476 secs passed Thread #6: 1250000 reads finished. 590 secs passed Thread #4: 1300000 reads finished. 590 secs passed Thread #2: 1350000 reads finished. 593 secs passed Thread #1: 1400000 reads finished. 595 secs passed Thread #5: 1450000 reads finished. 599 secs passed Thread #7: 1500000 reads finished. 608 secs passed Thread #3: 1550000 reads finished. 621 secs passed Thread #0: 1600000 reads finished. 627 secs passed Thread #6: 1650000 reads finished. 731 secs passed Thread #4: 1700000 reads finished. 731 secs passed Thread #2: 1750000 reads finished. 735 secs passed Thread #1: 1800000 reads finished. 737 secs passed Thread #5: 1850000 reads finished. 742 secs passed Thread #7: 1900000 reads finished. 754 secs passed Thread #3: 1950000 reads finished. 769 secs passed Thread #0: 2000000 reads finished. 777 secs passed Thread #6: 2050000 reads finished. 873 secs passed Thread #4: 2100000 reads finished. 873 secs passed Thread #2: 2150000 reads finished. 877 secs passed Thread #1: 2200000 reads finished. 880 secs passed Thread #5: 2250000 reads finished. 884 secs passed Thread #7: 2300000 reads finished. 899 secs passed Thread #3: 2350000 reads finished. 917 secs passed Thread #0: 2400000 reads finished. 926 secs passed Thread #6: 2450000 reads finished. 1013 secs passed Thread #4: 2500000 reads finished. 1014 secs passed Thread #2: 2550000 reads finished. 1019 secs passed Thread #1: 2600000 reads finished. 1022 secs passed Thread #5: 2650000 reads finished. 1025 secs passed Thread #7: 2700000 reads finished. 1044 secs passed Thread #3: 2750000 reads finished. 1066 secs passed Thread #0: 2800000 reads finished. 1077 secs passed Thread #6: 2850000 reads finished. 1153 secs passed Thread #4: 2900000 reads finished. 1154 secs passed Thread #2: 2950000 reads finished. 1161 secs passed Thread #1: 3000000 reads finished. 1164 secs passed Thread #5: 3050000 reads finished. 1167 secs passed Thread #7: 3100000 reads finished. 1189 secs passed Thread #3: 3150000 reads finished. 1215 secs passed Thread #0: 3200000 reads finished. 1228 secs passed Thread #6: 3250000 reads finished. 1293 secs passed Thread #4: 3300000 reads finished. 1295 secs passed Thread #2: 3350000 reads finished. 1302 secs passed Thread #1: 3400000 reads finished. 1306 secs passed Thread #5: 3450000 reads finished. 1310 secs passed Thread #7: 3500000 reads finished. 1334 secs passed Thread #3: 3550000 reads finished. 1363 secs passed Thread #0: 3600000 reads finished. 1379 secs passed Thread #6: 3650000 reads finished. 1433 secs passed Thread #4: 3700000 reads finished. 1436 secs passed Thread #2: 3750000 reads finished. 1444 secs passed Thread #1: 3800000 reads finished. 1447 secs passed Thread #5: 3850000 reads finished. 1452 secs passed Thread #7: 3900000 reads finished. 1480 secs passed Thread #3: 3950000 reads finished. 1512 secs passed Thread #0: 4000000 reads finished. 1529 secs passed Thread #6: 4050000 reads finished. 1572 secs passed Thread #4: 4100000 reads finished. 1576 secs passed Thread #2: 4150000 reads finished. 1587 secs passed Thread #1: 4200000 reads finished. 1592 secs passed Thread #5: 4250000 reads finished. 1593 secs passed Thread #7: 4300000 reads finished. 1625 secs passed Thread #3: 4350000 reads finished. 1660 secs passed Thread #0: 4400000 reads finished. 1679 secs passed Thread #6: 4450000 reads finished. 1712 secs passed Thread #4: 4500000 reads finished. 1718 secs passed Thread #2: 4550000 reads finished. 1728 secs passed Thread #1: 4600000 reads finished. 1734 secs passed Thread #5: 4650000 reads finished. 1736 secs passed Thread #7: 4700000 reads finished. 1771 secs passed Thread #3: 4750000 reads finished. 1809 secs passed Thread #0: 4800000 reads finished. 1829 secs passed Thread #6: 4850000 reads finished. 1852 secs passed Thread #4: 4900000 reads finished. 1858 secs passed Thread #2: 4950000 reads finished. 1871 secs passed Thread #1: 5000000 reads finished. 1876 secs passed Thread #5: 5050000 reads finished. 1879 secs passed Thread #7: 5100000 reads finished. 1916 secs passed Thread #3: 5150000 reads finished. 1957 secs passed Thread #0: 5200000 reads finished. 1980 secs passed Thread #6: 5250000 reads finished. 1992 secs passed Thread #4: 5300000 reads finished. 2000 secs passed Thread #2: 5350000 reads finished. 2013 secs passed Thread #1: 5400000 reads finished. 2019 secs passed Thread #5: 5450000 reads finished. 2021 secs passed Thread #7: 5500000 reads finished. 2062 secs passed Thread #3: 5550000 reads finished. 2106 secs passed Thread #0: 5600000 reads finished. 2130 secs passed Thread #6: 5650000 reads finished. 2132 secs passed Thread #4: 5700000 reads finished. 2140 secs passed Thread #2: 5750000 reads finished. 2155 secs passed Thread #1: 5800000 reads finished. 2161 secs passed Thread #5: 5850000 reads finished. 2163 secs passed Thread #7: 5900000 reads finished. 2207 secs passed Thread #3: 5950000 reads finished. 2255 secs passed Thread #6: 6050000 reads finished. 2272 secs passed Thread #0: 6000000 reads finished. 2280 secs passed Thread #4: 6100000 reads finished. 2280 secs passed Thread #2: 6150000 reads finished. 2297 secs passed Thread #1: 6200000 reads finished. 2302 secs passed Thread #5: 6250000 reads finished. 2305 secs passed Thread #7: 6300000 reads finished. 2354 secs passed Thread #3: 6350000 reads finished. 2404 secs passed Thread #6: 6400000 reads finished. 2413 secs passed Thread #4: 6500000 reads finished. 2421 secs passed Thread #0: 6450000 reads finished. 2431 secs passed Thread #2: 6550000 reads finished. 2438 secs passed Thread #1: 6600000 reads finished. 2444 secs passed Thread #5: 6650000 reads finished. 2448 secs passed Thread #7: 6700000 reads finished. 2500 secs passed Thread #6: 6800000 reads finished. 2553 secs passed Thread #3: 6750000 reads finished. 2553 secs passed Thread #4: 6850000 reads finished. 2560 secs passed Thread #0: 6900000 reads finished. 2581 secs passed Thread #2: 6950000 reads finished. 2581 secs passed Thread #1: 7000000 reads finished. 2587 secs passed Thread #5: 7050000 reads finished. 2591 secs passed Thread #7: 7100000 reads finished. 2647 secs passed Thread #6: 7150000 reads finished. 2692 secs passed Thread #3: 7200000 reads finished. 2701 secs passed Thread #4: 7250000 reads finished. 2702 secs passed Thread #2: 7350000 reads finished. 2723 secs passed Thread #1: 7400000 reads finished. 2729 secs passed Thread #0: 7300000 reads finished. 2732 secs passed Thread #5: 7450000 reads finished. 2732 secs passed Thread #7: 7500000 reads finished. 2792 secs passed Thread #6: 7550000 reads finished. 2832 secs passed Thread #4: 7650000 reads finished. 2843 secs passed Thread #3: 7600000 reads finished. 2849 secs passed Thread #2: 7700000 reads finished. 2867 secs passed Thread #1: 7750000 reads finished. 2871 secs passed Thread #5: 7850000 reads finished. 2875 secs passed Thread #0: 7800000 reads finished. 2883 secs passed Thread #7: 7900000 reads finished. 2937 secs passed Thread #6: 7950000 reads finished. 2973 secs passed Thread #4: 8000000 reads finished. 2984 secs passed Thread #3: 8050000 reads finished. 2998 secs passed Thread #2: 8100000 reads finished. 3009 secs passed Thread #1: 8150000 reads finished. 3013 secs passed Thread #5: 8200000 reads finished. 3017 secs passed Thread #0: 8250000 reads finished. 3035 secs passed Thread #7: 8300000 reads finished. 3082 secs passed Thread #6: 8350000 reads finished. 3113 secs passed Thread #4: 8400000 reads finished. 3124 secs passed Thread #3: 8450000 reads finished. 3146 secs passed Thread #2: 8500000 reads finished. 3150 secs passed Thread #1: 8550000 reads finished. 3154 secs passed Thread #5: 8600000 reads finished. 3160 secs passed Thread #0: 8650000 reads finished. 3187 secs passed Thread #7: 8700000 reads finished. 3229 secs passed Thread #6: 8750000 reads finished. 3255 secs passed Thread #4: 8800000 reads finished. 3265 secs passed Thread #2: 8900000 reads finished. 3292 secs passed Thread #3: 8850000 reads finished. 3295 secs passed Thread #1: 8950000 reads finished. 3296 secs passed Thread #5: 9000000 reads finished. 3302 secs passed Thread #0: 9050000 reads finished. 3338 secs passed Thread #7: 9100000 reads finished. 3374 secs passed Thread #6: 9150000 reads finished. 3396 secs passed Thread #4: 9200000 reads finished. 3406 secs passed Thread #2: 9250000 reads finished. 3434 secs passed Thread #1: 9350000 reads finished. 3439 secs passed Thread #3: 9300000 reads finished. 3444 secs passed Thread #5: 9400000 reads finished. 3446 secs passed Thread #0: 9450000 reads finished. 3488 secs passed Thread #7: 9500000 reads finished. 3520 secs passed Thread #6: 9550000 reads finished. 3535 secs passed Thread #4: 9600000 reads finished. 3547 secs passed Thread #2: 9650000 reads finished. 3576 secs passed Thread #1: 9700000 reads finished. 3581 secs passed Thread #5: 9800000 reads finished. 3588 secs passed Thread #3: 9750000 reads finished. 3593 secs passed Thread #0: 9850000 reads finished. 3640 secs passed Thread #7: 9900000 reads finished. 3665 secs passed Thread #6: 9950000 reads finished. 3676 secs passed Thread #4: 10000000 reads finished. 3689 secs passed Thread #2: 10050000 reads finished. 3718 secs passed Thread #1: 10100000 reads finished. 3723 secs passed Thread #5: 10150000 reads finished. 3731 secs passed Thread #3: 10200000 reads finished. 3742 secs passed Thread #0: 10250000 reads finished. 3790 secs passed Thread #7: 10300000 reads finished. 3812 secs passed Thread #6: 10350000 reads finished. 3816 secs passed Thread #4: 10400000 reads finished. 3830 secs passed Thread #2: 10450000 reads finished. 3859 secs passed Thread #1: 10500000 reads finished. 3866 secs passed Thread #5: 10550000 reads finished. 3874 secs passed Thread #3: 10600000 reads finished. 3891 secs passed Thread #0: 10650000 reads finished. 3940 secs passed Thread #6: 10750000 reads finished. 3956 secs passed Thread #7: 10700000 reads finished. 3957 secs passed Thread #4: 10800000 reads finished. 3971 secs passed Thread #2: 10850000 reads finished. 4000 secs passed Thread #1: 10900000 reads finished. 4008 secs passed Thread #5: 10950000 reads finished. 4016 secs passed Thread #3: 11000000 reads finished. 4039 secs passed Thread #0: 11050000 reads finished. 4090 secs passed Thread #6: 11100000 reads finished. 4095 secs passed Thread #7: 11150000 reads finished. 4102 secs passed Thread #4: 11200000 reads finished. 4112 secs passed Thread #2: 11250000 reads finished. 4142 secs passed Thread #1: 11300000 reads finished. 4150 secs passed Thread #5: 11350000 reads finished. 4158 secs passed Thread #2: 11606618 reads finished. 4159 secs passed Thread #3: 11400000 reads finished. 4175 secs passed Thread #6: 11500000 reads finished. 4195 secs passed Thread #0: 11450000 reads finished. 4196 secs passed Thread #7: 11550000 reads finished. 4196 secs passed Thread #4: 11600000 reads finished. 4197 secs passed Total number of aligned reads: 1866901 (16%) Done. Finished at Wed Mar 7 18:02:26 2018 Total time consumed: 4197 secs BSMAP v2.74 Start at: Wed Mar 7 18:02:27 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly10k.fa (format: FASTA) Load in 35320 db seqs, total size 691523275 bp. 7 secs passed total_kmers: 43046721 Create seed table. 27 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: /Volumes/Serine/wd/18-03-07/WG-BS/5_ACAGTG_L001_R1_001.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/Serine/wd/18-03-07/bsmap/5_ACAGTG_L001_R1_001-bsmap_out_jelly10k.sam (format: SAM) Thread #2: 50000 reads finished. 154 secs passed Thread #4: 150000 reads finished. 155 secs passed Thread #0: 100000 reads finished. 155 secs passed Thread #6: 350000 reads finished. 155 secs passed Thread #7: 300000 reads finished. 156 secs passed Thread #1: 400000 reads finished. 157 secs passed Thread #3: 200000 reads finished. 162 secs passed Thread #5: 250000 reads finished. 164 secs passed Thread #6: 600000 reads finished. 283 secs passed Thread #2: 450000 reads finished. 283 secs passed Thread #4: 500000 reads finished. 283 secs passed Thread #0: 550000 reads finished. 283 secs passed Thread #1: 700000 reads finished. 285 secs passed Thread #7: 650000 reads finished. 285 secs passed Thread #3: 750000 reads finished. 296 secs passed Thread #5: 800000 reads finished. 300 secs passed Thread #6: 850000 reads finished. 412 secs passed Thread #4: 950000 reads finished. 412 secs passed Thread #0: 1000000 reads finished. 413 secs passed Thread #7: 1100000 reads finished. 413 secs passed Thread #1: 1050000 reads finished. 413 secs passed Thread #2: 900000 reads finished. 413 secs passed Thread #3: 1150000 reads finished. 431 secs passed Thread #5: 1200000 reads finished. 436 secs passed Thread #6: 1250000 reads finished. 540 secs passed Thread #4: 1300000 reads finished. 540 secs passed Thread #0: 1350000 reads finished. 541 secs passed Thread #7: 1400000 reads finished. 541 secs passed Thread #1: 1450000 reads finished. 542 secs passed Thread #2: 1500000 reads finished. 544 secs passed Thread #3: 1550000 reads finished. 565 secs passed Thread #5: 1600000 reads finished. 572 secs passed Thread #6: 1650000 reads finished. 668 secs passed Thread #4: 1700000 reads finished. 669 secs passed Thread #0: 1750000 reads finished. 670 secs passed Thread #7: 1800000 reads finished. 670 secs passed Thread #1: 1850000 reads finished. 670 secs passed Thread #2: 1900000 reads finished. 673 secs passed Thread #3: 1950000 reads finished. 699 secs passed Thread #5: 2000000 reads finished. 708 secs passed Thread #6: 2050000 reads finished. 796 secs passed Thread #4: 2100000 reads finished. 797 secs passed Thread #0: 2150000 reads finished. 798 secs passed Thread #7: 2200000 reads finished. 799 secs passed Thread #1: 2250000 reads finished. 799 secs passed Thread #2: 2300000 reads finished. 803 secs passed Thread #3: 2350000 reads finished. 834 secs passed Thread #5: 2400000 reads finished. 845 secs passed Thread #6: 2450000 reads finished. 924 secs passed Thread #4: 2500000 reads finished. 926 secs passed Thread #0: 2550000 reads finished. 927 secs passed Thread #1: 2650000 reads finished. 927 secs passed Thread #7: 2600000 reads finished. 928 secs passed Thread #2: 2700000 reads finished. 932 secs passed Thread #3: 2750000 reads finished. 968 secs passed Thread #5: 2800000 reads finished. 981 secs passed Thread #6: 2850000 reads finished. 1052 secs passed Thread #4: 2900000 reads finished. 1055 secs passed Thread #0: 2950000 reads finished. 1056 secs passed Thread #1: 3000000 reads finished. 1056 secs passed Thread #7: 3050000 reads finished. 1056 secs passed Thread #2: 3100000 reads finished. 1061 secs passed Thread #3: 3150000 reads finished. 1103 secs passed Thread #5: 3200000 reads finished. 1118 secs passed Thread #6: 3250000 reads finished. 1180 secs passed Thread #4: 3300000 reads finished. 1183 secs passed Thread #1: 3400000 reads finished. 1184 secs passed Thread #7: 3450000 reads finished. 1185 secs passed Thread #0: 3350000 reads finished. 1185 secs passed Thread #2: 3500000 reads finished. 1192 secs passed Thread #3: 3550000 reads finished. 1238 secs passed Thread #5: 3600000 reads finished. 1253 secs passed Thread #6: 3650000 reads finished. 1307 secs passed Thread #4: 3700000 reads finished. 1311 secs passed Thread #1: 3750000 reads finished. 1313 secs passed Thread #7: 3800000 reads finished. 1313 secs passed Thread #0: 3850000 reads finished. 1315 secs passed Thread #2: 3900000 reads finished. 1321 secs passed Thread #3: 3950000 reads finished. 1372 secs passed Thread #5: 4000000 reads finished. 1389 secs passed Thread #6: 4050000 reads finished. 1436 secs passed Thread #4: 4100000 reads finished. 1439 secs passed Thread #7: 4200000 reads finished. 1442 secs passed Thread #1: 4150000 reads finished. 1442 secs passed Thread #0: 4250000 reads finished. 1443 secs passed Thread #2: 4300000 reads finished. 1451 secs passed Thread #3: 4350000 reads finished. 1505 secs passed Thread #5: 4400000 reads finished. 1525 secs passed Thread #6: 4450000 reads finished. 1564 secs passed Thread #4: 4500000 reads finished. 1569 secs passed Thread #1: 4600000 reads finished. 1570 secs passed Thread #0: 4650000 reads finished. 1571 secs passed Thread #7: 4550000 reads finished. 1574 secs passed Thread #2: 4700000 reads finished. 1579 secs passed Thread #3: 4750000 reads finished. 1639 secs passed Thread #5: 4800000 reads finished. 1661 secs passed Thread #6: 4850000 reads finished. 1692 secs passed Thread #4: 4900000 reads finished. 1697 secs passed Thread #1: 4950000 reads finished. 1699 secs passed Thread #0: 5000000 reads finished. 1700 secs passed Thread #7: 5050000 reads finished. 1703 secs passed Thread #2: 5100000 reads finished. 1709 secs passed Thread #3: 5150000 reads finished. 1774 secs passed Thread #5: 5200000 reads finished. 1797 secs passed Thread #6: 5250000 reads finished. 1820 secs passed Thread #4: 5300000 reads finished. 1826 secs passed Thread #1: 5350000 reads finished. 1827 secs passed Thread #0: 5400000 reads finished. 1829 secs passed Thread #7: 5450000 reads finished. 1832 secs passed Thread #2: 5500000 reads finished. 1839 secs passed Thread #3: 5550000 reads finished. 1908 secs passed Thread #5: 5600000 reads finished. 1933 secs passed Thread #6: 5650000 reads finished. 1948 secs passed Thread #4: 5700000 reads finished. 1954 secs passed Thread #1: 5750000 reads finished. 1956 secs passed Thread #0: 5800000 reads finished. 1958 secs passed Thread #7: 5850000 reads finished. 1960 secs passed Thread #2: 5900000 reads finished. 1969 secs passed Thread #3: 5950000 reads finished. 2043 secs passed Thread #5: 6000000 reads finished. 2069 secs passed Thread #6: 6050000 reads finished. 2076 secs passed Thread #4: 6100000 reads finished. 2082 secs passed Thread #1: 6150000 reads finished. 2084 secs passed Thread #0: 6200000 reads finished. 2087 secs passed Thread #7: 6250000 reads finished. 2088 secs passed Thread #2: 6300000 reads finished. 2100 secs passed Thread #3: 6350000 reads finished. 2179 secs passed Thread #6: 6450000 reads finished. 2204 secs passed Thread #5: 6400000 reads finished. 2206 secs passed Thread #4: 6500000 reads finished. 2210 secs passed Thread #1: 6550000 reads finished. 2212 secs passed Thread #0: 6600000 reads finished. 2217 secs passed Thread #7: 6650000 reads finished. 2217 secs passed Thread #2: 6700000 reads finished. 2229 secs passed Thread #3: 6750000 reads finished. 2313 secs passed Thread #6: 6800000 reads finished. 2331 secs passed Thread #4: 6900000 reads finished. 2339 secs passed Thread #1: 6950000 reads finished. 2341 secs passed Thread #5: 6850000 reads finished. 2343 secs passed Thread #0: 7000000 reads finished. 2346 secs passed Thread #7: 7050000 reads finished. 2346 secs passed Thread #2: 7100000 reads finished. 2359 secs passed Thread #3: 7150000 reads finished. 2448 secs passed Thread #6: 7200000 reads finished. 2459 secs passed Thread #4: 7250000 reads finished. 2468 secs passed Thread #1: 7300000 reads finished. 2470 secs passed Thread #0: 7400000 reads finished. 2474 secs passed Thread #7: 7450000 reads finished. 2475 secs passed Thread #5: 7350000 reads finished. 2479 secs passed Thread #2: 7500000 reads finished. 2489 secs passed Thread #3: 7550000 reads finished. 2583 secs passed Thread #6: 7600000 reads finished. 2588 secs passed Thread #4: 7650000 reads finished. 2597 secs passed Thread #1: 7700000 reads finished. 2601 secs passed Thread #0: 7750000 reads finished. 2602 secs passed Thread #7: 7800000 reads finished. 2603 secs passed Thread #5: 7850000 reads finished. 2615 secs passed Thread #2: 7900000 reads finished. 2619 secs passed Thread #6: 8000000 reads finished. 2716 secs passed Thread #3: 7950000 reads finished. 2719 secs passed Thread #4: 8050000 reads finished. 2724 secs passed Thread #1: 8100000 reads finished. 2730 secs passed Thread #0: 8150000 reads finished. 2731 secs passed Thread #7: 8200000 reads finished. 2731 secs passed Thread #2: 8300000 reads finished. 2751 secs passed Thread #5: 8250000 reads finished. 2752 secs passed Thread #6: 8350000 reads finished. 2846 secs passed Thread #4: 8450000 reads finished. 2854 secs passed Thread #3: 8400000 reads finished. 2854 secs passed Thread #7: 8600000 reads finished. 2858 secs passed Thread #1: 8500000 reads finished. 2858 secs passed Thread #0: 8550000 reads finished. 2859 secs passed Thread #2: 8650000 reads finished. 2879 secs passed Thread #5: 8700000 reads finished. 2888 secs passed Thread #6: 8750000 reads finished. 2974 secs passed Thread #4: 8800000 reads finished. 2982 secs passed Thread #1: 8950000 reads finished. 2987 secs passed Thread #7: 8900000 reads finished. 2987 secs passed Thread #0: 9000000 reads finished. 2988 secs passed Thread #3: 8850000 reads finished. 2988 secs passed Thread #2: 9050000 reads finished. 3008 secs passed Thread #5: 9100000 reads finished. 3024 secs passed Thread #6: 9150000 reads finished. 3100 secs passed Thread #4: 9200000 reads finished. 3109 secs passed Thread #1: 9250000 reads finished. 3115 secs passed Thread #7: 9300000 reads finished. 3115 secs passed Thread #0: 9350000 reads finished. 3118 secs passed Thread #3: 9400000 reads finished. 3125 secs passed Thread #2: 9450000 reads finished. 3140 secs passed Thread #5: 9500000 reads finished. 3163 secs passed Thread #6: 9550000 reads finished. 3227 secs passed Thread #4: 9600000 reads finished. 3237 secs passed Thread #1: 9650000 reads finished. 3243 secs passed Thread #7: 9700000 reads finished. 3244 secs passed Thread #0: 9750000 reads finished. 3247 secs passed Thread #3: 9800000 reads finished. 3260 secs passed Thread #2: 9850000 reads finished. 3269 secs passed Thread #5: 9900000 reads finished. 3300 secs passed Thread #6: 9950000 reads finished. 3356 secs passed Thread #4: 10000000 reads finished. 3366 secs passed Thread #1: 10050000 reads finished. 3372 secs passed Thread #7: 10100000 reads finished. 3374 secs passed Thread #0: 10150000 reads finished. 3377 secs passed Thread #3: 10200000 reads finished. 3394 secs passed Thread #2: 10250000 reads finished. 3398 secs passed Thread #5: 10300000 reads finished. 3436 secs passed Thread #6: 10350000 reads finished. 3483 secs passed Thread #4: 10400000 reads finished. 3495 secs passed Thread #1: 10450000 reads finished. 3501 secs passed Thread #7: 10500000 reads finished. 3502 secs passed Thread #0: 10550000 reads finished. 3506 secs passed Thread #2: 10650000 reads finished. 3527 secs passed Thread #3: 10600000 reads finished. 3529 secs passed Thread #5: 10700000 reads finished. 3573 secs passed Thread #6: 10750000 reads finished. 3611 secs passed Thread #4: 10800000 reads finished. 3623 secs passed Thread #7: 10900000 reads finished. 3629 secs passed Thread #1: 10850000 reads finished. 3630 secs passed Thread #0: 10950000 reads finished. 3635 secs passed Thread #2: 11000000 reads finished. 3656 secs passed Thread #3: 11050000 reads finished. 3664 secs passed Thread #5: 11100000 reads finished. 3709 secs passed Thread #6: 11150000 reads finished. 3739 secs passed Thread #4: 11200000 reads finished. 3751 secs passed Thread #7: 11250000 reads finished. 3758 secs passed Thread #1: 11300000 reads finished. 3758 secs passed Thread #0: 11350000 reads finished. 3763 secs passed Thread #2: 11400000 reads finished. 3786 secs passed Thread #3: 11450000 reads finished. 3799 secs passed Thread #5: 11500000 reads finished. 3845 secs passed Thread #6: 11550000 reads finished. 3868 secs passed Thread #4: 11600000 reads finished. 3879 secs passed Thread #7: 11650000 reads finished. 3886 secs passed Thread #1: 11700000 reads finished. 3888 secs passed Thread #0: 11750000 reads finished. 3892 secs passed Thread #2: 11800000 reads finished. 3915 secs passed Thread #3: 11850000 reads finished. 3934 secs passed Thread #5: 11900000 reads finished. 3981 secs passed Thread #6: 11950000 reads finished. 3996 secs passed Thread #4: 12000000 reads finished. 4007 secs passed Thread #7: 12050000 reads finished. 4013 secs passed Thread #1: 12100000 reads finished. 4015 secs passed Thread #0: 12150000 reads finished. 4022 secs passed Thread #2: 12200000 reads finished. 4045 secs passed Thread #3: 12250000 reads finished. 4068 secs passed Thread #5: 12300000 reads finished. 4111 secs passed Thread #6: 12350000 reads finished. 4114 secs passed Thread #4: 12400000 reads finished. 4121 secs passed Thread #7: 12450000 reads finished. 4123 secs passed Thread #1: 12500000 reads finished. 4123 secs passed Thread #2: 12589609 reads finished. 4124 secs passed Thread #0: 12550000 reads finished. 4124 secs passed Total number of aligned reads: 1941301 (15%) Done. Finished at Wed Mar 7 19:11:11 2018 Total time consumed: 4124 secs BSMAP v2.74 Start at: Wed Mar 7 19:11:12 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly10k.fa (format: FASTA) Load in 35320 db seqs, total size 691523275 bp. 7 secs passed total_kmers: 43046721 Create seed table. 27 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: /Volumes/Serine/wd/18-03-07/WG-BS/6_GCCAAT_L001_R1_001.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/Serine/wd/18-03-07/bsmap/6_GCCAAT_L001_R1_001-bsmap_out_jelly10k.sam (format: SAM) Thread #5: 50000 reads finished. 147 secs passed Thread #7: 100000 reads finished. 149 secs passed Thread #1: 200000 reads finished. 151 secs passed Thread #0: 350000 reads finished. 152 secs passed Thread #6: 400000 reads finished. 153 secs passed Thread #2: 250000 reads finished. 166 secs passed Thread #4: 150000 reads finished. 169 secs passed Thread #3: 300000 reads finished. 172 secs passed Thread #5: 450000 reads finished. 271 secs passed Thread #7: 500000 reads finished. 272 secs passed Thread #1: 550000 reads finished. 274 secs passed Thread #0: 600000 reads finished. 276 secs passed Thread #6: 650000 reads finished. 276 secs passed Thread #2: 700000 reads finished. 305 secs passed Thread #4: 750000 reads finished. 312 secs passed Thread #3: 800000 reads finished. 316 secs passed Thread #5: 850000 reads finished. 394 secs passed Thread #7: 900000 reads finished. 396 secs passed Thread #1: 950000 reads finished. 398 secs passed Thread #6: 1050000 reads finished. 401 secs passed Thread #0: 1000000 reads finished. 401 secs passed Thread #2: 1100000 reads finished. 444 secs passed Thread #4: 1150000 reads finished. 454 secs passed Thread #3: 1200000 reads finished. 461 secs passed Thread #5: 1250000 reads finished. 518 secs passed Thread #7: 1300000 reads finished. 520 secs passed Thread #1: 1350000 reads finished. 522 secs passed Thread #6: 1400000 reads finished. 525 secs passed Thread #0: 1450000 reads finished. 526 secs passed Thread #2: 1500000 reads finished. 583 secs passed Thread #4: 1550000 reads finished. 597 secs passed Thread #3: 1600000 reads finished. 607 secs passed Thread #5: 1650000 reads finished. 641 secs passed Thread #7: 1700000 reads finished. 644 secs passed Thread #1: 1750000 reads finished. 646 secs passed Thread #6: 1800000 reads finished. 649 secs passed Thread #0: 1850000 reads finished. 650 secs passed Thread #2: 1900000 reads finished. 721 secs passed Thread #4: 1950000 reads finished. 740 secs passed Thread #3: 2000000 reads finished. 751 secs passed Thread #5: 2050000 reads finished. 765 secs passed Thread #7: 2100000 reads finished. 768 secs passed Thread #1: 2150000 reads finished. 770 secs passed Thread #6: 2200000 reads finished. 773 secs passed Thread #0: 2250000 reads finished. 775 secs passed Thread #2: 2300000 reads finished. 861 secs passed Thread #4: 2350000 reads finished. 883 secs passed Thread #5: 2450000 reads finished. 888 secs passed Thread #7: 2500000 reads finished. 890 secs passed Thread #1: 2550000 reads finished. 894 secs passed Thread #3: 2400000 reads finished. 896 secs passed Thread #6: 2600000 reads finished. 898 secs passed Thread #0: 2650000 reads finished. 900 secs passed Thread #2: 2700000 reads finished. 999 secs passed Thread #5: 2800000 reads finished. 1012 secs passed Thread #7: 2850000 reads finished. 1014 secs passed Thread #1: 2900000 reads finished. 1018 secs passed Thread #6: 3000000 reads finished. 1022 secs passed Thread #0: 3050000 reads finished. 1026 secs passed Thread #4: 2750000 reads finished. 1026 secs passed Thread #3: 2950000 reads finished. 1041 secs passed Thread #5: 3150000 reads finished. 1136 secs passed Thread #7: 3200000 reads finished. 1137 secs passed Thread #2: 3100000 reads finished. 1139 secs passed Thread #1: 3250000 reads finished. 1142 secs passed Thread #6: 3300000 reads finished. 1146 secs passed Thread #0: 3350000 reads finished. 1150 secs passed Thread #4: 3400000 reads finished. 1168 secs passed Thread #3: 3450000 reads finished. 1187 secs passed Thread #5: 3500000 reads finished. 1259 secs passed Thread #7: 3550000 reads finished. 1260 secs passed Thread #1: 3650000 reads finished. 1266 secs passed Thread #6: 3700000 reads finished. 1271 secs passed Thread #0: 3750000 reads finished. 1275 secs passed Thread #2: 3600000 reads finished. 1278 secs passed Thread #4: 3800000 reads finished. 1311 secs passed Thread #3: 3850000 reads finished. 1332 secs passed Thread #5: 3900000 reads finished. 1382 secs passed Thread #7: 3950000 reads finished. 1383 secs passed Thread #1: 4000000 reads finished. 1390 secs passed Thread #6: 4050000 reads finished. 1396 secs passed Thread #0: 4100000 reads finished. 1400 secs passed Thread #2: 4150000 reads finished. 1417 secs passed Thread #4: 4200000 reads finished. 1453 secs passed Thread #3: 4250000 reads finished. 1476 secs passed Thread #5: 4300000 reads finished. 1505 secs passed Thread #7: 4350000 reads finished. 1506 secs passed Thread #1: 4400000 reads finished. 1513 secs passed Thread #6: 4450000 reads finished. 1521 secs passed Thread #0: 4500000 reads finished. 1526 secs passed Thread #2: 4550000 reads finished. 1556 secs passed Thread #4: 4600000 reads finished. 1596 secs passed Thread #3: 4650000 reads finished. 1621 secs passed Thread #7: 4750000 reads finished. 1630 secs passed Thread #5: 4700000 reads finished. 1631 secs passed Thread #1: 4800000 reads finished. 1638 secs passed Thread #6: 4850000 reads finished. 1646 secs passed Thread #0: 4900000 reads finished. 1652 secs passed Thread #2: 4950000 reads finished. 1696 secs passed Thread #4: 5000000 reads finished. 1740 secs passed Thread #7: 5100000 reads finished. 1755 secs passed Thread #5: 5150000 reads finished. 1756 secs passed Thread #1: 5200000 reads finished. 1765 secs passed Thread #3: 5050000 reads finished. 1766 secs passed Thread #6: 5250000 reads finished. 1773 secs passed Thread #0: 5300000 reads finished. 1778 secs passed Thread #2: 5350000 reads finished. 1837 secs passed Thread #7: 5450000 reads finished. 1879 secs passed Thread #5: 5500000 reads finished. 1881 secs passed Thread #4: 5400000 reads finished. 1883 secs passed Thread #1: 5550000 reads finished. 1889 secs passed Thread #6: 5650000 reads finished. 1898 secs passed Thread #0: 5700000 reads finished. 1903 secs passed Thread #3: 5600000 reads finished. 1911 secs passed Thread #2: 5750000 reads finished. 1976 secs passed Thread #7: 5800000 reads finished. 2003 secs passed Thread #5: 5850000 reads finished. 2005 secs passed Thread #1: 5950000 reads finished. 2013 secs passed Thread #6: 6000000 reads finished. 2022 secs passed Thread #4: 5900000 reads finished. 2026 secs passed Thread #0: 6050000 reads finished. 2027 secs passed Thread #3: 6100000 reads finished. 2056 secs passed Thread #2: 6150000 reads finished. 2116 secs passed Thread #7: 6200000 reads finished. 2126 secs passed Thread #5: 6250000 reads finished. 2129 secs passed Thread #1: 6300000 reads finished. 2137 secs passed Thread #6: 6350000 reads finished. 2146 secs passed Thread #0: 6450000 reads finished. 2152 secs passed Thread #4: 6400000 reads finished. 2169 secs passed Thread #3: 6500000 reads finished. 2200 secs passed Thread #7: 6600000 reads finished. 2249 secs passed Thread #5: 6650000 reads finished. 2253 secs passed Thread #2: 6550000 reads finished. 2255 secs passed Thread #1: 6700000 reads finished. 2260 secs passed Thread #6: 6750000 reads finished. 2271 secs passed Thread #0: 6800000 reads finished. 2278 secs passed Thread #4: 6850000 reads finished. 2311 secs passed Thread #3: 6900000 reads finished. 2345 secs passed Thread #7: 6950000 reads finished. 2372 secs passed Thread #5: 7000000 reads finished. 2376 secs passed Thread #1: 7100000 reads finished. 2384 secs passed Thread #2: 7050000 reads finished. 2393 secs passed Thread #6: 7150000 reads finished. 2396 secs passed Thread #0: 7200000 reads finished. 2403 secs passed Thread #4: 7250000 reads finished. 2454 secs passed Thread #3: 7300000 reads finished. 2489 secs passed Thread #7: 7350000 reads finished. 2495 secs passed Thread #5: 7400000 reads finished. 2499 secs passed Thread #1: 7450000 reads finished. 2507 secs passed Thread #6: 7550000 reads finished. 2521 secs passed Thread #0: 7600000 reads finished. 2531 secs passed Thread #2: 7500000 reads finished. 2533 secs passed Thread #4: 7650000 reads finished. 2596 secs passed Thread #7: 7750000 reads finished. 2619 secs passed Thread #5: 7800000 reads finished. 2624 secs passed Thread #1: 7850000 reads finished. 2632 secs passed Thread #3: 7700000 reads finished. 2633 secs passed Thread #6: 7900000 reads finished. 2646 secs passed Thread #0: 7950000 reads finished. 2654 secs passed Thread #2: 8000000 reads finished. 2672 secs passed Thread #4: 8050000 reads finished. 2738 secs passed Thread #7: 8100000 reads finished. 2741 secs passed Thread #5: 8150000 reads finished. 2749 secs passed Thread #1: 8200000 reads finished. 2756 secs passed Thread #6: 8300000 reads finished. 2770 secs passed Thread #0: 8350000 reads finished. 2780 secs passed Thread #3: 8250000 reads finished. 2780 secs passed Thread #2: 8400000 reads finished. 2812 secs passed Thread #7: 8500000 reads finished. 2863 secs passed Thread #5: 8550000 reads finished. 2872 secs passed Thread #1: 8600000 reads finished. 2879 secs passed Thread #4: 8450000 reads finished. 2880 secs passed Thread #6: 8650000 reads finished. 2893 secs passed Thread #0: 8700000 reads finished. 2903 secs passed Thread #3: 8750000 reads finished. 2926 secs passed Thread #2: 8800000 reads finished. 2950 secs passed Thread #7: 8850000 reads finished. 2987 secs passed Thread #5: 8900000 reads finished. 2995 secs passed Thread #1: 8950000 reads finished. 3003 secs passed Thread #6: 9050000 reads finished. 3018 secs passed Thread #4: 9000000 reads finished. 3022 secs passed Thread #0: 9100000 reads finished. 3028 secs passed Thread #3: 9150000 reads finished. 3070 secs passed Thread #2: 9200000 reads finished. 3087 secs passed Thread #7: 9250000 reads finished. 3111 secs passed Thread #5: 9300000 reads finished. 3121 secs passed Thread #1: 9350000 reads finished. 3129 secs passed Thread #6: 9400000 reads finished. 3145 secs passed Thread #0: 9500000 reads finished. 3152 secs passed Thread #4: 9450000 reads finished. 3164 secs passed Thread #3: 9550000 reads finished. 3214 secs passed Thread #2: 9600000 reads finished. 3226 secs passed Thread #7: 9650000 reads finished. 3234 secs passed Thread #5: 9700000 reads finished. 3245 secs passed Thread #1: 9750000 reads finished. 3253 secs passed Thread #6: 9800000 reads finished. 3269 secs passed Thread #0: 9850000 reads finished. 3278 secs passed Thread #4: 9900000 reads finished. 3307 secs passed Thread #3: 9950000 reads finished. 3359 secs passed Thread #7: 10050000 reads finished. 3359 secs passed Thread #2: 10000000 reads finished. 3366 secs passed Thread #5: 10100000 reads finished. 3368 secs passed Thread #1: 10150000 reads finished. 3376 secs passed Thread #6: 10200000 reads finished. 3393 secs passed Thread #0: 10250000 reads finished. 3402 secs passed Thread #4: 10300000 reads finished. 3449 secs passed Thread #7: 10400000 reads finished. 3482 secs passed Thread #5: 10500000 reads finished. 3492 secs passed Thread #1: 10550000 reads finished. 3500 secs passed Thread #3: 10350000 reads finished. 3503 secs passed Thread #2: 10450000 reads finished. 3505 secs passed Thread #6: 10600000 reads finished. 3518 secs passed Thread #0: 10650000 reads finished. 3527 secs passed Thread #4: 10700000 reads finished. 3592 secs passed Thread #7: 10750000 reads finished. 3605 secs passed Thread #5: 10800000 reads finished. 3614 secs passed Thread #1: 10850000 reads finished. 3623 secs passed Thread #6: 11000000 reads finished. 3643 secs passed Thread #2: 10950000 reads finished. 3644 secs passed Thread #3: 10900000 reads finished. 3648 secs passed Thread #0: 11050000 reads finished. 3652 secs passed Thread #7: 11150000 reads finished. 3729 secs passed Thread #4: 11100000 reads finished. 3736 secs passed Thread #5: 11200000 reads finished. 3737 secs passed Thread #1: 11250000 reads finished. 3747 secs passed Thread #6: 11300000 reads finished. 3768 secs passed Thread #0: 11450000 reads finished. 3777 secs passed Thread #2: 11350000 reads finished. 3783 secs passed Thread #3: 11400000 reads finished. 3793 secs passed Thread #7: 11500000 reads finished. 3852 secs passed Thread #5: 11600000 reads finished. 3861 secs passed Thread #1: 11650000 reads finished. 3872 secs passed Thread #4: 11550000 reads finished. 3880 secs passed Thread #6: 11700000 reads finished. 3892 secs passed Thread #0: 11750000 reads finished. 3901 secs passed Thread #2: 11800000 reads finished. 3922 secs passed Thread #3: 11850000 reads finished. 3938 secs passed Thread #7: 11900000 reads finished. 3976 secs passed Thread #5: 11950000 reads finished. 3984 secs passed Thread #1: 12000000 reads finished. 3997 secs passed Thread #6: 12100000 reads finished. 4016 secs passed Thread #4: 12050000 reads finished. 4022 secs passed Thread #0: 12150000 reads finished. 4026 secs passed Thread #2: 12200000 reads finished. 4056 secs passed Thread #3: 12250000 reads finished. 4071 secs passed Thread #7: 12300000 reads finished. 4080 secs passed Thread #5: 12350000 reads finished. 4082 secs passed Thread #1: 12400000 reads finished. 4085 secs passed Thread #4: 12489766 reads finished. 4087 secs passed Thread #6: 12450000 reads finished. 4087 secs passed Total number of aligned reads: 1917041 (15%) Done. Finished at Wed Mar 7 20:19:19 2018 Total time consumed: 4087 secs BSMAP v2.74 Start at: Wed Mar 7 20:19:20 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly10k.fa (format: FASTA) Load in 35320 db seqs, total size 691523275 bp. 7 secs passed total_kmers: 43046721 Create seed table. 29 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: /Volumes/Serine/wd/18-03-07/WG-BS/7_CAGATC_L001_R1_001.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/Serine/wd/18-03-07/bsmap/7_CAGATC_L001_R1_001-bsmap_out_jelly10k.sam (format: SAM) Thread #5: 150000 reads finished. 157 secs passed Thread #0: 200000 reads finished. 157 secs passed Thread #4: 300000 reads finished. 157 secs passed Thread #1: 250000 reads finished. 157 secs passed Thread #3: 400000 reads finished. 158 secs passed Thread #6: 50000 reads finished. 161 secs passed Thread #2: 100000 reads finished. 162 secs passed Thread #7: 350000 reads finished. 165 secs passed Thread #0: 500000 reads finished. 284 secs passed Thread #4: 550000 reads finished. 284 secs passed Thread #3: 650000 reads finished. 285 secs passed Thread #1: 600000 reads finished. 286 secs passed Thread #5: 450000 reads finished. 286 secs passed Thread #2: 750000 reads finished. 296 secs passed Thread #6: 700000 reads finished. 297 secs passed Thread #7: 800000 reads finished. 299 secs passed Thread #0: 850000 reads finished. 410 secs passed Thread #4: 900000 reads finished. 412 secs passed Thread #3: 950000 reads finished. 412 secs passed Thread #1: 1000000 reads finished. 414 secs passed Thread #5: 1050000 reads finished. 414 secs passed Thread #2: 1100000 reads finished. 431 secs passed Thread #6: 1150000 reads finished. 432 secs passed Thread #7: 1200000 reads finished. 435 secs passed Thread #0: 1250000 reads finished. 537 secs passed Thread #4: 1300000 reads finished. 538 secs passed Thread #3: 1350000 reads finished. 540 secs passed Thread #5: 1450000 reads finished. 542 secs passed Thread #1: 1400000 reads finished. 543 secs passed Thread #2: 1500000 reads finished. 565 secs passed Thread #6: 1550000 reads finished. 568 secs passed Thread #7: 1600000 reads finished. 569 secs passed Thread #0: 1650000 reads finished. 663 secs passed Thread #4: 1700000 reads finished. 666 secs passed Thread #3: 1750000 reads finished. 668 secs passed Thread #5: 1800000 reads finished. 671 secs passed Thread #1: 1850000 reads finished. 671 secs passed Thread #2: 1900000 reads finished. 699 secs passed Thread #6: 1950000 reads finished. 704 secs passed Thread #7: 2000000 reads finished. 705 secs passed Thread #0: 2050000 reads finished. 791 secs passed Thread #4: 2100000 reads finished. 793 secs passed Thread #3: 2150000 reads finished. 796 secs passed Thread #1: 2250000 reads finished. 799 secs passed Thread #5: 2200000 reads finished. 799 secs passed Thread #2: 2300000 reads finished. 833 secs passed Thread #7: 2400000 reads finished. 839 secs passed Thread #6: 2350000 reads finished. 840 secs passed Thread #0: 2450000 reads finished. 918 secs passed Thread #4: 2500000 reads finished. 921 secs passed Thread #3: 2550000 reads finished. 923 secs passed Thread #1: 2600000 reads finished. 927 secs passed Thread #5: 2650000 reads finished. 929 secs passed Thread #2: 2700000 reads finished. 968 secs passed Thread #7: 2750000 reads finished. 975 secs passed Thread #6: 2800000 reads finished. 975 secs passed Thread #0: 2850000 reads finished. 1046 secs passed Thread #4: 2900000 reads finished. 1048 secs passed Thread #3: 2950000 reads finished. 1051 secs passed Thread #1: 3000000 reads finished. 1055 secs passed Thread #5: 3050000 reads finished. 1057 secs passed Thread #2: 3100000 reads finished. 1102 secs passed Thread #7: 3150000 reads finished. 1109 secs passed Thread #6: 3200000 reads finished. 1112 secs passed Thread #0: 3250000 reads finished. 1173 secs passed Thread #4: 3300000 reads finished. 1176 secs passed Thread #3: 3350000 reads finished. 1179 secs passed Thread #1: 3400000 reads finished. 1183 secs passed Thread #5: 3450000 reads finished. 1186 secs passed Thread #2: 3500000 reads finished. 1236 secs passed Thread #7: 3550000 reads finished. 1244 secs passed Thread #6: 3600000 reads finished. 1247 secs passed Thread #0: 3650000 reads finished. 1301 secs passed Thread #4: 3700000 reads finished. 1304 secs passed Thread #3: 3750000 reads finished. 1305 secs passed Thread #1: 3800000 reads finished. 1310 secs passed Thread #5: 3850000 reads finished. 1314 secs passed Thread #2: 3900000 reads finished. 1370 secs passed Thread #7: 3950000 reads finished. 1379 secs passed Thread #6: 4000000 reads finished. 1383 secs passed Thread #0: 4050000 reads finished. 1428 secs passed Thread #4: 4100000 reads finished. 1432 secs passed Thread #3: 4150000 reads finished. 1433 secs passed Thread #1: 4200000 reads finished. 1438 secs passed Thread #5: 4250000 reads finished. 1443 secs passed Thread #2: 4300000 reads finished. 1504 secs passed Thread #7: 4350000 reads finished. 1513 secs passed Thread #6: 4400000 reads finished. 1519 secs passed Thread #0: 4450000 reads finished. 1555 secs passed Thread #4: 4500000 reads finished. 1560 secs passed Thread #3: 4550000 reads finished. 1560 secs passed Thread #1: 4600000 reads finished. 1567 secs passed Thread #5: 4650000 reads finished. 1572 secs passed Thread #2: 4700000 reads finished. 1638 secs passed Thread #7: 4750000 reads finished. 1648 secs passed Thread #6: 4800000 reads finished. 1655 secs passed Thread #0: 4850000 reads finished. 1682 secs passed Thread #3: 4950000 reads finished. 1687 secs passed Thread #4: 4900000 reads finished. 1688 secs passed Thread #1: 5000000 reads finished. 1695 secs passed Thread #5: 5050000 reads finished. 1700 secs passed Thread #2: 5100000 reads finished. 1772 secs passed Thread #7: 5150000 reads finished. 1783 secs passed Thread #6: 5200000 reads finished. 1790 secs passed Thread #0: 5250000 reads finished. 1810 secs passed Thread #4: 5350000 reads finished. 1815 secs passed Thread #3: 5300000 reads finished. 1815 secs passed Thread #1: 5400000 reads finished. 1823 secs passed Thread #5: 5450000 reads finished. 1829 secs passed Thread #2: 5500000 reads finished. 1906 secs passed Thread #7: 5550000 reads finished. 1918 secs passed Thread #6: 5600000 reads finished. 1925 secs passed Thread #0: 5650000 reads finished. 1938 secs passed Thread #4: 5700000 reads finished. 1942 secs passed Thread #3: 5750000 reads finished. 1943 secs passed Thread #1: 5800000 reads finished. 1952 secs passed Thread #5: 5850000 reads finished. 1958 secs passed Thread #2: 5900000 reads finished. 2040 secs passed Thread #7: 5950000 reads finished. 2053 secs passed Thread #6: 6000000 reads finished. 2060 secs passed Thread #0: 6050000 reads finished. 2064 secs passed Thread #4: 6100000 reads finished. 2069 secs passed Thread #3: 6150000 reads finished. 2072 secs passed Thread #1: 6200000 reads finished. 2081 secs passed Thread #5: 6250000 reads finished. 2089 secs passed Thread #2: 6300000 reads finished. 2174 secs passed Thread #7: 6350000 reads finished. 2187 secs passed Thread #0: 6450000 reads finished. 2191 secs passed Thread #6: 6400000 reads finished. 2196 secs passed Thread #4: 6500000 reads finished. 2198 secs passed Thread #3: 6550000 reads finished. 2199 secs passed Thread #1: 6600000 reads finished. 2209 secs passed Thread #5: 6650000 reads finished. 2218 secs passed Thread #2: 6700000 reads finished. 2308 secs passed Thread #0: 6800000 reads finished. 2321 secs passed Thread #7: 6750000 reads finished. 2323 secs passed Thread #4: 6900000 reads finished. 2326 secs passed Thread #3: 6950000 reads finished. 2326 secs passed Thread #6: 6850000 reads finished. 2332 secs passed Thread #1: 7000000 reads finished. 2336 secs passed Thread #5: 7050000 reads finished. 2346 secs passed Thread #2: 7100000 reads finished. 2442 secs passed Thread #0: 7150000 reads finished. 2448 secs passed Thread #3: 7300000 reads finished. 2454 secs passed Thread #4: 7250000 reads finished. 2454 secs passed Thread #7: 7200000 reads finished. 2458 secs passed Thread #1: 7400000 reads finished. 2464 secs passed Thread #6: 7350000 reads finished. 2467 secs passed Thread #5: 7450000 reads finished. 2474 secs passed Thread #0: 7550000 reads finished. 2573 secs passed Thread #2: 7500000 reads finished. 2574 secs passed Thread #3: 7600000 reads finished. 2581 secs passed Thread #4: 7650000 reads finished. 2584 secs passed Thread #1: 7750000 reads finished. 2594 secs passed Thread #7: 7700000 reads finished. 2595 secs passed Thread #6: 7800000 reads finished. 2602 secs passed Thread #5: 7850000 reads finished. 2602 secs passed Thread #0: 7900000 reads finished. 2700 secs passed Thread #3: 8000000 reads finished. 2709 secs passed Thread #2: 7950000 reads finished. 2709 secs passed Thread #4: 8050000 reads finished. 2712 secs passed Thread #1: 8100000 reads finished. 2722 secs passed Thread #7: 8150000 reads finished. 2730 secs passed Thread #5: 8250000 reads finished. 2731 secs passed Thread #6: 8200000 reads finished. 2737 secs passed Thread #0: 8300000 reads finished. 2829 secs passed Thread #3: 8350000 reads finished. 2837 secs passed Thread #4: 8450000 reads finished. 2839 secs passed Thread #2: 8400000 reads finished. 2843 secs passed Thread #1: 8500000 reads finished. 2850 secs passed Thread #5: 8600000 reads finished. 2859 secs passed Thread #7: 8550000 reads finished. 2864 secs passed Thread #6: 8650000 reads finished. 2873 secs passed Thread #0: 8700000 reads finished. 2955 secs passed Thread #3: 8750000 reads finished. 2965 secs passed Thread #4: 8800000 reads finished. 2967 secs passed Thread #2: 8850000 reads finished. 2978 secs passed Thread #1: 8900000 reads finished. 2979 secs passed Thread #5: 8950000 reads finished. 2988 secs passed Thread #7: 9000000 reads finished. 3000 secs passed Thread #6: 9050000 reads finished. 3009 secs passed Thread #0: 9100000 reads finished. 3082 secs passed Thread #3: 9150000 reads finished. 3093 secs passed Thread #4: 9200000 reads finished. 3096 secs passed Thread #1: 9300000 reads finished. 3107 secs passed Thread #2: 9250000 reads finished. 3112 secs passed Thread #5: 9350000 reads finished. 3118 secs passed Thread #7: 9400000 reads finished. 3135 secs passed Thread #6: 9450000 reads finished. 3144 secs passed Thread #0: 9500000 reads finished. 3210 secs passed Thread #3: 9550000 reads finished. 3220 secs passed Thread #4: 9600000 reads finished. 3222 secs passed Thread #1: 9650000 reads finished. 3235 secs passed Thread #2: 9700000 reads finished. 3246 secs passed Thread #5: 9750000 reads finished. 3247 secs passed Thread #7: 9800000 reads finished. 3270 secs passed Thread #6: 9850000 reads finished. 3280 secs passed Thread #0: 9900000 reads finished. 3337 secs passed Thread #3: 9950000 reads finished. 3347 secs passed Thread #4: 10000000 reads finished. 3349 secs passed Thread #1: 10050000 reads finished. 3359 secs passed Thread #5: 10150000 reads finished. 3366 secs passed Thread #2: 10100000 reads finished. 3367 secs passed Thread #7: 10200000 reads finished. 3371 secs passed Thread #6: 10250000 reads finished. 3372 secs passed Thread #0: 10295293 reads finished. 3376 secs passed Total number of aligned reads: 1631447 (16%) Done. Finished at Wed Mar 7 21:15:36 2018 Total time consumed: 3376 secs BSMAP v2.74 Start at: Wed Mar 7 21:15:36 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly10k.fa (format: FASTA) Load in 35320 db seqs, total size 691523275 bp. 8 secs passed total_kmers: 43046721 Create seed table. 29 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: /Volumes/Serine/wd/18-03-07/WG-BS/8_ACTTGA_L001_R1_001.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/Serine/wd/18-03-07/bsmap/8_ACTTGA_L001_R1_001-bsmap_out_jelly10k.sam (format: SAM) Thread #2: 50000 reads finished. 165 secs passed Thread #3: 100000 reads finished. 166 secs passed Thread #1: 250000 reads finished. 167 secs passed Thread #5: 150000 reads finished. 167 secs passed Thread #7: 350000 reads finished. 168 secs passed Thread #4: 300000 reads finished. 169 secs passed Thread #0: 400000 reads finished. 169 secs passed Thread #6: 200000 reads finished. 209 secs passed Thread #2: 450000 reads finished. 303 secs passed Thread #1: 550000 reads finished. 304 secs passed Thread #3: 500000 reads finished. 306 secs passed Thread #5: 600000 reads finished. 306 secs passed Thread #7: 650000 reads finished. 306 secs passed Thread #4: 700000 reads finished. 307 secs passed Thread #0: 750000 reads finished. 308 secs passed Thread #6: 800000 reads finished. 393 secs passed Thread #1: 900000 reads finished. 439 secs passed Thread #2: 850000 reads finished. 440 secs passed Thread #3: 950000 reads finished. 443 secs passed Thread #5: 1000000 reads finished. 443 secs passed Thread #7: 1050000 reads finished. 443 secs passed Thread #4: 1100000 reads finished. 443 secs passed Thread #0: 1150000 reads finished. 445 secs passed Thread #1: 1250000 reads finished. 573 secs passed Thread #2: 1300000 reads finished. 574 secs passed Thread #3: 1350000 reads finished. 577 secs passed Thread #4: 1500000 reads finished. 578 secs passed Thread #5: 1400000 reads finished. 578 secs passed Thread #7: 1450000 reads finished. 578 secs passed Thread #6: 1200000 reads finished. 578 secs passed Thread #0: 1550000 reads finished. 579 secs passed Thread #1: 1600000 reads finished. 704 secs passed Thread #2: 1650000 reads finished. 707 secs passed Thread #4: 1750000 reads finished. 709 secs passed Thread #3: 1700000 reads finished. 709 secs passed Thread #7: 1850000 reads finished. 710 secs passed Thread #5: 1800000 reads finished. 711 secs passed Thread #0: 1950000 reads finished. 713 secs passed Thread #6: 1900000 reads finished. 764 secs passed Thread #1: 2000000 reads finished. 841 secs passed Thread #2: 2050000 reads finished. 844 secs passed Thread #7: 2200000 reads finished. 848 secs passed Thread #4: 2100000 reads finished. 848 secs passed Thread #3: 2150000 reads finished. 848 secs passed Thread #5: 2250000 reads finished. 849 secs passed Thread #0: 2300000 reads finished. 851 secs passed Thread #6: 2350000 reads finished. 947 secs passed Thread #1: 2400000 reads finished. 977 secs passed Thread #2: 2450000 reads finished. 982 secs passed Thread #7: 2500000 reads finished. 985 secs passed Thread #4: 2550000 reads finished. 986 secs passed Thread #3: 2600000 reads finished. 986 secs passed Thread #5: 2650000 reads finished. 988 secs passed Thread #0: 2700000 reads finished. 991 secs passed Thread #1: 2800000 reads finished. 1115 secs passed Thread #2: 2850000 reads finished. 1121 secs passed Thread #7: 2900000 reads finished. 1123 secs passed Thread #4: 2950000 reads finished. 1123 secs passed Thread #3: 3000000 reads finished. 1124 secs passed Thread #5: 3050000 reads finished. 1127 secs passed Thread #0: 3100000 reads finished. 1129 secs passed Thread #6: 2750000 reads finished. 1131 secs passed Thread #1: 3150000 reads finished. 1250 secs passed Thread #2: 3200000 reads finished. 1257 secs passed Thread #7: 3250000 reads finished. 1260 secs passed Thread #4: 3300000 reads finished. 1260 secs passed Thread #3: 3350000 reads finished. 1261 secs passed Thread #5: 3400000 reads finished. 1265 secs passed Thread #0: 3450000 reads finished. 1268 secs passed Thread #6: 3500000 reads finished. 1314 secs passed Thread #1: 3550000 reads finished. 1388 secs passed Thread #2: 3600000 reads finished. 1396 secs passed Thread #4: 3700000 reads finished. 1397 secs passed Thread #7: 3650000 reads finished. 1399 secs passed Thread #3: 3750000 reads finished. 1399 secs passed Thread #5: 3800000 reads finished. 1404 secs passed Thread #0: 3850000 reads finished. 1406 secs passed Thread #6: 3900000 reads finished. 1496 secs passed Thread #1: 3950000 reads finished. 1525 secs passed Thread #2: 4000000 reads finished. 1535 secs passed Thread #4: 4050000 reads finished. 1535 secs passed Thread #7: 4100000 reads finished. 1537 secs passed Thread #3: 4150000 reads finished. 1537 secs passed Thread #5: 4200000 reads finished. 1542 secs passed Thread #0: 4250000 reads finished. 1546 secs passed Thread #1: 4350000 reads finished. 1658 secs passed Thread #4: 4450000 reads finished. 1672 secs passed Thread #2: 4400000 reads finished. 1672 secs passed Thread #7: 4500000 reads finished. 1673 secs passed Thread #3: 4550000 reads finished. 1674 secs passed Thread #6: 4300000 reads finished. 1678 secs passed Thread #5: 4600000 reads finished. 1679 secs passed Thread #0: 4650000 reads finished. 1682 secs passed Thread #1: 4700000 reads finished. 1796 secs passed Thread #2: 4800000 reads finished. 1810 secs passed Thread #4: 4750000 reads finished. 1810 secs passed Thread #7: 4850000 reads finished. 1812 secs passed Thread #3: 4900000 reads finished. 1813 secs passed Thread #5: 5000000 reads finished. 1818 secs passed Thread #0: 5050000 reads finished. 1822 secs passed Thread #6: 4950000 reads finished. 1856 secs passed Thread #1: 5100000 reads finished. 1936 secs passed Thread #4: 5200000 reads finished. 1949 secs passed Thread #2: 5150000 reads finished. 1951 secs passed Thread #7: 5250000 reads finished. 1951 secs passed Thread #3: 5300000 reads finished. 1953 secs passed Thread #5: 5350000 reads finished. 1958 secs passed Thread #0: 5400000 reads finished. 1961 secs passed Thread #6: 5450000 reads finished. 2036 secs passed Thread #1: 5500000 reads finished. 2073 secs passed Thread #4: 5550000 reads finished. 2087 secs passed Thread #7: 5650000 reads finished. 2089 secs passed Thread #2: 5600000 reads finished. 2090 secs passed Thread #3: 5700000 reads finished. 2092 secs passed Thread #5: 5750000 reads finished. 2098 secs passed Thread #0: 5800000 reads finished. 2100 secs passed Thread #1: 5900000 reads finished. 2212 secs passed Thread #6: 5850000 reads finished. 2215 secs passed Thread #4: 5950000 reads finished. 2226 secs passed Thread #7: 6000000 reads finished. 2228 secs passed Thread #2: 6050000 reads finished. 2229 secs passed Thread #3: 6100000 reads finished. 2231 secs passed Thread #5: 6150000 reads finished. 2238 secs passed Thread #0: 6200000 reads finished. 2239 secs passed Thread #1: 6250000 reads finished. 2349 secs passed Thread #4: 6350000 reads finished. 2365 secs passed Thread #7: 6400000 reads finished. 2368 secs passed Thread #2: 6450000 reads finished. 2369 secs passed Thread #3: 6500000 reads finished. 2371 secs passed Thread #5: 6550000 reads finished. 2378 secs passed Thread #0: 6600000 reads finished. 2378 secs passed Thread #6: 6300000 reads finished. 2394 secs passed Thread #1: 6650000 reads finished. 2487 secs passed Thread #4: 6700000 reads finished. 2503 secs passed Thread #7: 6750000 reads finished. 2505 secs passed Thread #2: 6800000 reads finished. 2507 secs passed Thread #3: 6850000 reads finished. 2508 secs passed Thread #5: 6900000 reads finished. 2516 secs passed Thread #0: 6950000 reads finished. 2517 secs passed Thread #6: 7000000 reads finished. 2573 secs passed Thread #1: 7050000 reads finished. 2624 secs passed Thread #4: 7100000 reads finished. 2641 secs passed Thread #7: 7150000 reads finished. 2644 secs passed Thread #2: 7200000 reads finished. 2645 secs passed Thread #3: 7250000 reads finished. 2647 secs passed Thread #5: 7300000 reads finished. 2655 secs passed Thread #0: 7350000 reads finished. 2656 secs passed Thread #6: 7400000 reads finished. 2754 secs passed Thread #1: 7450000 reads finished. 2761 secs passed Thread #4: 7500000 reads finished. 2779 secs passed Thread #7: 7550000 reads finished. 2783 secs passed Thread #2: 7600000 reads finished. 2784 secs passed Thread #3: 7650000 reads finished. 2786 secs passed Thread #5: 7700000 reads finished. 2795 secs passed Thread #0: 7750000 reads finished. 2795 secs passed Thread #1: 7850000 reads finished. 2900 secs passed Thread #4: 7900000 reads finished. 2918 secs passed Thread #7: 7950000 reads finished. 2922 secs passed Thread #2: 8000000 reads finished. 2924 secs passed Thread #3: 8050000 reads finished. 2926 secs passed Thread #5: 8100000 reads finished. 2934 secs passed Thread #6: 7800000 reads finished. 2935 secs passed Thread #0: 8150000 reads finished. 2936 secs passed Thread #1: 8200000 reads finished. 3038 secs passed Thread #4: 8250000 reads finished. 3056 secs passed Thread #7: 8300000 reads finished. 3060 secs passed Thread #2: 8350000 reads finished. 3062 secs passed Thread #3: 8400000 reads finished. 3065 secs passed Thread #5: 8450000 reads finished. 3072 secs passed Thread #0: 8550000 reads finished. 3075 secs passed Thread #6: 8500000 reads finished. 3116 secs passed Thread #1: 8600000 reads finished. 3176 secs passed Thread #4: 8650000 reads finished. 3194 secs passed Thread #7: 8700000 reads finished. 3200 secs passed Thread #2: 8750000 reads finished. 3200 secs passed Thread #3: 8800000 reads finished. 3203 secs passed Thread #5: 8850000 reads finished. 3211 secs passed Thread #0: 8900000 reads finished. 3216 secs passed Thread #6: 8950000 reads finished. 3297 secs passed Thread #1: 9000000 reads finished. 3314 secs passed Thread #4: 9050000 reads finished. 3334 secs passed Thread #7: 9100000 reads finished. 3338 secs passed Thread #2: 9150000 reads finished. 3339 secs passed Thread #3: 9200000 reads finished. 3342 secs passed Thread #5: 9250000 reads finished. 3351 secs passed Thread #0: 9300000 reads finished. 3355 secs passed Thread #1: 9400000 reads finished. 3452 secs passed Thread #4: 9450000 reads finished. 3473 secs passed Thread #7: 9500000 reads finished. 3476 secs passed Thread #6: 9350000 reads finished. 3476 secs passed Thread #2: 9550000 reads finished. 3478 secs passed Thread #3: 9600000 reads finished. 3481 secs passed Thread #5: 9650000 reads finished. 3490 secs passed Thread #0: 9700000 reads finished. 3494 secs passed Thread #1: 9750000 reads finished. 3589 secs passed Thread #4: 9800000 reads finished. 3612 secs passed Thread #7: 9850000 reads finished. 3616 secs passed Thread #2: 9950000 reads finished. 3618 secs passed Thread #3: 10000000 reads finished. 3621 secs passed Thread #5: 10050000 reads finished. 3629 secs passed Thread #0: 10100000 reads finished. 3634 secs passed Thread #6: 9900000 reads finished. 3653 secs passed Thread #1: 10150000 reads finished. 3728 secs passed Thread #4: 10200000 reads finished. 3751 secs passed Thread #7: 10250000 reads finished. 3755 secs passed Thread #2: 10300000 reads finished. 3758 secs passed Thread #3: 10350000 reads finished. 3760 secs passed Thread #5: 10400000 reads finished. 3770 secs passed Thread #0: 10450000 reads finished. 3774 secs passed Thread #6: 10500000 reads finished. 3829 secs passed Thread #1: 10550000 reads finished. 3866 secs passed Thread #4: 10600000 reads finished. 3889 secs passed Thread #7: 10650000 reads finished. 3895 secs passed Thread #2: 10700000 reads finished. 3899 secs passed Thread #3: 10750000 reads finished. 3901 secs passed Thread #5: 10800000 reads finished. 3911 secs passed Thread #0: 10850000 reads finished. 3913 secs passed Thread #1: 10950000 reads finished. 4004 secs passed Thread #6: 10900000 reads finished. 4010 secs passed Thread #4: 11000000 reads finished. 4027 secs passed Thread #7: 11050000 reads finished. 4034 secs passed Thread #2: 11100000 reads finished. 4039 secs passed Thread #3: 11150000 reads finished. 4040 secs passed Thread #5: 11200000 reads finished. 4051 secs passed Thread #0: 11250000 reads finished. 4053 secs passed Thread #1: 11300000 reads finished. 4141 secs passed Thread #4: 11400000 reads finished. 4167 secs passed Thread #7: 11450000 reads finished. 4174 secs passed Thread #2: 11500000 reads finished. 4180 secs passed Thread #3: 11550000 reads finished. 4180 secs passed Thread #6: 11350000 reads finished. 4190 secs passed Thread #5: 11600000 reads finished. 4192 secs passed Thread #0: 11650000 reads finished. 4193 secs passed Thread #1: 11700000 reads finished. 4280 secs passed Thread #4: 11750000 reads finished. 4306 secs passed Thread #7: 11800000 reads finished. 4313 secs passed Thread #2: 11850000 reads finished. 4319 secs passed Thread #3: 11900000 reads finished. 4320 secs passed Thread #5: 12000000 reads finished. 4332 secs passed Thread #0: 12050000 reads finished. 4332 secs passed Thread #6: 11950000 reads finished. 4364 secs passed Thread #1: 12100000 reads finished. 4418 secs passed Thread #4: 12150000 reads finished. 4444 secs passed Thread #7: 12200000 reads finished. 4451 secs passed Thread #2: 12250000 reads finished. 4459 secs passed Thread #3: 12300000 reads finished. 4459 secs passed Thread #5: 12350000 reads finished. 4470 secs passed Thread #0: 12400000 reads finished. 4470 secs passed Thread #6: 12450000 reads finished. 4535 secs passed Thread #1: 12500000 reads finished. 4555 secs passed Thread #4: 12550000 reads finished. 4583 secs passed Thread #7: 12600000 reads finished. 4590 secs passed Thread #2: 12650000 reads finished. 4597 secs passed Thread #3: 12700000 reads finished. 4598 secs passed Thread #5: 12750000 reads finished. 4609 secs passed Thread #0: 12800000 reads finished. 4609 secs passed Thread #1: 12900000 reads finished. 4693 secs passed Thread #6: 12850000 reads finished. 4704 secs passed Thread #4: 12950000 reads finished. 4721 secs passed Thread #7: 13000000 reads finished. 4729 secs passed Thread #2: 13050000 reads finished. 4736 secs passed Thread #3: 13100000 reads finished. 4737 secs passed Thread #5: 13150000 reads finished. 4749 secs passed Thread #0: 13200000 reads finished. 4750 secs passed Thread #1: 13250000 reads finished. 4831 secs passed Thread #4: 13350000 reads finished. 4860 secs passed Thread #7: 13400000 reads finished. 4868 secs passed Thread #6: 13300000 reads finished. 4872 secs passed Thread #2: 13450000 reads finished. 4876 secs passed Thread #3: 13500000 reads finished. 4876 secs passed Thread #5: 13550000 reads finished. 4890 secs passed Thread #0: 13600000 reads finished. 4890 secs passed Thread #1: 13650000 reads finished. 4970 secs passed Thread #4: 13700000 reads finished. 4999 secs passed Thread #7: 13750000 reads finished. 5008 secs passed Thread #2: 13850000 reads finished. 5015 secs passed Thread #3: 13900000 reads finished. 5016 secs passed Thread #0: 14000000 reads finished. 5028 secs passed Thread #5: 13950000 reads finished. 5029 secs passed Thread #6: 13800000 reads finished. 5040 secs passed Thread #1: 14050000 reads finished. 5106 secs passed Thread #6: 14374642 reads finished. 5123 secs passed Thread #4: 14100000 reads finished. 5127 secs passed Thread #7: 14150000 reads finished. 5131 secs passed Thread #2: 14200000 reads finished. 5133 secs passed Thread #3: 14250000 reads finished. 5133 secs passed Thread #0: 14300000 reads finished. 5135 secs passed Thread #5: 14350000 reads finished. 5135 secs passed Total number of aligned reads: 2204953 (15%) Done. Finished at Wed Mar 7 22:41:11 2018 Total time consumed: 5135 secs