BSMAP v2.74 Start at: Sun Mar 11 09:41:57 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly1k.fa (format: FASTA) Load in 159429 db seqs, total size 1140787867 bp. 29 secs passed total_kmers: 43046721 Create seed table. 64 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_jelly1k.sam (format: SAM) Thread #0: 50000 reads finished. 699 secs passed Thread #1: 200000 reads finished. 700 secs passed Thread #5: 100000 reads finished. 700 secs passed Thread #4: 300000 reads finished. 702 secs passed Thread #2: 150000 reads finished. 702 secs passed Thread #6: 250000 reads finished. 703 secs passed Thread #7: 400000 reads finished. 705 secs passed Thread #3: 350000 reads finished. 779 secs passed Thread #0: 450000 reads finished. 1332 secs passed Thread #1: 500000 reads finished. 1332 secs passed Thread #5: 550000 reads finished. 1335 secs passed Thread #4: 600000 reads finished. 1335 secs passed Thread #6: 700000 reads finished. 1339 secs passed Thread #2: 650000 reads finished. 1339 secs passed Thread #7: 750000 reads finished. 1342 secs passed Thread #3: 800000 reads finished. 1490 secs passed Thread #1: 900000 reads finished. 1964 secs passed Thread #0: 850000 reads finished. 1965 secs passed Thread #4: 1000000 reads finished. 1968 secs passed Thread #5: 950000 reads finished. 1969 secs passed Thread #6: 1050000 reads finished. 1975 secs passed Thread #2: 1100000 reads finished. 1976 secs passed Thread #7: 1150000 reads finished. 1980 secs passed Thread #3: 1200000 reads finished. 2202 secs passed Thread #0: 1300000 reads finished. 2598 secs passed Thread #1: 1250000 reads finished. 2598 secs passed Thread #4: 1350000 reads finished. 2602 secs passed Thread #5: 1400000 reads finished. 2604 secs passed Thread #6: 1450000 reads finished. 2611 secs passed Thread #2: 1500000 reads finished. 2613 secs passed Thread #7: 1550000 reads finished. 2617 secs passed Thread #3: 1600000 reads finished. 2914 secs passed Thread #0: 1650000 reads finished. 3230 secs passed Thread #1: 1700000 reads finished. 3231 secs passed Thread #4: 1750000 reads finished. 3236 secs passed Thread #5: 1800000 reads finished. 3240 secs passed Thread #6: 1850000 reads finished. 3246 secs passed Thread #2: 1900000 reads finished. 3250 secs passed Thread #7: 1950000 reads finished. 3254 secs passed Thread #3: 2000000 reads finished. 3626 secs passed Thread #0: 2050000 reads finished. 3864 secs passed Thread #1: 2100000 reads finished. 3864 secs passed Thread #4: 2150000 reads finished. 3869 secs passed Thread #5: 2200000 reads finished. 3876 secs passed Thread #6: 2250000 reads finished. 3883 secs passed Thread #2: 2300000 reads finished. 3887 secs passed Thread #7: 2350000 reads finished. 3893 secs passed Thread #3: 2400000 reads finished. 4338 secs passed Thread #1: 2500000 reads finished. 4497 secs passed Thread #0: 2450000 reads finished. 4499 secs passed Thread #4: 2550000 reads finished. 4504 secs passed Thread #5: 2600000 reads finished. 4512 secs passed Thread #6: 2650000 reads finished. 4520 secs passed Thread #2: 2700000 reads finished. 4525 secs passed Thread #7: 2750000 reads finished. 4531 secs passed Thread #3: 2800000 reads finished. 5050 secs passed Thread #1: 2850000 reads finished. 5130 secs passed Thread #0: 2900000 reads finished. 5132 secs passed Thread #4: 2950000 reads finished. 5138 secs passed Thread #5: 3000000 reads finished. 5148 secs passed Thread #6: 3050000 reads finished. 5156 secs passed Thread #2: 3100000 reads finished. 5161 secs passed Thread #7: 3150000 reads finished. 5170 secs passed Thread #3: 3200000 reads finished. 5761 secs passed Thread #1: 3250000 reads finished. 5762 secs passed Thread #0: 3300000 reads finished. 5765 secs passed Thread #4: 3350000 reads finished. 5772 secs passed Thread #5: 3400000 reads finished. 5788 secs passed Thread #6: 3450000 reads finished. 5793 secs passed Thread #2: 3500000 reads finished. 5799 secs passed Thread #7: 3550000 reads finished. 5808 secs passed Thread #1: 3650000 reads finished. 6395 secs passed Thread #0: 3700000 reads finished. 6398 secs passed Thread #4: 3750000 reads finished. 6405 secs passed Thread #5: 3800000 reads finished. 6424 secs passed Thread #6: 3850000 reads finished. 6429 secs passed Thread #2: 3900000 reads finished. 6436 secs passed Thread #7: 3950000 reads finished. 6445 secs passed Thread #3: 3600000 reads finished. 6471 secs passed Thread #1: 4000000 reads finished. 7028 secs passed Thread #0: 4050000 reads finished. 7031 secs passed Thread #4: 4100000 reads finished. 7038 secs passed Thread #5: 4150000 reads finished. 7059 secs passed Thread #6: 4200000 reads finished. 7064 secs passed Thread #2: 4250000 reads finished. 7073 secs passed Thread #7: 4300000 reads finished. 7081 secs passed Thread #3: 4350000 reads finished. 7182 secs passed Thread #1: 4400000 reads finished. 7661 secs passed Thread #0: 4450000 reads finished. 7664 secs passed Thread #4: 4500000 reads finished. 7671 secs passed Thread #5: 4550000 reads finished. 7694 secs passed Thread #6: 4600000 reads finished. 7700 secs passed Thread #2: 4650000 reads finished. 7710 secs passed Thread #7: 4700000 reads finished. 7718 secs passed Thread #3: 4750000 reads finished. 7893 secs passed Thread #1: 4800000 reads finished. 8294 secs passed Thread #0: 4850000 reads finished. 8297 secs passed Thread #4: 4900000 reads finished. 8305 secs passed Thread #5: 4950000 reads finished. 8328 secs passed Thread #6: 5000000 reads finished. 8337 secs passed Thread #2: 5050000 reads finished. 8347 secs passed Thread #7: 5100000 reads finished. 8357 secs passed Thread #3: 5150000 reads finished. 8604 secs passed Thread #1: 5200000 reads finished. 8927 secs passed Thread #0: 5250000 reads finished. 8929 secs passed Thread #4: 5300000 reads finished. 8938 secs passed Thread #5: 5350000 reads finished. 8963 secs passed Thread #6: 5400000 reads finished. 8974 secs passed Thread #2: 5450000 reads finished. 8985 secs passed Thread #7: 5500000 reads finished. 8994 secs passed Thread #3: 5550000 reads finished. 9314 secs passed Thread #1: 5600000 reads finished. 9558 secs passed Thread #0: 5650000 reads finished. 9565 secs passed Thread #4: 5700000 reads finished. 9570 secs passed Thread #5: 5750000 reads finished. 9601 secs passed Thread #6: 5800000 reads finished. 9608 secs passed Thread #2: 5850000 reads finished. 9622 secs passed Thread #7: 5900000 reads finished. 9632 secs passed Thread #3: 5950000 reads finished. 10027 secs passed Thread #1: 6000000 reads finished. 10189 secs passed Thread #0: 6050000 reads finished. 10197 secs passed Thread #4: 6100000 reads finished. 10203 secs passed Thread #5: 6150000 reads finished. 10235 secs passed Thread #6: 6200000 reads finished. 10247 secs passed Thread #2: 6250000 reads finished. 10262 secs passed Thread #7: 6300000 reads finished. 10270 secs passed Thread #3: 6350000 reads finished. 10739 secs passed Thread #1: 6400000 reads finished. 10822 secs passed Thread #0: 6450000 reads finished. 10831 secs passed Thread #4: 6500000 reads finished. 10837 secs passed Thread #5: 6550000 reads finished. 10871 secs passed Thread #6: 6600000 reads finished. 10884 secs passed Thread #2: 6650000 reads finished. 10899 secs passed Thread #7: 6700000 reads finished. 10907 secs passed Thread #3: 6750000 reads finished. 11448 secs passed Thread #1: 6800000 reads finished. 11451 secs passed Thread #0: 6850000 reads finished. 11461 secs passed Thread #4: 6900000 reads finished. 11469 secs passed Thread #5: 6950000 reads finished. 11506 secs passed Thread #6: 7000000 reads finished. 11525 secs passed Thread #2: 7050000 reads finished. 11541 secs passed Thread #7: 7100000 reads finished. 11549 secs passed Thread #1: 7200000 reads finished. 12084 secs passed Thread #0: 7250000 reads finished. 12094 secs passed Thread #4: 7300000 reads finished. 12102 secs passed Thread #5: 7350000 reads finished. 12142 secs passed Thread #3: 7150000 reads finished. 12159 secs passed Thread #6: 7400000 reads finished. 12161 secs passed Thread #2: 7450000 reads finished. 12178 secs passed Thread #7: 7500000 reads finished. 12187 secs passed Thread #1: 7550000 reads finished. 12720 secs passed Thread #0: 7600000 reads finished. 12729 secs passed Thread #4: 7650000 reads finished. 12736 secs passed Thread #5: 7700000 reads finished. 12777 secs passed Thread #6: 7800000 reads finished. 12796 secs passed Thread #2: 7850000 reads finished. 12815 secs passed Thread #7: 7900000 reads finished. 12824 secs passed Thread #3: 7750000 reads finished. 12869 secs passed Thread #1: 7950000 reads finished. 13353 secs passed Thread #0: 8000000 reads finished. 13362 secs passed Thread #4: 8050000 reads finished. 13370 secs passed Thread #5: 8100000 reads finished. 13412 secs passed Thread #6: 8150000 reads finished. 13433 secs passed Thread #2: 8200000 reads finished. 13452 secs passed Thread #7: 8250000 reads finished. 13461 secs passed Thread #3: 8300000 reads finished. 13581 secs passed Thread #1: 8350000 reads finished. 13986 secs passed Thread #0: 8400000 reads finished. 13996 secs passed Thread #4: 8450000 reads finished. 14003 secs passed Thread #5: 8500000 reads finished. 14046 secs passed Thread #6: 8550000 reads finished. 14069 secs passed Thread #2: 8600000 reads finished. 14090 secs passed Thread #7: 8650000 reads finished. 14098 secs passed Thread #3: 8700000 reads finished. 14292 secs passed Thread #1: 8750000 reads finished. 14620 secs passed Thread #0: 8800000 reads finished. 14630 secs passed Thread #4: 8850000 reads finished. 14637 secs passed Thread #5: 8900000 reads finished. 14682 secs passed Thread #6: 8950000 reads finished. 14706 secs passed Thread #2: 9000000 reads finished. 14728 secs passed Thread #7: 9050000 reads finished. 14736 secs passed Thread #7: 9402890 reads finished. 14773 secs passed Thread #3: 9100000 reads finished. 14973 secs passed Thread #1: 9150000 reads finished. 15160 secs passed Thread #0: 9200000 reads finished. 15167 secs passed Thread #4: 9250000 reads finished. 15170 secs passed Thread #5: 9300000 reads finished. 15187 secs passed Thread #6: 9350000 reads finished. 15194 secs passed Thread #2: 9400000 reads finished. 15196 secs passed Total number of aligned reads: 1657135 (18%) Done. Finished at Sun Mar 11 13:55:13 2018 Total time consumed: 15196 secs BSMAP v2.74 Start at: Sun Mar 11 13:55:14 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly1k.fa (format: FASTA) Load in 159429 db seqs, total size 1140787867 bp. 10 secs passed total_kmers: 43046721 Create seed table. 41 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_jelly1k.sam (format: SAM) Thread #7: 100000 reads finished. 678 secs passed Thread #4: 200000 reads finished. 679 secs passed Thread #6: 50000 reads finished. 679 secs passed Thread #1: 400000 reads finished. 682 secs passed Thread #5: 150000 reads finished. 682 secs passed Thread #3: 250000 reads finished. 682 secs passed Thread #2: 350000 reads finished. 693 secs passed Thread #0: 300000 reads finished. 695 secs passed Thread #7: 450000 reads finished. 1315 secs passed Thread #4: 500000 reads finished. 1317 secs passed Thread #6: 550000 reads finished. 1318 secs passed Thread #1: 600000 reads finished. 1321 secs passed Thread #3: 700000 reads finished. 1323 secs passed Thread #5: 650000 reads finished. 1324 secs passed Thread #2: 750000 reads finished. 1345 secs passed Thread #0: 800000 reads finished. 1349 secs passed Thread #7: 850000 reads finished. 1951 secs passed Thread #4: 900000 reads finished. 1954 secs passed Thread #6: 950000 reads finished. 1958 secs passed Thread #1: 1000000 reads finished. 1961 secs passed Thread #3: 1050000 reads finished. 1964 secs passed Thread #5: 1100000 reads finished. 1966 secs passed Thread #2: 1150000 reads finished. 1997 secs passed Thread #0: 1200000 reads finished. 2002 secs passed Thread #7: 1250000 reads finished. 2589 secs passed Thread #4: 1300000 reads finished. 2591 secs passed Thread #6: 1350000 reads finished. 2597 secs passed Thread #1: 1400000 reads finished. 2601 secs passed Thread #3: 1450000 reads finished. 2605 secs passed Thread #5: 1500000 reads finished. 2607 secs passed Thread #2: 1550000 reads finished. 2649 secs passed Thread #0: 1600000 reads finished. 2656 secs passed Thread #7: 1650000 reads finished. 3226 secs passed Thread #4: 1700000 reads finished. 3228 secs passed Thread #6: 1750000 reads finished. 3235 secs passed Thread #1: 1800000 reads finished. 3241 secs passed Thread #3: 1850000 reads finished. 3246 secs passed Thread #5: 1900000 reads finished. 3249 secs passed Thread #2: 1950000 reads finished. 3302 secs passed Thread #0: 2000000 reads finished. 3310 secs passed Thread #7: 2050000 reads finished. 3863 secs passed Thread #4: 2100000 reads finished. 3865 secs passed Thread #6: 2150000 reads finished. 3874 secs passed Thread #1: 2200000 reads finished. 3880 secs passed Thread #3: 2250000 reads finished. 3889 secs passed Thread #5: 2300000 reads finished. 3891 secs passed Thread #2: 2350000 reads finished. 3953 secs passed Thread #0: 2400000 reads finished. 3962 secs passed Thread #7: 2450000 reads finished. 4501 secs passed Thread #4: 2500000 reads finished. 4503 secs passed Thread #6: 2550000 reads finished. 4512 secs passed Thread #1: 2600000 reads finished. 4520 secs passed Thread #3: 2650000 reads finished. 4530 secs passed Thread #5: 2700000 reads finished. 4532 secs passed Thread #2: 2750000 reads finished. 4605 secs passed Thread #0: 2800000 reads finished. 4617 secs passed Thread #7: 2850000 reads finished. 5137 secs passed Thread #4: 2900000 reads finished. 5140 secs passed Thread #6: 2950000 reads finished. 5152 secs passed Thread #1: 3000000 reads finished. 5160 secs passed Thread #3: 3050000 reads finished. 5170 secs passed Thread #5: 3100000 reads finished. 5174 secs passed Thread #2: 3150000 reads finished. 5257 secs passed Thread #0: 3200000 reads finished. 5270 secs passed Thread #7: 3250000 reads finished. 5774 secs passed Thread #4: 3300000 reads finished. 5777 secs passed Thread #6: 3350000 reads finished. 5791 secs passed Thread #1: 3400000 reads finished. 5800 secs passed Thread #3: 3450000 reads finished. 5811 secs passed Thread #5: 3500000 reads finished. 5816 secs passed Thread #2: 3550000 reads finished. 5909 secs passed Thread #0: 3600000 reads finished. 5924 secs passed Thread #7: 3650000 reads finished. 6412 secs passed Thread #4: 3700000 reads finished. 6416 secs passed Thread #6: 3750000 reads finished. 6431 secs passed Thread #1: 3800000 reads finished. 6441 secs passed Thread #3: 3850000 reads finished. 6452 secs passed Thread #5: 3900000 reads finished. 6458 secs passed Thread #2: 3950000 reads finished. 6560 secs passed Thread #0: 4000000 reads finished. 6578 secs passed Thread #7: 4050000 reads finished. 7048 secs passed Thread #4: 4100000 reads finished. 7052 secs passed Thread #6: 4150000 reads finished. 7070 secs passed Thread #1: 4200000 reads finished. 7081 secs passed Thread #3: 4250000 reads finished. 7095 secs passed Thread #5: 4300000 reads finished. 7100 secs passed Thread #2: 4350000 reads finished. 7211 secs passed Thread #0: 4400000 reads finished. 7232 secs passed Thread #7: 4450000 reads finished. 7685 secs passed Thread #4: 4500000 reads finished. 7690 secs passed Thread #6: 4550000 reads finished. 7710 secs passed Thread #1: 4600000 reads finished. 7722 secs passed Thread #3: 4650000 reads finished. 7737 secs passed Thread #5: 4700000 reads finished. 7742 secs passed Thread #2: 4750000 reads finished. 7862 secs passed Thread #0: 4800000 reads finished. 7885 secs passed Thread #7: 4850000 reads finished. 8323 secs passed Thread #4: 4900000 reads finished. 8328 secs passed Thread #6: 4950000 reads finished. 8350 secs passed Thread #1: 5000000 reads finished. 8363 secs passed Thread #3: 5050000 reads finished. 8377 secs passed Thread #5: 5100000 reads finished. 8384 secs passed Thread #2: 5150000 reads finished. 8514 secs passed Thread #0: 5200000 reads finished. 8539 secs passed Thread #7: 5250000 reads finished. 8960 secs passed Thread #4: 5300000 reads finished. 8967 secs passed Thread #6: 5350000 reads finished. 8989 secs passed Thread #1: 5400000 reads finished. 9004 secs passed Thread #3: 5450000 reads finished. 9019 secs passed Thread #5: 5500000 reads finished. 9026 secs passed Thread #2: 5550000 reads finished. 9165 secs passed Thread #0: 5600000 reads finished. 9193 secs passed Thread #7: 5650000 reads finished. 9597 secs passed Thread #4: 5700000 reads finished. 9605 secs passed Thread #6: 5750000 reads finished. 9628 secs passed Thread #1: 5800000 reads finished. 9643 secs passed Thread #3: 5850000 reads finished. 9660 secs passed Thread #5: 5900000 reads finished. 9667 secs passed Thread #2: 5950000 reads finished. 9816 secs passed Thread #0: 6000000 reads finished. 9847 secs passed Thread #7: 6050000 reads finished. 10234 secs passed Thread #4: 6100000 reads finished. 10242 secs passed Thread #6: 6150000 reads finished. 10267 secs passed Thread #1: 6200000 reads finished. 10284 secs passed Thread #3: 6250000 reads finished. 10302 secs passed Thread #5: 6300000 reads finished. 10308 secs passed Thread #2: 6350000 reads finished. 10468 secs passed Thread #0: 6400000 reads finished. 10501 secs passed Thread #7: 6450000 reads finished. 10871 secs passed Thread #4: 6500000 reads finished. 10880 secs passed Thread #6: 6550000 reads finished. 10906 secs passed Thread #1: 6600000 reads finished. 10924 secs passed Thread #3: 6650000 reads finished. 10943 secs passed Thread #5: 6700000 reads finished. 10950 secs passed Thread #2: 6750000 reads finished. 11119 secs passed Thread #0: 6800000 reads finished. 11156 secs passed Thread #7: 6850000 reads finished. 11510 secs passed Thread #4: 6900000 reads finished. 11517 secs passed Thread #6: 6950000 reads finished. 11545 secs passed Thread #1: 7000000 reads finished. 11563 secs passed Thread #3: 7050000 reads finished. 11582 secs passed Thread #5: 7100000 reads finished. 11593 secs passed Thread #2: 7150000 reads finished. 11774 secs passed Thread #0: 7200000 reads finished. 11810 secs passed Thread #7: 7250000 reads finished. 12151 secs passed Thread #4: 7300000 reads finished. 12153 secs passed Thread #6: 7350000 reads finished. 12182 secs passed Thread #1: 7400000 reads finished. 12202 secs passed Thread #3: 7450000 reads finished. 12225 secs passed Thread #5: 7500000 reads finished. 12234 secs passed Thread #2: 7550000 reads finished. 12425 secs passed Thread #0: 7600000 reads finished. 12462 secs passed Thread #7: 7650000 reads finished. 12787 secs passed Thread #4: 7700000 reads finished. 12790 secs passed Thread #6: 7750000 reads finished. 12820 secs passed Thread #1: 7800000 reads finished. 12844 secs passed Thread #3: 7850000 reads finished. 12868 secs passed Thread #5: 7900000 reads finished. 12879 secs passed Thread #2: 7950000 reads finished. 13076 secs passed Thread #0: 8000000 reads finished. 13117 secs passed Thread #7: 8050000 reads finished. 13424 secs passed Thread #4: 8100000 reads finished. 13427 secs passed Thread #6: 8150000 reads finished. 13460 secs passed Thread #1: 8200000 reads finished. 13484 secs passed Thread #3: 8250000 reads finished. 13509 secs passed Thread #5: 8300000 reads finished. 13519 secs passed Thread #2: 8350000 reads finished. 13728 secs passed Thread #0: 8400000 reads finished. 13771 secs passed Thread #7: 8450000 reads finished. 14060 secs passed Thread #4: 8500000 reads finished. 14064 secs passed Thread #6: 8550000 reads finished. 14098 secs passed Thread #1: 8600000 reads finished. 14124 secs passed Thread #3: 8650000 reads finished. 14150 secs passed Thread #5: 8700000 reads finished. 14160 secs passed Thread #2: 8750000 reads finished. 14379 secs passed Thread #0: 8800000 reads finished. 14425 secs passed Thread #7: 8850000 reads finished. 14699 secs passed Thread #4: 8900000 reads finished. 14706 secs passed Thread #6: 8950000 reads finished. 14741 secs passed Thread #1: 9000000 reads finished. 14767 secs passed Thread #3: 9050000 reads finished. 14790 secs passed Thread #5: 9100000 reads finished. 14800 secs passed Thread #2: 9150000 reads finished. 15030 secs passed Thread #0: 9200000 reads finished. 15078 secs passed Thread #7: 9250000 reads finished. 15336 secs passed Thread #4: 9300000 reads finished. 15343 secs passed Thread #6: 9350000 reads finished. 15381 secs passed Thread #1: 9400000 reads finished. 15407 secs passed Thread #3: 9450000 reads finished. 15431 secs passed Thread #5: 9500000 reads finished. 15442 secs passed Thread #2: 9550000 reads finished. 15682 secs passed Thread #0: 9600000 reads finished. 15733 secs passed Thread #7: 9650000 reads finished. 15974 secs passed Thread #4: 9700000 reads finished. 15980 secs passed Thread #6: 9750000 reads finished. 16019 secs passed Thread #1: 9800000 reads finished. 16047 secs passed Thread #3: 9850000 reads finished. 16072 secs passed Thread #5: 9900000 reads finished. 16083 secs passed Thread #2: 9950000 reads finished. 16334 secs passed Thread #0: 10000000 reads finished. 16386 secs passed Thread #7: 10050000 reads finished. 16610 secs passed Thread #4: 10100000 reads finished. 16618 secs passed Thread #6: 10150000 reads finished. 16658 secs passed Thread #1: 10200000 reads finished. 16687 secs passed Thread #3: 10250000 reads finished. 16713 secs passed Thread #5: 10300000 reads finished. 16725 secs passed Thread #2: 10350000 reads finished. 16985 secs passed Thread #0: 10400000 reads finished. 17041 secs passed Thread #7: 10450000 reads finished. 17247 secs passed Thread #4: 10500000 reads finished. 17256 secs passed Thread #6: 10550000 reads finished. 17298 secs passed Thread #1: 10600000 reads finished. 17327 secs passed Thread #3: 10650000 reads finished. 17356 secs passed Thread #5: 10700000 reads finished. 17368 secs passed Thread #2: 10750000 reads finished. 17638 secs passed Thread #0: 10800000 reads finished. 17695 secs passed Thread #7: 10850000 reads finished. 17884 secs passed Thread #4: 10900000 reads finished. 17894 secs passed Thread #6: 10950000 reads finished. 17938 secs passed Thread #1: 11000000 reads finished. 17968 secs passed Thread #3: 11050000 reads finished. 17998 secs passed Thread #5: 11100000 reads finished. 18010 secs passed Thread #2: 11150000 reads finished. 18290 secs passed Thread #0: 11200000 reads finished. 18350 secs passed Thread #7: 11250000 reads finished. 18522 secs passed Thread #4: 11300000 reads finished. 18532 secs passed Thread #6: 11350000 reads finished. 18578 secs passed Thread #1: 11400000 reads finished. 18609 secs passed Thread #3: 11450000 reads finished. 18640 secs passed Thread #5: 11500000 reads finished. 18653 secs passed Thread #2: 11550000 reads finished. 18942 secs passed Thread #0: 11600000 reads finished. 19004 secs passed Thread #0: 11954873 reads finished. 19069 secs passed Thread #7: 11650000 reads finished. 19149 secs passed Thread #4: 11700000 reads finished. 19157 secs passed Thread #6: 11750000 reads finished. 19185 secs passed Thread #1: 11800000 reads finished. 19201 secs passed Thread #3: 11850000 reads finished. 19213 secs passed Thread #5: 11900000 reads finished. 19216 secs passed Thread #2: 11950000 reads finished. 19248 secs passed Total number of aligned reads: 2060372 (17%) Done. Finished at Sun Mar 11 19:16:02 2018 Total time consumed: 19248 secs BSMAP v2.74 Start at: Sun Mar 11 19:16:03 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly1k.fa (format: FASTA) Load in 159429 db seqs, total size 1140787867 bp. 11 secs passed total_kmers: 43046721 Create seed table. 41 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_jelly1k.sam (format: SAM) Thread #2: 50000 reads finished. 679 secs passed Thread #5: 350000 reads finished. 681 secs passed Thread #6: 150000 reads finished. 683 secs passed Thread #0: 250000 reads finished. 684 secs passed Thread #1: 300000 reads finished. 684 secs passed Thread #3: 400000 reads finished. 686 secs passed Thread #7: 100000 reads finished. 687 secs passed Thread #4: 200000 reads finished. 689 secs passed Thread #2: 450000 reads finished. 1317 secs passed Thread #5: 500000 reads finished. 1322 secs passed Thread #0: 600000 reads finished. 1324 secs passed Thread #6: 550000 reads finished. 1325 secs passed Thread #1: 650000 reads finished. 1326 secs passed Thread #3: 700000 reads finished. 1328 secs passed Thread #7: 750000 reads finished. 1334 secs passed Thread #4: 800000 reads finished. 1336 secs passed Thread #2: 850000 reads finished. 1955 secs passed Thread #5: 900000 reads finished. 1960 secs passed Thread #0: 950000 reads finished. 1965 secs passed Thread #6: 1000000 reads finished. 1966 secs passed Thread #1: 1050000 reads finished. 1969 secs passed Thread #3: 1100000 reads finished. 1971 secs passed Thread #7: 1150000 reads finished. 1980 secs passed Thread #4: 1200000 reads finished. 1982 secs passed Thread #2: 1250000 reads finished. 2593 secs passed Thread #5: 1300000 reads finished. 2599 secs passed Thread #0: 1350000 reads finished. 2606 secs passed Thread #6: 1400000 reads finished. 2608 secs passed Thread #1: 1450000 reads finished. 2611 secs passed Thread #3: 1500000 reads finished. 2614 secs passed Thread #7: 1550000 reads finished. 2626 secs passed Thread #4: 1600000 reads finished. 2629 secs passed Thread #2: 1650000 reads finished. 3231 secs passed Thread #5: 1700000 reads finished. 3237 secs passed Thread #0: 1750000 reads finished. 3247 secs passed Thread #6: 1800000 reads finished. 3250 secs passed Thread #1: 1850000 reads finished. 3252 secs passed Thread #3: 1900000 reads finished. 3256 secs passed Thread #7: 1950000 reads finished. 3272 secs passed Thread #4: 2000000 reads finished. 3275 secs passed Thread #2: 2050000 reads finished. 3869 secs passed Thread #5: 2100000 reads finished. 3876 secs passed Thread #0: 2150000 reads finished. 3887 secs passed Thread #6: 2200000 reads finished. 3893 secs passed Thread #1: 2250000 reads finished. 3896 secs passed Thread #3: 2300000 reads finished. 3898 secs passed Thread #7: 2350000 reads finished. 3917 secs passed Thread #4: 2400000 reads finished. 3921 secs passed Thread #2: 2450000 reads finished. 4509 secs passed Thread #5: 2500000 reads finished. 4517 secs passed Thread #0: 2550000 reads finished. 4529 secs passed Thread #6: 2600000 reads finished. 4536 secs passed Thread #1: 2650000 reads finished. 4539 secs passed Thread #3: 2700000 reads finished. 4542 secs passed Thread #7: 2750000 reads finished. 4565 secs passed Thread #4: 2800000 reads finished. 4570 secs passed Thread #2: 2850000 reads finished. 5153 secs passed Thread #5: 2900000 reads finished. 5163 secs passed Thread #0: 2950000 reads finished. 5175 secs passed Thread #6: 3000000 reads finished. 5183 secs passed Thread #1: 3050000 reads finished. 5187 secs passed Thread #3: 3100000 reads finished. 5190 secs passed Thread #7: 3150000 reads finished. 5215 secs passed Thread #4: 3200000 reads finished. 5222 secs passed Thread #2: 3250000 reads finished. 5792 secs passed Thread #5: 3300000 reads finished. 5803 secs passed Thread #0: 3350000 reads finished. 5817 secs passed Thread #6: 3400000 reads finished. 5825 secs passed Thread #1: 3450000 reads finished. 5830 secs passed Thread #3: 3500000 reads finished. 5833 secs passed Thread #7: 3550000 reads finished. 5861 secs passed Thread #4: 3600000 reads finished. 5869 secs passed Thread #2: 3650000 reads finished. 6431 secs passed Thread #5: 3700000 reads finished. 6443 secs passed Thread #0: 3750000 reads finished. 6459 secs passed Thread #6: 3800000 reads finished. 6466 secs passed Thread #1: 3850000 reads finished. 6471 secs passed Thread #3: 3900000 reads finished. 6475 secs passed Thread #7: 3950000 reads finished. 6507 secs passed Thread #4: 4000000 reads finished. 6515 secs passed Thread #2: 4050000 reads finished. 7066 secs passed Thread #5: 4100000 reads finished. 7079 secs passed Thread #0: 4150000 reads finished. 7097 secs passed Thread #6: 4200000 reads finished. 7107 secs passed Thread #1: 4250000 reads finished. 7116 secs passed Thread #3: 4300000 reads finished. 7126 secs passed Thread #7: 4350000 reads finished. 7156 secs passed Thread #4: 4400000 reads finished. 7159 secs passed Thread #2: 4450000 reads finished. 7705 secs passed Thread #5: 4500000 reads finished. 7719 secs passed Thread #0: 4550000 reads finished. 7738 secs passed Thread #6: 4600000 reads finished. 7748 secs passed Thread #1: 4650000 reads finished. 7758 secs passed Thread #3: 4700000 reads finished. 7770 secs passed Thread #7: 4750000 reads finished. 7802 secs passed Thread #4: 4800000 reads finished. 7806 secs passed Thread #2: 4850000 reads finished. 8342 secs passed Thread #5: 4900000 reads finished. 8358 secs passed Thread #0: 4950000 reads finished. 8379 secs passed Thread #6: 5000000 reads finished. 8389 secs passed Thread #1: 5050000 reads finished. 8401 secs passed Thread #3: 5100000 reads finished. 8413 secs passed Thread #7: 5150000 reads finished. 8448 secs passed Thread #4: 5200000 reads finished. 8453 secs passed Thread #2: 5250000 reads finished. 8981 secs passed Thread #5: 5300000 reads finished. 8997 secs passed Thread #0: 5350000 reads finished. 9019 secs passed Thread #6: 5400000 reads finished. 9030 secs passed Thread #1: 5450000 reads finished. 9042 secs passed Thread #3: 5500000 reads finished. 9055 secs passed Thread #7: 5550000 reads finished. 9094 secs passed Thread #4: 5600000 reads finished. 9100 secs passed Thread #2: 5650000 reads finished. 9619 secs passed Thread #5: 5700000 reads finished. 9637 secs passed Thread #0: 5750000 reads finished. 9659 secs passed Thread #6: 5800000 reads finished. 9672 secs passed Thread #1: 5850000 reads finished. 9684 secs passed Thread #3: 5900000 reads finished. 9697 secs passed Thread #7: 5950000 reads finished. 9741 secs passed Thread #4: 6000000 reads finished. 9747 secs passed Thread #2: 6050000 reads finished. 10258 secs passed Thread #5: 6100000 reads finished. 10277 secs passed Thread #0: 6150000 reads finished. 10300 secs passed Thread #6: 6200000 reads finished. 10313 secs passed Thread #1: 6250000 reads finished. 10327 secs passed Thread #3: 6300000 reads finished. 10340 secs passed Thread #7: 6350000 reads finished. 10386 secs passed Thread #4: 6400000 reads finished. 10395 secs passed Thread #2: 6450000 reads finished. 10899 secs passed Thread #5: 6500000 reads finished. 10916 secs passed Thread #0: 6550000 reads finished. 10941 secs passed Thread #6: 6600000 reads finished. 10956 secs passed Thread #1: 6650000 reads finished. 10969 secs passed Thread #3: 6700000 reads finished. 10981 secs passed Thread #7: 6750000 reads finished. 11032 secs passed Thread #4: 6800000 reads finished. 11041 secs passed Thread #2: 6850000 reads finished. 11539 secs passed Thread #5: 6900000 reads finished. 11555 secs passed Thread #0: 6950000 reads finished. 11581 secs passed Thread #6: 7000000 reads finished. 11596 secs passed Thread #1: 7050000 reads finished. 11610 secs passed Thread #3: 7100000 reads finished. 11624 secs passed Thread #7: 7150000 reads finished. 11682 secs passed Thread #4: 7200000 reads finished. 11689 secs passed Thread #2: 7250000 reads finished. 12179 secs passed Thread #5: 7300000 reads finished. 12196 secs passed Thread #0: 7350000 reads finished. 12220 secs passed Thread #6: 7400000 reads finished. 12239 secs passed Thread #1: 7450000 reads finished. 12253 secs passed Thread #3: 7500000 reads finished. 12266 secs passed Thread #7: 7550000 reads finished. 12328 secs passed Thread #4: 7600000 reads finished. 12335 secs passed Thread #2: 7650000 reads finished. 12816 secs passed Thread #5: 7700000 reads finished. 12835 secs passed Thread #0: 7750000 reads finished. 12860 secs passed Thread #6: 7800000 reads finished. 12881 secs passed Thread #1: 7850000 reads finished. 12898 secs passed Thread #3: 7900000 reads finished. 12912 secs passed Thread #7: 7950000 reads finished. 12974 secs passed Thread #4: 8000000 reads finished. 12984 secs passed Thread #2: 8050000 reads finished. 13454 secs passed Thread #5: 8100000 reads finished. 13474 secs passed Thread #0: 8150000 reads finished. 13501 secs passed Thread #6: 8200000 reads finished. 13523 secs passed Thread #1: 8250000 reads finished. 13541 secs passed Thread #3: 8300000 reads finished. 13554 secs passed Thread #7: 8350000 reads finished. 13620 secs passed Thread #4: 8400000 reads finished. 13630 secs passed Thread #2: 8450000 reads finished. 14092 secs passed Thread #5: 8500000 reads finished. 14112 secs passed Thread #0: 8550000 reads finished. 14142 secs passed Thread #6: 8600000 reads finished. 14165 secs passed Thread #1: 8650000 reads finished. 14182 secs passed Thread #3: 8700000 reads finished. 14198 secs passed Thread #7: 8750000 reads finished. 14268 secs passed Thread #4: 8800000 reads finished. 14280 secs passed Thread #2: 8850000 reads finished. 14735 secs passed Thread #5: 8900000 reads finished. 14756 secs passed Thread #0: 8950000 reads finished. 14786 secs passed Thread #6: 9000000 reads finished. 14805 secs passed Thread #1: 9050000 reads finished. 14823 secs passed Thread #3: 9100000 reads finished. 14839 secs passed Thread #7: 9150000 reads finished. 14914 secs passed Thread #4: 9200000 reads finished. 14926 secs passed Thread #2: 9250000 reads finished. 15374 secs passed Thread #5: 9300000 reads finished. 15396 secs passed Thread #0: 9350000 reads finished. 15429 secs passed Thread #6: 9400000 reads finished. 15449 secs passed Thread #1: 9450000 reads finished. 15466 secs passed Thread #3: 9500000 reads finished. 15484 secs passed Thread #7: 9550000 reads finished. 15562 secs passed Thread #4: 9600000 reads finished. 15574 secs passed Thread #2: 9650000 reads finished. 16013 secs passed Thread #5: 9700000 reads finished. 16036 secs passed Thread #0: 9750000 reads finished. 16071 secs passed Thread #6: 9800000 reads finished. 16092 secs passed Thread #1: 9850000 reads finished. 16109 secs passed Thread #3: 9900000 reads finished. 16127 secs passed Thread #7: 9950000 reads finished. 16209 secs passed Thread #4: 10000000 reads finished. 16223 secs passed Thread #2: 10050000 reads finished. 16653 secs passed Thread #5: 10100000 reads finished. 16676 secs passed Thread #0: 10150000 reads finished. 16712 secs passed Thread #6: 10200000 reads finished. 16735 secs passed Thread #1: 10250000 reads finished. 16752 secs passed Thread #3: 10300000 reads finished. 16770 secs passed Thread #7: 10350000 reads finished. 16856 secs passed Thread #4: 10400000 reads finished. 16871 secs passed Thread #2: 10450000 reads finished. 17293 secs passed Thread #5: 10500000 reads finished. 17317 secs passed Thread #0: 10550000 reads finished. 17355 secs passed Thread #6: 10600000 reads finished. 17379 secs passed Thread #1: 10650000 reads finished. 17396 secs passed Thread #3: 10700000 reads finished. 17414 secs passed Thread #7: 10750000 reads finished. 17504 secs passed Thread #4: 10800000 reads finished. 17521 secs passed Thread #2: 10850000 reads finished. 17933 secs passed Thread #5: 10900000 reads finished. 17958 secs passed Thread #0: 10950000 reads finished. 17997 secs passed Thread #6: 11000000 reads finished. 18022 secs passed Thread #1: 11050000 reads finished. 18039 secs passed Thread #3: 11100000 reads finished. 18058 secs passed Thread #7: 11150000 reads finished. 18151 secs passed Thread #4: 11200000 reads finished. 18169 secs passed Thread #2: 11250000 reads finished. 18574 secs passed Thread #5: 11300000 reads finished. 18599 secs passed Thread #0: 11350000 reads finished. 18640 secs passed Thread #6: 11400000 reads finished. 18667 secs passed Thread #1: 11450000 reads finished. 18683 secs passed Thread #3: 11500000 reads finished. 18702 secs passed Thread #7: 11550000 reads finished. 18786 secs passed Thread #4: 11600000 reads finished. 18800 secs passed Thread #1: 11817358 reads finished. 18856 secs passed Thread #2: 11650000 reads finished. 19005 secs passed Thread #5: 11700000 reads finished. 19013 secs passed Thread #0: 11750000 reads finished. 19024 secs passed Thread #6: 11800000 reads finished. 19027 secs passed Total number of aligned reads: 2046229 (17%) Done. Finished at Mon Mar 12 00:33:10 2018 Total time consumed: 19027 secs BSMAP v2.74 Start at: Mon Mar 12 00:33:11 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly1k.fa (format: FASTA) Load in 159429 db seqs, total size 1140787867 bp. 11 secs passed total_kmers: 43046721 Create seed table. 41 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_jelly1k.sam (format: SAM) Thread #0: 350000 reads finished. 683 secs passed Thread #5: 150000 reads finished. 685 secs passed Thread #4: 300000 reads finished. 687 secs passed Thread #3: 100000 reads finished. 689 secs passed Thread #1: 50000 reads finished. 692 secs passed Thread #7: 400000 reads finished. 692 secs passed Thread #6: 200000 reads finished. 693 secs passed Thread #2: 250000 reads finished. 693 secs passed Thread #0: 450000 reads finished. 1322 secs passed Thread #5: 500000 reads finished. 1328 secs passed Thread #4: 550000 reads finished. 1330 secs passed Thread #3: 600000 reads finished. 1336 secs passed Thread #7: 700000 reads finished. 1341 secs passed Thread #1: 650000 reads finished. 1342 secs passed Thread #6: 750000 reads finished. 1342 secs passed Thread #2: 800000 reads finished. 1343 secs passed Thread #0: 850000 reads finished. 1959 secs passed Thread #5: 900000 reads finished. 1969 secs passed Thread #4: 950000 reads finished. 1972 secs passed Thread #3: 1000000 reads finished. 1981 secs passed Thread #7: 1050000 reads finished. 1986 secs passed Thread #6: 1150000 reads finished. 1990 secs passed Thread #2: 1200000 reads finished. 1991 secs passed Thread #1: 1100000 reads finished. 1991 secs passed Thread #0: 1250000 reads finished. 2597 secs passed Thread #5: 1300000 reads finished. 2610 secs passed Thread #4: 1350000 reads finished. 2615 secs passed Thread #3: 1400000 reads finished. 2626 secs passed Thread #7: 1450000 reads finished. 2632 secs passed Thread #6: 1500000 reads finished. 2639 secs passed Thread #2: 1550000 reads finished. 2640 secs passed Thread #1: 1600000 reads finished. 2641 secs passed Thread #0: 1650000 reads finished. 3235 secs passed Thread #5: 1700000 reads finished. 3252 secs passed Thread #4: 1750000 reads finished. 3257 secs passed Thread #3: 1800000 reads finished. 3273 secs passed Thread #7: 1850000 reads finished. 3279 secs passed Thread #6: 1900000 reads finished. 3287 secs passed Thread #2: 1950000 reads finished. 3287 secs passed Thread #1: 2000000 reads finished. 3291 secs passed Thread #0: 2050000 reads finished. 3872 secs passed Thread #5: 2100000 reads finished. 3892 secs passed Thread #4: 2150000 reads finished. 3899 secs passed Thread #3: 2200000 reads finished. 3919 secs passed Thread #7: 2250000 reads finished. 3924 secs passed Thread #2: 2350000 reads finished. 3934 secs passed Thread #6: 2300000 reads finished. 3934 secs passed Thread #1: 2400000 reads finished. 3939 secs passed Thread #0: 2450000 reads finished. 4510 secs passed Thread #5: 2500000 reads finished. 4534 secs passed Thread #4: 2550000 reads finished. 4541 secs passed Thread #3: 2600000 reads finished. 4565 secs passed Thread #7: 2650000 reads finished. 4572 secs passed Thread #6: 2750000 reads finished. 4583 secs passed Thread #2: 2700000 reads finished. 4584 secs passed Thread #1: 2800000 reads finished. 4590 secs passed Thread #0: 2850000 reads finished. 5147 secs passed Thread #5: 2900000 reads finished. 5175 secs passed Thread #4: 2950000 reads finished. 5182 secs passed Thread #3: 3000000 reads finished. 5211 secs passed Thread #7: 3050000 reads finished. 5218 secs passed Thread #6: 3100000 reads finished. 5231 secs passed Thread #2: 3150000 reads finished. 5232 secs passed Thread #1: 3200000 reads finished. 5239 secs passed Thread #0: 3250000 reads finished. 5787 secs passed Thread #5: 3300000 reads finished. 5819 secs passed Thread #4: 3350000 reads finished. 5825 secs passed Thread #3: 3400000 reads finished. 5857 secs passed Thread #7: 3450000 reads finished. 5865 secs passed Thread #6: 3500000 reads finished. 5880 secs passed Thread #2: 3550000 reads finished. 5882 secs passed Thread #1: 3600000 reads finished. 5891 secs passed Thread #0: 3650000 reads finished. 6426 secs passed Thread #5: 3700000 reads finished. 6460 secs passed Thread #4: 3750000 reads finished. 6468 secs passed Thread #3: 3800000 reads finished. 6503 secs passed Thread #7: 3850000 reads finished. 6513 secs passed Thread #6: 3900000 reads finished. 6529 secs passed Thread #2: 3950000 reads finished. 6530 secs passed Thread #1: 4000000 reads finished. 6542 secs passed Thread #0: 4050000 reads finished. 7062 secs passed Thread #5: 4100000 reads finished. 7101 secs passed Thread #4: 4150000 reads finished. 7112 secs passed Thread #3: 4200000 reads finished. 7155 secs passed Thread #7: 4250000 reads finished. 7159 secs passed Thread #6: 4300000 reads finished. 7176 secs passed Thread #2: 4350000 reads finished. 7178 secs passed Thread #1: 4400000 reads finished. 7191 secs passed Thread #0: 4450000 reads finished. 7699 secs passed Thread #5: 4500000 reads finished. 7741 secs passed Thread #4: 4550000 reads finished. 7753 secs passed Thread #3: 4600000 reads finished. 7799 secs passed Thread #7: 4650000 reads finished. 7805 secs passed Thread #6: 4700000 reads finished. 7823 secs passed Thread #2: 4750000 reads finished. 7825 secs passed Thread #1: 4800000 reads finished. 7839 secs passed Thread #0: 4850000 reads finished. 8335 secs passed Thread #5: 4900000 reads finished. 8381 secs passed Thread #4: 4950000 reads finished. 8394 secs passed Thread #3: 5000000 reads finished. 8444 secs passed Thread #7: 5050000 reads finished. 8450 secs passed Thread #6: 5100000 reads finished. 8470 secs passed Thread #2: 5150000 reads finished. 8472 secs passed Thread #1: 5200000 reads finished. 8487 secs passed Thread #0: 5250000 reads finished. 8970 secs passed Thread #5: 5300000 reads finished. 9022 secs passed Thread #4: 5350000 reads finished. 9035 secs passed Thread #3: 5400000 reads finished. 9089 secs passed Thread #7: 5450000 reads finished. 9097 secs passed Thread #6: 5500000 reads finished. 9119 secs passed Thread #2: 5550000 reads finished. 9119 secs passed Thread #1: 5600000 reads finished. 9136 secs passed Thread #0: 5650000 reads finished. 9608 secs passed Thread #5: 5700000 reads finished. 9664 secs passed Thread #4: 5750000 reads finished. 9678 secs passed Thread #3: 5800000 reads finished. 9735 secs passed Thread #7: 5850000 reads finished. 9744 secs passed Thread #6: 5900000 reads finished. 9768 secs passed Thread #2: 5950000 reads finished. 9769 secs passed Thread #1: 6000000 reads finished. 9786 secs passed Thread #0: 6050000 reads finished. 10246 secs passed Thread #5: 6100000 reads finished. 10305 secs passed Thread #4: 6150000 reads finished. 10320 secs passed Thread #3: 6200000 reads finished. 10381 secs passed Thread #7: 6250000 reads finished. 10392 secs passed Thread #2: 6350000 reads finished. 10418 secs passed Thread #6: 6300000 reads finished. 10419 secs passed Thread #1: 6400000 reads finished. 10437 secs passed Thread #0: 6450000 reads finished. 10885 secs passed Thread #5: 6500000 reads finished. 10946 secs passed Thread #4: 6550000 reads finished. 10962 secs passed Thread #3: 6600000 reads finished. 11027 secs passed Thread #7: 6650000 reads finished. 11040 secs passed Thread #6: 6750000 reads finished. 11068 secs passed Thread #2: 6700000 reads finished. 11070 secs passed Thread #1: 6800000 reads finished. 11088 secs passed Thread #0: 6850000 reads finished. 11523 secs passed Thread #5: 6900000 reads finished. 11587 secs passed Thread #4: 6950000 reads finished. 11605 secs passed Thread #3: 7000000 reads finished. 11677 secs passed Thread #7: 7050000 reads finished. 11687 secs passed Thread #2: 7150000 reads finished. 11717 secs passed Thread #6: 7100000 reads finished. 11721 secs passed Thread #1: 7200000 reads finished. 11738 secs passed Thread #0: 7250000 reads finished. 12162 secs passed Thread #5: 7300000 reads finished. 12231 secs passed Thread #4: 7350000 reads finished. 12249 secs passed Thread #3: 7400000 reads finished. 12324 secs passed Thread #7: 7450000 reads finished. 12334 secs passed Thread #2: 7500000 reads finished. 12367 secs passed Thread #6: 7550000 reads finished. 12372 secs passed Thread #1: 7600000 reads finished. 12388 secs passed Thread #0: 7650000 reads finished. 12804 secs passed Thread #5: 7700000 reads finished. 12877 secs passed Thread #4: 7750000 reads finished. 12892 secs passed Thread #3: 7800000 reads finished. 12972 secs passed Thread #7: 7850000 reads finished. 12982 secs passed Thread #2: 7900000 reads finished. 13014 secs passed Thread #6: 7950000 reads finished. 13020 secs passed Thread #1: 8000000 reads finished. 13037 secs passed Thread #0: 8050000 reads finished. 13443 secs passed Thread #5: 8100000 reads finished. 13520 secs passed Thread #4: 8150000 reads finished. 13535 secs passed Thread #3: 8200000 reads finished. 13619 secs passed Thread #7: 8250000 reads finished. 13630 secs passed Thread #2: 8300000 reads finished. 13663 secs passed Thread #6: 8350000 reads finished. 13669 secs passed Thread #1: 8400000 reads finished. 13688 secs passed Thread #0: 8450000 reads finished. 14079 secs passed Thread #5: 8500000 reads finished. 14160 secs passed Thread #4: 8550000 reads finished. 14179 secs passed Thread #3: 8600000 reads finished. 14265 secs passed Thread #7: 8650000 reads finished. 14282 secs passed Thread #2: 8700000 reads finished. 14316 secs passed Thread #6: 8750000 reads finished. 14321 secs passed Thread #1: 8800000 reads finished. 14340 secs passed Thread #0: 8850000 reads finished. 14717 secs passed Thread #5: 8900000 reads finished. 14802 secs passed Thread #4: 8950000 reads finished. 14822 secs passed Thread #3: 9000000 reads finished. 14913 secs passed Thread #7: 9050000 reads finished. 14930 secs passed Thread #2: 9100000 reads finished. 14967 secs passed Thread #6: 9150000 reads finished. 14972 secs passed Thread #1: 9200000 reads finished. 14990 secs passed Thread #0: 9250000 reads finished. 15357 secs passed Thread #5: 9300000 reads finished. 15448 secs passed Thread #4: 9350000 reads finished. 15467 secs passed Thread #3: 9400000 reads finished. 15562 secs passed Thread #7: 9450000 reads finished. 15578 secs passed Thread #2: 9500000 reads finished. 15616 secs passed Thread #6: 9550000 reads finished. 15620 secs passed Thread #1: 9600000 reads finished. 15641 secs passed Thread #0: 9650000 reads finished. 15996 secs passed Thread #5: 9700000 reads finished. 16091 secs passed Thread #4: 9750000 reads finished. 16110 secs passed Thread #3: 9800000 reads finished. 16209 secs passed Thread #7: 9850000 reads finished. 16226 secs passed Thread #2: 9900000 reads finished. 16266 secs passed Thread #6: 9950000 reads finished. 16270 secs passed Thread #1: 10000000 reads finished. 16292 secs passed Thread #0: 10050000 reads finished. 16635 secs passed Thread #5: 10100000 reads finished. 16734 secs passed Thread #4: 10150000 reads finished. 16754 secs passed Thread #3: 10200000 reads finished. 16855 secs passed Thread #7: 10250000 reads finished. 16874 secs passed Thread #2: 10300000 reads finished. 16915 secs passed Thread #6: 10350000 reads finished. 16919 secs passed Thread #1: 10400000 reads finished. 16942 secs passed Thread #0: 10450000 reads finished. 17273 secs passed Thread #5: 10500000 reads finished. 17376 secs passed Thread #4: 10550000 reads finished. 17397 secs passed Thread #3: 10600000 reads finished. 17501 secs passed Thread #7: 10650000 reads finished. 17521 secs passed Thread #2: 10700000 reads finished. 17565 secs passed Thread #6: 10750000 reads finished. 17568 secs passed Thread #1: 10800000 reads finished. 17593 secs passed Thread #0: 10850000 reads finished. 17912 secs passed Thread #5: 10900000 reads finished. 18018 secs passed Thread #4: 10950000 reads finished. 18041 secs passed Thread #3: 11000000 reads finished. 18149 secs passed Thread #7: 11050000 reads finished. 18170 secs passed Thread #2: 11100000 reads finished. 18214 secs passed Thread #6: 11150000 reads finished. 18217 secs passed Thread #1: 11200000 reads finished. 18244 secs passed Thread #0: 11250000 reads finished. 18551 secs passed Thread #0: 11606618 reads finished. 18636 secs passed Thread #5: 11300000 reads finished. 18659 secs passed Thread #4: 11350000 reads finished. 18675 secs passed Thread #3: 11400000 reads finished. 18742 secs passed Thread #7: 11450000 reads finished. 18754 secs passed Thread #2: 11500000 reads finished. 18770 secs passed Thread #6: 11550000 reads finished. 18771 secs passed Thread #1: 11600000 reads finished. 18774 secs passed Total number of aligned reads: 2050966 (18%) Done. Finished at Mon Mar 12 05:46:05 2018 Total time consumed: 18774 secs BSMAP v2.74 Start at: Mon Mar 12 05:46:05 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly1k.fa (format: FASTA) Load in 159429 db seqs, total size 1140787867 bp. 11 secs passed total_kmers: 43046721 Create seed table. 42 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_jelly1k.sam (format: SAM) Thread #1: 100000 reads finished. 679 secs passed Thread #0: 300000 reads finished. 679 secs passed Thread #5: 200000 reads finished. 681 secs passed Thread #7: 250000 reads finished. 682 secs passed Thread #6: 350000 reads finished. 688 secs passed Thread #3: 400000 reads finished. 689 secs passed Thread #2: 50000 reads finished. 694 secs passed Thread #4: 150000 reads finished. 697 secs passed Thread #0: 500000 reads finished. 1316 secs passed Thread #1: 450000 reads finished. 1317 secs passed Thread #5: 550000 reads finished. 1321 secs passed Thread #7: 600000 reads finished. 1322 secs passed Thread #6: 650000 reads finished. 1333 secs passed Thread #3: 700000 reads finished. 1335 secs passed Thread #2: 750000 reads finished. 1347 secs passed Thread #4: 800000 reads finished. 1352 secs passed Thread #0: 850000 reads finished. 1953 secs passed Thread #1: 900000 reads finished. 1955 secs passed Thread #5: 950000 reads finished. 1959 secs passed Thread #7: 1000000 reads finished. 1961 secs passed Thread #6: 1050000 reads finished. 1979 secs passed Thread #3: 1100000 reads finished. 1980 secs passed Thread #2: 1150000 reads finished. 2000 secs passed Thread #4: 1200000 reads finished. 2005 secs passed Thread #0: 1250000 reads finished. 2589 secs passed Thread #1: 1300000 reads finished. 2593 secs passed Thread #5: 1350000 reads finished. 2598 secs passed Thread #7: 1400000 reads finished. 2600 secs passed Thread #6: 1450000 reads finished. 2625 secs passed Thread #3: 1500000 reads finished. 2626 secs passed Thread #2: 1550000 reads finished. 2652 secs passed Thread #4: 1600000 reads finished. 2660 secs passed Thread #0: 1650000 reads finished. 3227 secs passed Thread #1: 1700000 reads finished. 3230 secs passed Thread #5: 1750000 reads finished. 3237 secs passed Thread #7: 1800000 reads finished. 3239 secs passed Thread #6: 1850000 reads finished. 3270 secs passed Thread #3: 1900000 reads finished. 3272 secs passed Thread #2: 1950000 reads finished. 3304 secs passed Thread #4: 2000000 reads finished. 3314 secs passed Thread #0: 2050000 reads finished. 3863 secs passed Thread #1: 2100000 reads finished. 3867 secs passed Thread #5: 2150000 reads finished. 3876 secs passed Thread #7: 2200000 reads finished. 3879 secs passed Thread #6: 2250000 reads finished. 3915 secs passed Thread #3: 2300000 reads finished. 3917 secs passed Thread #2: 2350000 reads finished. 3957 secs passed Thread #4: 2400000 reads finished. 3969 secs passed Thread #0: 2450000 reads finished. 4500 secs passed Thread #1: 2500000 reads finished. 4504 secs passed Thread #5: 2550000 reads finished. 4515 secs passed Thread #7: 2600000 reads finished. 4519 secs passed Thread #6: 2650000 reads finished. 4561 secs passed Thread #3: 2700000 reads finished. 4563 secs passed Thread #2: 2750000 reads finished. 4610 secs passed Thread #4: 2800000 reads finished. 4624 secs passed Thread #0: 2850000 reads finished. 5135 secs passed Thread #1: 2900000 reads finished. 5142 secs passed Thread #5: 2950000 reads finished. 5155 secs passed Thread #7: 3000000 reads finished. 5158 secs passed Thread #6: 3050000 reads finished. 5206 secs passed Thread #3: 3100000 reads finished. 5209 secs passed Thread #2: 3150000 reads finished. 5263 secs passed Thread #4: 3200000 reads finished. 5279 secs passed Thread #0: 3250000 reads finished. 5772 secs passed Thread #1: 3300000 reads finished. 5780 secs passed Thread #5: 3350000 reads finished. 5794 secs passed Thread #7: 3400000 reads finished. 5797 secs passed Thread #6: 3450000 reads finished. 5850 secs passed Thread #3: 3500000 reads finished. 5855 secs passed Thread #2: 3550000 reads finished. 5916 secs passed Thread #4: 3600000 reads finished. 5932 secs passed Thread #0: 3650000 reads finished. 6408 secs passed Thread #1: 3700000 reads finished. 6417 secs passed Thread #5: 3750000 reads finished. 6433 secs passed Thread #7: 3800000 reads finished. 6435 secs passed Thread #6: 3850000 reads finished. 6496 secs passed Thread #3: 3900000 reads finished. 6500 secs passed Thread #2: 3950000 reads finished. 6568 secs passed Thread #4: 4000000 reads finished. 6586 secs passed Thread #0: 4050000 reads finished. 7044 secs passed Thread #1: 4100000 reads finished. 7054 secs passed Thread #5: 4150000 reads finished. 7072 secs passed Thread #7: 4200000 reads finished. 7074 secs passed Thread #6: 4250000 reads finished. 7141 secs passed Thread #3: 4300000 reads finished. 7146 secs passed Thread #2: 4350000 reads finished. 7220 secs passed Thread #4: 4400000 reads finished. 7240 secs passed Thread #0: 4450000 reads finished. 7681 secs passed Thread #1: 4500000 reads finished. 7694 secs passed Thread #7: 4600000 reads finished. 7713 secs passed Thread #5: 4550000 reads finished. 7720 secs passed Thread #6: 4650000 reads finished. 7787 secs passed Thread #3: 4700000 reads finished. 7790 secs passed Thread #2: 4750000 reads finished. 7871 secs passed Thread #4: 4800000 reads finished. 7893 secs passed Thread #0: 4850000 reads finished. 8317 secs passed Thread #1: 4900000 reads finished. 8332 secs passed Thread #7: 4950000 reads finished. 8353 secs passed Thread #5: 5000000 reads finished. 8359 secs passed Thread #6: 5050000 reads finished. 8432 secs passed Thread #3: 5100000 reads finished. 8437 secs passed Thread #2: 5150000 reads finished. 8525 secs passed Thread #4: 5200000 reads finished. 8548 secs passed Thread #0: 5250000 reads finished. 8959 secs passed Thread #1: 5300000 reads finished. 8973 secs passed Thread #7: 5350000 reads finished. 8996 secs passed Thread #5: 5400000 reads finished. 9002 secs passed Thread #6: 5450000 reads finished. 9082 secs passed Thread #3: 5500000 reads finished. 9087 secs passed Thread #2: 5550000 reads finished. 9182 secs passed Thread #4: 5600000 reads finished. 9207 secs passed Thread #0: 5650000 reads finished. 9597 secs passed Thread #1: 5700000 reads finished. 9611 secs passed Thread #7: 5750000 reads finished. 9635 secs passed Thread #5: 5800000 reads finished. 9642 secs passed Thread #6: 5850000 reads finished. 9729 secs passed Thread #3: 5900000 reads finished. 9733 secs passed Thread #2: 5950000 reads finished. 9836 secs passed Thread #4: 6000000 reads finished. 9863 secs passed Thread #0: 6050000 reads finished. 10234 secs passed Thread #1: 6100000 reads finished. 10248 secs passed Thread #7: 6150000 reads finished. 10274 secs passed Thread #5: 6200000 reads finished. 10281 secs passed Thread #6: 6250000 reads finished. 10373 secs passed Thread #3: 6300000 reads finished. 10379 secs passed Thread #2: 6350000 reads finished. 10491 secs passed Thread #4: 6400000 reads finished. 10520 secs passed Thread #0: 6450000 reads finished. 10870 secs passed Thread #1: 6500000 reads finished. 10885 secs passed Thread #7: 6550000 reads finished. 10912 secs passed Thread #5: 6600000 reads finished. 10921 secs passed Thread #6: 6650000 reads finished. 11018 secs passed Thread #3: 6700000 reads finished. 11025 secs passed Thread #2: 6750000 reads finished. 11147 secs passed Thread #4: 6800000 reads finished. 11177 secs passed Thread #0: 6850000 reads finished. 11507 secs passed Thread #1: 6900000 reads finished. 11524 secs passed Thread #7: 6950000 reads finished. 11551 secs passed Thread #5: 7000000 reads finished. 11559 secs passed Thread #6: 7050000 reads finished. 11663 secs passed Thread #3: 7100000 reads finished. 11670 secs passed Thread #2: 7150000 reads finished. 11800 secs passed Thread #4: 7200000 reads finished. 11833 secs passed Thread #0: 7250000 reads finished. 12145 secs passed Thread #1: 7300000 reads finished. 12162 secs passed Thread #7: 7350000 reads finished. 12189 secs passed Thread #5: 7400000 reads finished. 12198 secs passed Thread #6: 7450000 reads finished. 12308 secs passed Thread #3: 7500000 reads finished. 12316 secs passed Thread #2: 7550000 reads finished. 12457 secs passed Thread #4: 7600000 reads finished. 12492 secs passed Thread #0: 7650000 reads finished. 12781 secs passed Thread #1: 7700000 reads finished. 12802 secs passed Thread #7: 7750000 reads finished. 12827 secs passed Thread #5: 7800000 reads finished. 12835 secs passed Thread #6: 7850000 reads finished. 12955 secs passed Thread #3: 7900000 reads finished. 12962 secs passed Thread #2: 7950000 reads finished. 13112 secs passed Thread #4: 8000000 reads finished. 13149 secs passed Thread #0: 8050000 reads finished. 13416 secs passed Thread #1: 8100000 reads finished. 13439 secs passed Thread #7: 8150000 reads finished. 13466 secs passed Thread #5: 8200000 reads finished. 13472 secs passed Thread #6: 8250000 reads finished. 13601 secs passed Thread #3: 8300000 reads finished. 13611 secs passed Thread #2: 8350000 reads finished. 13770 secs passed Thread #4: 8400000 reads finished. 13805 secs passed Thread #0: 8450000 reads finished. 14054 secs passed Thread #1: 8500000 reads finished. 14076 secs passed Thread #7: 8550000 reads finished. 14102 secs passed Thread #5: 8600000 reads finished. 14109 secs passed Thread #6: 8650000 reads finished. 14245 secs passed Thread #3: 8700000 reads finished. 14256 secs passed Thread #2: 8750000 reads finished. 14424 secs passed Thread #4: 8800000 reads finished. 14462 secs passed Thread #0: 8850000 reads finished. 14690 secs passed Thread #1: 8900000 reads finished. 14715 secs passed Thread #7: 8950000 reads finished. 14741 secs passed Thread #5: 9000000 reads finished. 14748 secs passed Thread #6: 9050000 reads finished. 14890 secs passed Thread #3: 9100000 reads finished. 14900 secs passed Thread #2: 9150000 reads finished. 15077 secs passed Thread #4: 9200000 reads finished. 15118 secs passed Thread #0: 9250000 reads finished. 15324 secs passed Thread #1: 9300000 reads finished. 15351 secs passed Thread #7: 9350000 reads finished. 15381 secs passed Thread #5: 9400000 reads finished. 15390 secs passed Thread #6: 9450000 reads finished. 15538 secs passed Thread #3: 9500000 reads finished. 15549 secs passed Thread #2: 9550000 reads finished. 15730 secs passed Thread #4: 9600000 reads finished. 15773 secs passed Thread #0: 9650000 reads finished. 15959 secs passed Thread #1: 9700000 reads finished. 15988 secs passed Thread #7: 9750000 reads finished. 16020 secs passed Thread #5: 9800000 reads finished. 16028 secs passed Thread #6: 9850000 reads finished. 16183 secs passed Thread #3: 9900000 reads finished. 16196 secs passed Thread #2: 9950000 reads finished. 16384 secs passed Thread #4: 10000000 reads finished. 16429 secs passed Thread #0: 10050000 reads finished. 16596 secs passed Thread #1: 10100000 reads finished. 16627 secs passed Thread #7: 10150000 reads finished. 16660 secs passed Thread #5: 10200000 reads finished. 16666 secs passed Thread #6: 10250000 reads finished. 16827 secs passed Thread #3: 10300000 reads finished. 16840 secs passed Thread #2: 10350000 reads finished. 17039 secs passed Thread #4: 10400000 reads finished. 17085 secs passed Thread #0: 10450000 reads finished. 17232 secs passed Thread #1: 10500000 reads finished. 17265 secs passed Thread #7: 10550000 reads finished. 17299 secs passed Thread #5: 10600000 reads finished. 17305 secs passed Thread #6: 10650000 reads finished. 17472 secs passed Thread #3: 10700000 reads finished. 17486 secs passed Thread #2: 10750000 reads finished. 17694 secs passed Thread #4: 10800000 reads finished. 17742 secs passed Thread #0: 10850000 reads finished. 17868 secs passed Thread #1: 10900000 reads finished. 17901 secs passed Thread #7: 10950000 reads finished. 17938 secs passed Thread #5: 11000000 reads finished. 17944 secs passed Thread #6: 11050000 reads finished. 18117 secs passed Thread #3: 11100000 reads finished. 18132 secs passed Thread #2: 11150000 reads finished. 18351 secs passed Thread #4: 11200000 reads finished. 18402 secs passed Thread #0: 11250000 reads finished. 18508 secs passed Thread #1: 11300000 reads finished. 18543 secs passed Thread #7: 11350000 reads finished. 18581 secs passed Thread #5: 11400000 reads finished. 18587 secs passed Thread #6: 11450000 reads finished. 18768 secs passed Thread #3: 11500000 reads finished. 18783 secs passed Thread #2: 11550000 reads finished. 19011 secs passed Thread #4: 11600000 reads finished. 19063 secs passed Thread #0: 11650000 reads finished. 19146 secs passed Thread #1: 11700000 reads finished. 19184 secs passed Thread #7: 11750000 reads finished. 19222 secs passed Thread #5: 11800000 reads finished. 19228 secs passed Thread #6: 11850000 reads finished. 19415 secs passed Thread #3: 11900000 reads finished. 19430 secs passed Thread #2: 11950000 reads finished. 19668 secs passed Thread #4: 12000000 reads finished. 19721 secs passed Thread #0: 12050000 reads finished. 19782 secs passed Thread #1: 12100000 reads finished. 19823 secs passed Thread #7: 12150000 reads finished. 19861 secs passed Thread #5: 12200000 reads finished. 19867 secs passed Thread #6: 12250000 reads finished. 20061 secs passed Thread #3: 12300000 reads finished. 20075 secs passed Thread #2: 12350000 reads finished. 20255 secs passed Thread #5: 12589609 reads finished. 20290 secs passed Thread #4: 12400000 reads finished. 20290 secs passed Thread #0: 12450000 reads finished. 20305 secs passed Thread #1: 12500000 reads finished. 20315 secs passed Thread #7: 12550000 reads finished. 20319 secs passed Total number of aligned reads: 2156556 (17%) Done. Finished at Mon Mar 12 11:24:45 2018 Total time consumed: 20320 secs BSMAP v2.74 Start at: Mon Mar 12 11:24:45 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly1k.fa (format: FASTA) Load in 159429 db seqs, total size 1140787867 bp. 11 secs passed total_kmers: 43046721 Create seed table. 41 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_jelly1k.sam (format: SAM) Thread #5: 100000 reads finished. 673 secs passed Thread #4: 200000 reads finished. 675 secs passed Thread #6: 150000 reads finished. 677 secs passed Thread #7: 400000 reads finished. 679 secs passed Thread #1: 300000 reads finished. 682 secs passed Thread #0: 350000 reads finished. 693 secs passed Thread #3: 250000 reads finished. 707 secs passed Thread #2: 50000 reads finished. 724 secs passed Thread #5: 450000 reads finished. 1307 secs passed Thread #4: 500000 reads finished. 1310 secs passed Thread #6: 550000 reads finished. 1313 secs passed Thread #7: 600000 reads finished. 1317 secs passed Thread #1: 650000 reads finished. 1324 secs passed Thread #0: 700000 reads finished. 1344 secs passed Thread #3: 750000 reads finished. 1373 secs passed Thread #2: 800000 reads finished. 1411 secs passed Thread #5: 850000 reads finished. 1942 secs passed Thread #4: 900000 reads finished. 1946 secs passed Thread #6: 950000 reads finished. 1951 secs passed Thread #7: 1000000 reads finished. 1957 secs passed Thread #1: 1050000 reads finished. 1967 secs passed Thread #0: 1100000 reads finished. 1997 secs passed Thread #3: 1150000 reads finished. 2039 secs passed Thread #2: 1200000 reads finished. 2096 secs passed Thread #5: 1250000 reads finished. 2576 secs passed Thread #4: 1300000 reads finished. 2581 secs passed Thread #6: 1350000 reads finished. 2587 secs passed Thread #7: 1400000 reads finished. 2595 secs passed Thread #1: 1450000 reads finished. 2611 secs passed Thread #0: 1500000 reads finished. 2648 secs passed Thread #3: 1550000 reads finished. 2705 secs passed Thread #2: 1600000 reads finished. 2781 secs passed Thread #5: 1650000 reads finished. 3211 secs passed Thread #4: 1700000 reads finished. 3217 secs passed Thread #6: 1750000 reads finished. 3224 secs passed Thread #7: 1800000 reads finished. 3234 secs passed Thread #1: 1850000 reads finished. 3252 secs passed Thread #0: 1900000 reads finished. 3299 secs passed Thread #3: 1950000 reads finished. 3370 secs passed Thread #2: 2000000 reads finished. 3465 secs passed Thread #5: 2050000 reads finished. 3843 secs passed Thread #4: 2100000 reads finished. 3850 secs passed Thread #6: 2150000 reads finished. 3859 secs passed Thread #7: 2200000 reads finished. 3871 secs passed Thread #1: 2250000 reads finished. 3893 secs passed Thread #0: 2300000 reads finished. 3950 secs passed Thread #3: 2350000 reads finished. 4035 secs passed Thread #2: 2400000 reads finished. 4150 secs passed Thread #5: 2450000 reads finished. 4476 secs passed Thread #4: 2500000 reads finished. 4483 secs passed Thread #6: 2550000 reads finished. 4495 secs passed Thread #7: 2600000 reads finished. 4508 secs passed Thread #1: 2650000 reads finished. 4534 secs passed Thread #0: 2700000 reads finished. 4600 secs passed Thread #3: 2750000 reads finished. 4700 secs passed Thread #2: 2800000 reads finished. 4834 secs passed Thread #5: 2850000 reads finished. 5107 secs passed Thread #4: 2900000 reads finished. 5116 secs passed Thread #6: 2950000 reads finished. 5129 secs passed Thread #7: 3000000 reads finished. 5143 secs passed Thread #1: 3050000 reads finished. 5174 secs passed Thread #0: 3100000 reads finished. 5249 secs passed Thread #3: 3150000 reads finished. 5363 secs passed Thread #2: 3200000 reads finished. 5520 secs passed Thread #5: 3250000 reads finished. 5737 secs passed Thread #4: 3300000 reads finished. 5747 secs passed Thread #6: 3350000 reads finished. 5763 secs passed Thread #7: 3400000 reads finished. 5778 secs passed Thread #1: 3450000 reads finished. 5812 secs passed Thread #0: 3500000 reads finished. 5898 secs passed Thread #3: 3550000 reads finished. 6028 secs passed Thread #2: 3600000 reads finished. 6207 secs passed Thread #5: 3650000 reads finished. 6368 secs passed Thread #4: 3700000 reads finished. 6380 secs passed Thread #6: 3750000 reads finished. 6397 secs passed Thread #7: 3800000 reads finished. 6412 secs passed Thread #1: 3850000 reads finished. 6452 secs passed Thread #0: 3900000 reads finished. 6547 secs passed Thread #3: 3950000 reads finished. 6692 secs passed Thread #2: 4000000 reads finished. 6893 secs passed Thread #5: 4050000 reads finished. 6999 secs passed Thread #4: 4100000 reads finished. 7011 secs passed Thread #6: 4150000 reads finished. 7030 secs passed Thread #7: 4200000 reads finished. 7046 secs passed Thread #1: 4250000 reads finished. 7090 secs passed Thread #0: 4300000 reads finished. 7196 secs passed Thread #3: 4350000 reads finished. 7355 secs passed Thread #2: 4400000 reads finished. 7578 secs passed Thread #5: 4450000 reads finished. 7631 secs passed Thread #4: 4500000 reads finished. 7646 secs passed Thread #6: 4550000 reads finished. 7663 secs passed Thread #7: 4600000 reads finished. 7680 secs passed Thread #1: 4650000 reads finished. 7729 secs passed Thread #0: 4700000 reads finished. 7845 secs passed Thread #3: 4750000 reads finished. 8020 secs passed Thread #5: 4850000 reads finished. 8262 secs passed Thread #2: 4800000 reads finished. 8264 secs passed Thread #4: 4900000 reads finished. 8277 secs passed Thread #6: 4950000 reads finished. 8296 secs passed Thread #7: 5000000 reads finished. 8315 secs passed Thread #1: 5050000 reads finished. 8367 secs passed Thread #0: 5100000 reads finished. 8494 secs passed Thread #3: 5150000 reads finished. 8685 secs passed Thread #5: 5200000 reads finished. 8894 secs passed Thread #4: 5300000 reads finished. 8910 secs passed Thread #6: 5350000 reads finished. 8931 secs passed Thread #7: 5400000 reads finished. 8951 secs passed Thread #2: 5250000 reads finished. 8951 secs passed Thread #1: 5450000 reads finished. 9007 secs passed Thread #0: 5500000 reads finished. 9145 secs passed Thread #3: 5550000 reads finished. 9350 secs passed Thread #5: 5600000 reads finished. 9524 secs passed Thread #4: 5650000 reads finished. 9542 secs passed Thread #6: 5700000 reads finished. 9565 secs passed Thread #7: 5750000 reads finished. 9587 secs passed Thread #2: 5800000 reads finished. 9637 secs passed Thread #1: 5850000 reads finished. 9646 secs passed Thread #0: 5900000 reads finished. 9795 secs passed Thread #3: 5950000 reads finished. 10014 secs passed Thread #5: 6000000 reads finished. 10155 secs passed Thread #4: 6050000 reads finished. 10174 secs passed Thread #6: 6100000 reads finished. 10199 secs passed Thread #7: 6150000 reads finished. 10223 secs passed Thread #1: 6250000 reads finished. 10286 secs passed Thread #2: 6200000 reads finished. 10322 secs passed Thread #0: 6300000 reads finished. 10444 secs passed Thread #3: 6350000 reads finished. 10679 secs passed Thread #5: 6400000 reads finished. 10786 secs passed Thread #4: 6450000 reads finished. 10806 secs passed Thread #6: 6500000 reads finished. 10834 secs passed Thread #7: 6550000 reads finished. 10859 secs passed Thread #1: 6600000 reads finished. 10924 secs passed Thread #2: 6650000 reads finished. 11009 secs passed Thread #0: 6700000 reads finished. 11093 secs passed Thread #3: 6750000 reads finished. 11345 secs passed Thread #5: 6800000 reads finished. 11418 secs passed Thread #4: 6850000 reads finished. 11438 secs passed Thread #6: 6900000 reads finished. 11469 secs passed Thread #7: 6950000 reads finished. 11494 secs passed Thread #1: 7000000 reads finished. 11565 secs passed Thread #2: 7050000 reads finished. 11695 secs passed Thread #0: 7100000 reads finished. 11743 secs passed Thread #3: 7150000 reads finished. 12012 secs passed Thread #5: 7200000 reads finished. 12051 secs passed Thread #4: 7250000 reads finished. 12070 secs passed Thread #6: 7300000 reads finished. 12102 secs passed Thread #7: 7350000 reads finished. 12128 secs passed Thread #1: 7400000 reads finished. 12204 secs passed Thread #2: 7450000 reads finished. 12383 secs passed Thread #0: 7500000 reads finished. 12396 secs passed Thread #3: 7550000 reads finished. 12677 secs passed Thread #5: 7600000 reads finished. 12687 secs passed Thread #4: 7650000 reads finished. 12700 secs passed Thread #6: 7700000 reads finished. 12735 secs passed Thread #7: 7750000 reads finished. 12765 secs passed Thread #1: 7800000 reads finished. 12845 secs passed Thread #0: 7900000 reads finished. 13046 secs passed Thread #2: 7850000 reads finished. 13069 secs passed Thread #5: 8000000 reads finished. 13317 secs passed Thread #4: 8050000 reads finished. 13332 secs passed Thread #3: 7950000 reads finished. 13340 secs passed Thread #6: 8100000 reads finished. 13368 secs passed Thread #7: 8150000 reads finished. 13400 secs passed Thread #1: 8200000 reads finished. 13486 secs passed Thread #0: 8250000 reads finished. 13701 secs passed Thread #2: 8300000 reads finished. 13756 secs passed Thread #5: 8350000 reads finished. 13950 secs passed Thread #4: 8400000 reads finished. 13966 secs passed Thread #6: 8500000 reads finished. 14001 secs passed Thread #3: 8450000 reads finished. 14004 secs passed Thread #7: 8550000 reads finished. 14034 secs passed Thread #1: 8600000 reads finished. 14125 secs passed Thread #0: 8650000 reads finished. 14350 secs passed Thread #2: 8700000 reads finished. 14440 secs passed Thread #5: 8750000 reads finished. 14582 secs passed Thread #4: 8800000 reads finished. 14598 secs passed Thread #6: 8850000 reads finished. 14634 secs passed Thread #3: 8900000 reads finished. 14667 secs passed Thread #7: 8950000 reads finished. 14670 secs passed Thread #1: 9000000 reads finished. 14763 secs passed Thread #0: 9050000 reads finished. 14999 secs passed Thread #2: 9100000 reads finished. 15124 secs passed Thread #5: 9150000 reads finished. 15212 secs passed Thread #4: 9200000 reads finished. 15229 secs passed Thread #6: 9250000 reads finished. 15269 secs passed Thread #7: 9350000 reads finished. 15310 secs passed Thread #3: 9300000 reads finished. 15336 secs passed Thread #1: 9400000 reads finished. 15407 secs passed Thread #0: 9450000 reads finished. 15649 secs passed Thread #2: 9500000 reads finished. 15810 secs passed Thread #5: 9550000 reads finished. 15843 secs passed Thread #4: 9600000 reads finished. 15861 secs passed Thread #6: 9650000 reads finished. 15904 secs passed Thread #7: 9700000 reads finished. 15945 secs passed Thread #3: 9750000 reads finished. 16001 secs passed Thread #1: 9800000 reads finished. 16046 secs passed Thread #0: 9850000 reads finished. 16300 secs passed Thread #5: 9950000 reads finished. 16476 secs passed Thread #4: 10000000 reads finished. 16496 secs passed Thread #2: 9900000 reads finished. 16496 secs passed Thread #6: 10050000 reads finished. 16539 secs passed Thread #7: 10100000 reads finished. 16581 secs passed Thread #3: 10150000 reads finished. 16665 secs passed Thread #1: 10200000 reads finished. 16684 secs passed Thread #0: 10250000 reads finished. 16948 secs passed Thread #5: 10300000 reads finished. 17107 secs passed Thread #4: 10350000 reads finished. 17128 secs passed Thread #6: 10450000 reads finished. 17174 secs passed Thread #2: 10400000 reads finished. 17182 secs passed Thread #7: 10500000 reads finished. 17217 secs passed Thread #1: 10600000 reads finished. 17325 secs passed Thread #3: 10550000 reads finished. 17330 secs passed Thread #0: 10650000 reads finished. 17600 secs passed Thread #5: 10700000 reads finished. 17739 secs passed Thread #4: 10750000 reads finished. 17761 secs passed Thread #6: 10800000 reads finished. 17808 secs passed Thread #7: 10900000 reads finished. 17854 secs passed Thread #2: 10850000 reads finished. 17867 secs passed Thread #1: 10950000 reads finished. 17965 secs passed Thread #3: 11000000 reads finished. 17995 secs passed Thread #0: 11050000 reads finished. 18250 secs passed Thread #5: 11100000 reads finished. 18371 secs passed Thread #4: 11150000 reads finished. 18394 secs passed Thread #6: 11200000 reads finished. 18443 secs passed Thread #7: 11250000 reads finished. 18489 secs passed Thread #2: 11300000 reads finished. 18553 secs passed Thread #1: 11350000 reads finished. 18605 secs passed Thread #3: 11400000 reads finished. 18660 secs passed Thread #0: 11450000 reads finished. 18900 secs passed Thread #5: 11500000 reads finished. 19002 secs passed Thread #4: 11550000 reads finished. 19027 secs passed Thread #6: 11600000 reads finished. 19077 secs passed Thread #7: 11650000 reads finished. 19125 secs passed Thread #2: 11700000 reads finished. 19240 secs passed Thread #1: 11750000 reads finished. 19245 secs passed Thread #3: 11800000 reads finished. 19325 secs passed Thread #0: 11850000 reads finished. 19551 secs passed Thread #5: 11900000 reads finished. 19633 secs passed Thread #4: 11950000 reads finished. 19660 secs passed Thread #6: 12000000 reads finished. 19711 secs passed Thread #7: 12050000 reads finished. 19759 secs passed Thread #1: 12150000 reads finished. 19884 secs passed Thread #2: 12100000 reads finished. 19925 secs passed Thread #3: 12200000 reads finished. 19981 secs passed Thread #0: 12250000 reads finished. 20140 secs passed Thread #5: 12300000 reads finished. 20180 secs passed Thread #4: 12350000 reads finished. 20193 secs passed Thread #6: 12400000 reads finished. 20213 secs passed Thread #1: 12489766 reads finished. 20225 secs passed Thread #7: 12450000 reads finished. 20225 secs passed Total number of aligned reads: 2116418 (17%) Done. Finished at Mon Mar 12 17:01:50 2018 Total time consumed: 20225 secs BSMAP v2.74 Start at: Mon Mar 12 17:01:50 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly1k.fa (format: FASTA) Load in 159429 db seqs, total size 1140787867 bp. 11 secs passed total_kmers: 43046721 Create seed table. 42 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_jelly1k.sam (format: SAM) Thread #4: 350000 reads finished. 681 secs passed Thread #2: 200000 reads finished. 682 secs passed Thread #6: 100000 reads finished. 682 secs passed Thread #1: 250000 reads finished. 686 secs passed Thread #0: 400000 reads finished. 686 secs passed Thread #5: 150000 reads finished. 691 secs passed Thread #7: 300000 reads finished. 692 secs passed Thread #3: 50000 reads finished. 712 secs passed Thread #4: 450000 reads finished. 1319 secs passed Thread #2: 500000 reads finished. 1321 secs passed Thread #6: 550000 reads finished. 1324 secs passed Thread #1: 600000 reads finished. 1329 secs passed Thread #0: 650000 reads finished. 1329 secs passed Thread #5: 700000 reads finished. 1340 secs passed Thread #7: 750000 reads finished. 1342 secs passed Thread #3: 800000 reads finished. 1384 secs passed Thread #4: 850000 reads finished. 1958 secs passed Thread #2: 900000 reads finished. 1960 secs passed Thread #6: 950000 reads finished. 1966 secs passed Thread #0: 1050000 reads finished. 1972 secs passed Thread #1: 1000000 reads finished. 1972 secs passed Thread #5: 1100000 reads finished. 1988 secs passed Thread #7: 1150000 reads finished. 1992 secs passed Thread #3: 1200000 reads finished. 2058 secs passed Thread #4: 1250000 reads finished. 2596 secs passed Thread #2: 1300000 reads finished. 2599 secs passed Thread #6: 1350000 reads finished. 2608 secs passed Thread #0: 1400000 reads finished. 2615 secs passed Thread #1: 1450000 reads finished. 2615 secs passed Thread #5: 1500000 reads finished. 2638 secs passed Thread #7: 1550000 reads finished. 2642 secs passed Thread #3: 1600000 reads finished. 2730 secs passed Thread #4: 1650000 reads finished. 3233 secs passed Thread #2: 1700000 reads finished. 3239 secs passed Thread #6: 1750000 reads finished. 3250 secs passed Thread #1: 1850000 reads finished. 3258 secs passed Thread #0: 1800000 reads finished. 3258 secs passed Thread #5: 1900000 reads finished. 3287 secs passed Thread #7: 1950000 reads finished. 3293 secs passed Thread #3: 2000000 reads finished. 3403 secs passed Thread #4: 2050000 reads finished. 3872 secs passed Thread #2: 2100000 reads finished. 3878 secs passed Thread #6: 2150000 reads finished. 3892 secs passed Thread #1: 2200000 reads finished. 3901 secs passed Thread #0: 2250000 reads finished. 3902 secs passed Thread #5: 2300000 reads finished. 3936 secs passed Thread #7: 2350000 reads finished. 3943 secs passed Thread #3: 2400000 reads finished. 4076 secs passed Thread #4: 2450000 reads finished. 4510 secs passed Thread #2: 2500000 reads finished. 4518 secs passed Thread #6: 2550000 reads finished. 4534 secs passed Thread #1: 2600000 reads finished. 4544 secs passed Thread #0: 2650000 reads finished. 4545 secs passed Thread #5: 2700000 reads finished. 4585 secs passed Thread #7: 2750000 reads finished. 4593 secs passed Thread #3: 2800000 reads finished. 4748 secs passed Thread #4: 2850000 reads finished. 5148 secs passed Thread #2: 2900000 reads finished. 5157 secs passed Thread #6: 2950000 reads finished. 5175 secs passed Thread #1: 3000000 reads finished. 5187 secs passed Thread #0: 3050000 reads finished. 5189 secs passed Thread #5: 3100000 reads finished. 5234 secs passed Thread #7: 3150000 reads finished. 5243 secs passed Thread #3: 3200000 reads finished. 5421 secs passed Thread #4: 3250000 reads finished. 5787 secs passed Thread #2: 3300000 reads finished. 5797 secs passed Thread #6: 3350000 reads finished. 5816 secs passed Thread #1: 3400000 reads finished. 5830 secs passed Thread #0: 3450000 reads finished. 5831 secs passed Thread #5: 3500000 reads finished. 5883 secs passed Thread #7: 3550000 reads finished. 5893 secs passed Thread #3: 3600000 reads finished. 6093 secs passed Thread #4: 3650000 reads finished. 6425 secs passed Thread #2: 3700000 reads finished. 6438 secs passed Thread #6: 3750000 reads finished. 6458 secs passed Thread #1: 3800000 reads finished. 6473 secs passed Thread #0: 3850000 reads finished. 6474 secs passed Thread #5: 3900000 reads finished. 6532 secs passed Thread #7: 3950000 reads finished. 6543 secs passed Thread #3: 4000000 reads finished. 6766 secs passed Thread #4: 4050000 reads finished. 7064 secs passed Thread #2: 4100000 reads finished. 7077 secs passed Thread #6: 4150000 reads finished. 7100 secs passed Thread #0: 4250000 reads finished. 7117 secs passed Thread #1: 4200000 reads finished. 7117 secs passed Thread #5: 4300000 reads finished. 7181 secs passed Thread #7: 4350000 reads finished. 7193 secs passed Thread #3: 4400000 reads finished. 7439 secs passed Thread #4: 4450000 reads finished. 7702 secs passed Thread #2: 4500000 reads finished. 7716 secs passed Thread #6: 4550000 reads finished. 7741 secs passed Thread #1: 4650000 reads finished. 7761 secs passed Thread #0: 4600000 reads finished. 7761 secs passed Thread #5: 4700000 reads finished. 7830 secs passed Thread #7: 4750000 reads finished. 7844 secs passed Thread #3: 4800000 reads finished. 8112 secs passed Thread #4: 4850000 reads finished. 8341 secs passed Thread #2: 4900000 reads finished. 8356 secs passed Thread #6: 4950000 reads finished. 8385 secs passed Thread #0: 5050000 reads finished. 8404 secs passed Thread #1: 5000000 reads finished. 8404 secs passed Thread #5: 5100000 reads finished. 8479 secs passed Thread #7: 5150000 reads finished. 8494 secs passed Thread #3: 5200000 reads finished. 8784 secs passed Thread #4: 5250000 reads finished. 8979 secs passed Thread #2: 5300000 reads finished. 8995 secs passed Thread #6: 5350000 reads finished. 9027 secs passed Thread #0: 5400000 reads finished. 9047 secs passed Thread #1: 5450000 reads finished. 9048 secs passed Thread #5: 5500000 reads finished. 9128 secs passed Thread #7: 5550000 reads finished. 9145 secs passed Thread #3: 5600000 reads finished. 9456 secs passed Thread #4: 5650000 reads finished. 9617 secs passed Thread #2: 5700000 reads finished. 9634 secs passed Thread #6: 5750000 reads finished. 9669 secs passed Thread #0: 5800000 reads finished. 9690 secs passed Thread #1: 5850000 reads finished. 9692 secs passed Thread #5: 5900000 reads finished. 9779 secs passed Thread #7: 5950000 reads finished. 9796 secs passed Thread #3: 6000000 reads finished. 10127 secs passed Thread #4: 6050000 reads finished. 10255 secs passed Thread #2: 6100000 reads finished. 10273 secs passed Thread #6: 6150000 reads finished. 10314 secs passed Thread #0: 6200000 reads finished. 10334 secs passed Thread #1: 6250000 reads finished. 10339 secs passed Thread #5: 6300000 reads finished. 10427 secs passed Thread #7: 6350000 reads finished. 10446 secs passed Thread #3: 6400000 reads finished. 10802 secs passed Thread #4: 6450000 reads finished. 10893 secs passed Thread #2: 6500000 reads finished. 10914 secs passed Thread #6: 6550000 reads finished. 10956 secs passed Thread #0: 6600000 reads finished. 10977 secs passed Thread #1: 6650000 reads finished. 10983 secs passed Thread #5: 6700000 reads finished. 11076 secs passed Thread #7: 6750000 reads finished. 11099 secs passed Thread #3: 6800000 reads finished. 11479 secs passed Thread #4: 6850000 reads finished. 11532 secs passed Thread #2: 6900000 reads finished. 11556 secs passed Thread #6: 6950000 reads finished. 11598 secs passed Thread #0: 7000000 reads finished. 11619 secs passed Thread #1: 7050000 reads finished. 11625 secs passed Thread #5: 7100000 reads finished. 11725 secs passed Thread #7: 7150000 reads finished. 11748 secs passed Thread #3: 7200000 reads finished. 12151 secs passed Thread #4: 7250000 reads finished. 12171 secs passed Thread #2: 7300000 reads finished. 12195 secs passed Thread #6: 7350000 reads finished. 12239 secs passed Thread #0: 7400000 reads finished. 12261 secs passed Thread #1: 7450000 reads finished. 12268 secs passed Thread #5: 7500000 reads finished. 12373 secs passed Thread #7: 7550000 reads finished. 12398 secs passed Thread #4: 7650000 reads finished. 12814 secs passed Thread #3: 7600000 reads finished. 12825 secs passed Thread #2: 7700000 reads finished. 12839 secs passed Thread #6: 7750000 reads finished. 12884 secs passed Thread #0: 7800000 reads finished. 12904 secs passed Thread #1: 7850000 reads finished. 12910 secs passed Thread #5: 7900000 reads finished. 13022 secs passed Thread #7: 7950000 reads finished. 13049 secs passed Thread #4: 8000000 reads finished. 13453 secs passed Thread #2: 8100000 reads finished. 13479 secs passed Thread #3: 8050000 reads finished. 13498 secs passed Thread #6: 8150000 reads finished. 13527 secs passed Thread #0: 8200000 reads finished. 13548 secs passed Thread #1: 8250000 reads finished. 13555 secs passed Thread #5: 8300000 reads finished. 13673 secs passed Thread #7: 8350000 reads finished. 13698 secs passed Thread #4: 8400000 reads finished. 14091 secs passed Thread #2: 8450000 reads finished. 14118 secs passed Thread #6: 8550000 reads finished. 14169 secs passed Thread #3: 8500000 reads finished. 14171 secs passed Thread #0: 8600000 reads finished. 14191 secs passed Thread #1: 8650000 reads finished. 14198 secs passed Thread #5: 8700000 reads finished. 14322 secs passed Thread #7: 8750000 reads finished. 14349 secs passed Thread #4: 8800000 reads finished. 14729 secs passed Thread #2: 8850000 reads finished. 14757 secs passed Thread #6: 8900000 reads finished. 14811 secs passed Thread #0: 9000000 reads finished. 14835 secs passed Thread #1: 9050000 reads finished. 14841 secs passed Thread #3: 8950000 reads finished. 14843 secs passed Thread #5: 9100000 reads finished. 14971 secs passed Thread #7: 9150000 reads finished. 14999 secs passed Thread #4: 9200000 reads finished. 15368 secs passed Thread #2: 9250000 reads finished. 15396 secs passed Thread #6: 9300000 reads finished. 15453 secs passed Thread #0: 9350000 reads finished. 15479 secs passed Thread #1: 9400000 reads finished. 15486 secs passed Thread #3: 9450000 reads finished. 15516 secs passed Thread #5: 9500000 reads finished. 15620 secs passed Thread #7: 9550000 reads finished. 15650 secs passed Thread #4: 9600000 reads finished. 16007 secs passed Thread #2: 9650000 reads finished. 16036 secs passed Thread #6: 9700000 reads finished. 16095 secs passed Thread #0: 9750000 reads finished. 16123 secs passed Thread #1: 9800000 reads finished. 16129 secs passed Thread #3: 9850000 reads finished. 16189 secs passed Thread #5: 9900000 reads finished. 16270 secs passed Thread #7: 9950000 reads finished. 16301 secs passed Thread #4: 10000000 reads finished. 16601 secs passed Thread #2: 10050000 reads finished. 16623 secs passed Thread #6: 10100000 reads finished. 16661 secs passed Thread #0: 10150000 reads finished. 16675 secs passed Thread #1: 10200000 reads finished. 16677 secs passed Thread #5: 10295293 reads finished. 16698 secs passed Thread #3: 10250000 reads finished. 16698 secs passed Total number of aligned reads: 1804355 (18%) Done. Finished at Mon Mar 12 21:40:08 2018 Total time consumed: 16698 secs BSMAP v2.74 Start at: Mon Mar 12 21:40:08 2018 Input reference file: /Volumes/Serine/wd/18-03-07/Ol-pbjelly1k.fa (format: FASTA) Load in 159429 db seqs, total size 1140787867 bp. 11 secs passed total_kmers: 43046721 Create seed table. 43 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_jelly1k.sam (format: SAM) Thread #0: 150000 reads finished. 677 secs passed Thread #1: 50000 reads finished. 678 secs passed Thread #5: 200000 reads finished. 680 secs passed Thread #2: 250000 reads finished. 687 secs passed Thread #3: 300000 reads finished. 687 secs passed Thread #4: 100000 reads finished. 693 secs passed Thread #7: 400000 reads finished. 699 secs passed Thread #6: 350000 reads finished. 709 secs passed Thread #0: 450000 reads finished. 1310 secs passed Thread #1: 500000 reads finished. 1316 secs passed Thread #5: 550000 reads finished. 1316 secs passed Thread #2: 600000 reads finished. 1329 secs passed Thread #3: 650000 reads finished. 1330 secs passed Thread #4: 700000 reads finished. 1343 secs passed Thread #7: 750000 reads finished. 1352 secs passed Thread #6: 800000 reads finished. 1373 secs passed Thread #0: 850000 reads finished. 1944 secs passed Thread #5: 950000 reads finished. 1952 secs passed Thread #1: 900000 reads finished. 1954 secs passed Thread #2: 1000000 reads finished. 1971 secs passed Thread #3: 1050000 reads finished. 1973 secs passed Thread #4: 1100000 reads finished. 1993 secs passed Thread #7: 1150000 reads finished. 2005 secs passed Thread #6: 1200000 reads finished. 2038 secs passed Thread #0: 1250000 reads finished. 2578 secs passed Thread #5: 1300000 reads finished. 2589 secs passed Thread #1: 1350000 reads finished. 2591 secs passed Thread #2: 1400000 reads finished. 2614 secs passed Thread #3: 1450000 reads finished. 2616 secs passed Thread #4: 1500000 reads finished. 2643 secs passed Thread #7: 1550000 reads finished. 2659 secs passed Thread #6: 1600000 reads finished. 2702 secs passed Thread #0: 1650000 reads finished. 3213 secs passed Thread #5: 1700000 reads finished. 3226 secs passed Thread #1: 1750000 reads finished. 3230 secs passed Thread #2: 1800000 reads finished. 3258 secs passed Thread #3: 1850000 reads finished. 3260 secs passed Thread #4: 1900000 reads finished. 3293 secs passed Thread #7: 1950000 reads finished. 3314 secs passed Thread #6: 2000000 reads finished. 3367 secs passed Thread #0: 2050000 reads finished. 3847 secs passed Thread #5: 2100000 reads finished. 3863 secs passed Thread #1: 2150000 reads finished. 3867 secs passed Thread #2: 2200000 reads finished. 3900 secs passed Thread #3: 2250000 reads finished. 3903 secs passed Thread #4: 2300000 reads finished. 3943 secs passed Thread #7: 2350000 reads finished. 3968 secs passed Thread #6: 2400000 reads finished. 4031 secs passed Thread #0: 2450000 reads finished. 4484 secs passed Thread #5: 2500000 reads finished. 4501 secs passed Thread #1: 2550000 reads finished. 4507 secs passed Thread #2: 2600000 reads finished. 4544 secs passed Thread #3: 2650000 reads finished. 4549 secs passed Thread #4: 2700000 reads finished. 4596 secs passed Thread #7: 2750000 reads finished. 4625 secs passed Thread #6: 2800000 reads finished. 4699 secs passed Thread #0: 2850000 reads finished. 5120 secs passed Thread #5: 2900000 reads finished. 5139 secs passed Thread #1: 2950000 reads finished. 5147 secs passed Thread #2: 3000000 reads finished. 5188 secs passed Thread #3: 3050000 reads finished. 5195 secs passed Thread #4: 3100000 reads finished. 5249 secs passed Thread #7: 3150000 reads finished. 5282 secs passed Thread #6: 3200000 reads finished. 5365 secs passed Thread #0: 3250000 reads finished. 5754 secs passed Thread #5: 3300000 reads finished. 5776 secs passed Thread #1: 3350000 reads finished. 5785 secs passed Thread #2: 3400000 reads finished. 5831 secs passed Thread #3: 3450000 reads finished. 5839 secs passed Thread #4: 3500000 reads finished. 5900 secs passed Thread #7: 3550000 reads finished. 5936 secs passed Thread #6: 3600000 reads finished. 6029 secs passed Thread #0: 3650000 reads finished. 6388 secs passed Thread #5: 3700000 reads finished. 6411 secs passed Thread #1: 3750000 reads finished. 6422 secs passed Thread #2: 3800000 reads finished. 6473 secs passed Thread #3: 3850000 reads finished. 6482 secs passed Thread #4: 3900000 reads finished. 6550 secs passed Thread #7: 3950000 reads finished. 6589 secs passed Thread #6: 4000000 reads finished. 6694 secs passed Thread #0: 4050000 reads finished. 7022 secs passed Thread #5: 4100000 reads finished. 7047 secs passed Thread #1: 4150000 reads finished. 7060 secs passed Thread #2: 4200000 reads finished. 7115 secs passed Thread #3: 4250000 reads finished. 7124 secs passed Thread #4: 4300000 reads finished. 7201 secs passed Thread #7: 4350000 reads finished. 7243 secs passed Thread #6: 4400000 reads finished. 7358 secs passed Thread #0: 4450000 reads finished. 7655 secs passed Thread #5: 4500000 reads finished. 7683 secs passed Thread #1: 4550000 reads finished. 7698 secs passed Thread #2: 4600000 reads finished. 7757 secs passed Thread #3: 4650000 reads finished. 7766 secs passed Thread #4: 4700000 reads finished. 7850 secs passed Thread #7: 4750000 reads finished. 7896 secs passed Thread #6: 4800000 reads finished. 8022 secs passed Thread #0: 4850000 reads finished. 8288 secs passed Thread #5: 4900000 reads finished. 8319 secs passed Thread #1: 4950000 reads finished. 8334 secs passed Thread #2: 5000000 reads finished. 8398 secs passed Thread #3: 5050000 reads finished. 8408 secs passed Thread #4: 5100000 reads finished. 8503 secs passed Thread #7: 5150000 reads finished. 8552 secs passed Thread #6: 5200000 reads finished. 8687 secs passed Thread #0: 5250000 reads finished. 8923 secs passed Thread #5: 5300000 reads finished. 8956 secs passed Thread #1: 5350000 reads finished. 8973 secs passed Thread #2: 5400000 reads finished. 9042 secs passed Thread #3: 5450000 reads finished. 9052 secs passed Thread #4: 5500000 reads finished. 9154 secs passed Thread #7: 5550000 reads finished. 9207 secs passed Thread #6: 5600000 reads finished. 9352 secs passed Thread #0: 5650000 reads finished. 9559 secs passed Thread #5: 5700000 reads finished. 9595 secs passed Thread #1: 5750000 reads finished. 9613 secs passed Thread #2: 5800000 reads finished. 9686 secs passed Thread #3: 5850000 reads finished. 9697 secs passed Thread #4: 5900000 reads finished. 9806 secs passed Thread #7: 5950000 reads finished. 9863 secs passed Thread #6: 6000000 reads finished. 10017 secs passed Thread #0: 6050000 reads finished. 10194 secs passed Thread #5: 6100000 reads finished. 10233 secs passed Thread #1: 6150000 reads finished. 10253 secs passed Thread #2: 6200000 reads finished. 10328 secs passed Thread #3: 6250000 reads finished. 10341 secs passed Thread #4: 6300000 reads finished. 10457 secs passed Thread #7: 6350000 reads finished. 10517 secs passed Thread #6: 6400000 reads finished. 10682 secs passed Thread #0: 6450000 reads finished. 10829 secs passed Thread #5: 6500000 reads finished. 10871 secs passed Thread #1: 6550000 reads finished. 10891 secs passed Thread #2: 6600000 reads finished. 10971 secs passed Thread #3: 6650000 reads finished. 10984 secs passed Thread #4: 6700000 reads finished. 11108 secs passed Thread #7: 6750000 reads finished. 11171 secs passed Thread #6: 6800000 reads finished. 11348 secs passed Thread #0: 6850000 reads finished. 11464 secs passed Thread #5: 6900000 reads finished. 11508 secs passed Thread #1: 6950000 reads finished. 11530 secs passed Thread #2: 7000000 reads finished. 11614 secs passed Thread #3: 7050000 reads finished. 11629 secs passed Thread #4: 7100000 reads finished. 11759 secs passed Thread #7: 7150000 reads finished. 11826 secs passed Thread #6: 7200000 reads finished. 12012 secs passed Thread #0: 7250000 reads finished. 12100 secs passed Thread #5: 7300000 reads finished. 12146 secs passed Thread #1: 7350000 reads finished. 12169 secs passed Thread #2: 7400000 reads finished. 12258 secs passed Thread #3: 7450000 reads finished. 12273 secs passed Thread #4: 7500000 reads finished. 12410 secs passed Thread #7: 7550000 reads finished. 12480 secs passed Thread #6: 7600000 reads finished. 12677 secs passed Thread #0: 7650000 reads finished. 12735 secs passed Thread #5: 7700000 reads finished. 12785 secs passed Thread #1: 7750000 reads finished. 12808 secs passed Thread #2: 7800000 reads finished. 12903 secs passed Thread #3: 7850000 reads finished. 12918 secs passed Thread #4: 7900000 reads finished. 13062 secs passed Thread #7: 7950000 reads finished. 13135 secs passed Thread #6: 8000000 reads finished. 13341 secs passed Thread #0: 8050000 reads finished. 13369 secs passed Thread #5: 8100000 reads finished. 13422 secs passed Thread #1: 8150000 reads finished. 13447 secs passed Thread #2: 8200000 reads finished. 13548 secs passed Thread #3: 8250000 reads finished. 13563 secs passed Thread #4: 8300000 reads finished. 13713 secs passed Thread #7: 8350000 reads finished. 13790 secs passed Thread #0: 8450000 reads finished. 14004 secs passed Thread #6: 8400000 reads finished. 14005 secs passed Thread #5: 8500000 reads finished. 14060 secs passed Thread #1: 8550000 reads finished. 14088 secs passed Thread #2: 8600000 reads finished. 14193 secs passed Thread #3: 8650000 reads finished. 14207 secs passed Thread #4: 8700000 reads finished. 14368 secs passed Thread #7: 8750000 reads finished. 14444 secs passed Thread #0: 8800000 reads finished. 14637 secs passed Thread #6: 8850000 reads finished. 14671 secs passed Thread #5: 8900000 reads finished. 14698 secs passed Thread #1: 8950000 reads finished. 14727 secs passed Thread #2: 9000000 reads finished. 14837 secs passed Thread #3: 9050000 reads finished. 14852 secs passed Thread #4: 9100000 reads finished. 15018 secs passed Thread #7: 9150000 reads finished. 15099 secs passed Thread #0: 9200000 reads finished. 15272 secs passed Thread #5: 9300000 reads finished. 15336 secs passed Thread #6: 9250000 reads finished. 15338 secs passed Thread #1: 9350000 reads finished. 15368 secs passed Thread #2: 9400000 reads finished. 15483 secs passed Thread #3: 9450000 reads finished. 15501 secs passed Thread #4: 9500000 reads finished. 15673 secs passed Thread #7: 9550000 reads finished. 15757 secs passed Thread #0: 9600000 reads finished. 15912 secs passed Thread #5: 9650000 reads finished. 15976 secs passed Thread #6: 9700000 reads finished. 16003 secs passed Thread #1: 9750000 reads finished. 16007 secs passed Thread #2: 9800000 reads finished. 16128 secs passed Thread #3: 9850000 reads finished. 16146 secs passed Thread #4: 9900000 reads finished. 16325 secs passed Thread #7: 9950000 reads finished. 16413 secs passed Thread #0: 10000000 reads finished. 16547 secs passed Thread #5: 10050000 reads finished. 16614 secs passed Thread #1: 10150000 reads finished. 16646 secs passed Thread #6: 10100000 reads finished. 16670 secs passed Thread #2: 10200000 reads finished. 16772 secs passed Thread #3: 10250000 reads finished. 16792 secs passed Thread #4: 10300000 reads finished. 16977 secs passed Thread #7: 10350000 reads finished. 17068 secs passed Thread #0: 10400000 reads finished. 17180 secs passed Thread #5: 10450000 reads finished. 17250 secs passed Thread #1: 10500000 reads finished. 17283 secs passed Thread #6: 10550000 reads finished. 17336 secs passed Thread #2: 10600000 reads finished. 17415 secs passed Thread #3: 10650000 reads finished. 17439 secs passed Thread #4: 10700000 reads finished. 17633 secs passed Thread #7: 10750000 reads finished. 17726 secs passed Thread #0: 10800000 reads finished. 17818 secs passed Thread #5: 10850000 reads finished. 17886 secs passed Thread #1: 10900000 reads finished. 17919 secs passed Thread #6: 10950000 reads finished. 18002 secs passed Thread #2: 11000000 reads finished. 18057 secs passed Thread #3: 11050000 reads finished. 18082 secs passed Thread #4: 11100000 reads finished. 18285 secs passed Thread #7: 11150000 reads finished. 18382 secs passed Thread #0: 11200000 reads finished. 18453 secs passed Thread #5: 11250000 reads finished. 18523 secs passed Thread #1: 11300000 reads finished. 18558 secs passed Thread #6: 11350000 reads finished. 18668 secs passed Thread #2: 11400000 reads finished. 18700 secs passed Thread #3: 11450000 reads finished. 18726 secs passed Thread #4: 11500000 reads finished. 18937 secs passed Thread #7: 11550000 reads finished. 19038 secs passed Thread #0: 11600000 reads finished. 19088 secs passed Thread #5: 11650000 reads finished. 19159 secs passed Thread #1: 11700000 reads finished. 19195 secs passed Thread #6: 11750000 reads finished. 19333 secs passed Thread #2: 11800000 reads finished. 19343 secs passed Thread #3: 11850000 reads finished. 19369 secs passed Thread #4: 11900000 reads finished. 19589 secs passed Thread #7: 11950000 reads finished. 19695 secs passed Thread #0: 12000000 reads finished. 19724 secs passed Thread #5: 12050000 reads finished. 19798 secs passed Thread #1: 12100000 reads finished. 19835 secs passed Thread #2: 12200000 reads finished. 19988 secs passed Thread #6: 12150000 reads finished. 20001 secs passed Thread #3: 12250000 reads finished. 20015 secs passed Thread #4: 12300000 reads finished. 20242 secs passed Thread #7: 12350000 reads finished. 20351 secs passed Thread #0: 12400000 reads finished. 20362 secs passed Thread #5: 12450000 reads finished. 20438 secs passed Thread #1: 12500000 reads finished. 20476 secs passed Thread #2: 12550000 reads finished. 20633 secs passed Thread #3: 12650000 reads finished. 20662 secs passed Thread #6: 12600000 reads finished. 20668 secs passed Thread #4: 12700000 reads finished. 20896 secs passed Thread #0: 12800000 reads finished. 20999 secs passed Thread #7: 12750000 reads finished. 21008 secs passed Thread #5: 12850000 reads finished. 21078 secs passed Thread #1: 12900000 reads finished. 21118 secs passed Thread #2: 12950000 reads finished. 21280 secs passed Thread #3: 13000000 reads finished. 21309 secs passed Thread #6: 13050000 reads finished. 21335 secs passed Thread #4: 13100000 reads finished. 21550 secs passed Thread #0: 13150000 reads finished. 21636 secs passed Thread #7: 13200000 reads finished. 21667 secs passed Thread #5: 13250000 reads finished. 21718 secs passed Thread #1: 13300000 reads finished. 21759 secs passed Thread #2: 13350000 reads finished. 21925 secs passed Thread #3: 13400000 reads finished. 21955 secs passed Thread #6: 13450000 reads finished. 22004 secs passed Thread #4: 13500000 reads finished. 22204 secs passed Thread #0: 13550000 reads finished. 22274 secs passed Thread #7: 13600000 reads finished. 22324 secs passed Thread #5: 13650000 reads finished. 22358 secs passed Thread #1: 13700000 reads finished. 22398 secs passed Thread #2: 13750000 reads finished. 22571 secs passed Thread #3: 13800000 reads finished. 22601 secs passed Thread #6: 13850000 reads finished. 22672 secs passed Thread #4: 13900000 reads finished. 22858 secs passed Thread #0: 13950000 reads finished. 22911 secs passed Thread #7: 14000000 reads finished. 22982 secs passed Thread #5: 14050000 reads finished. 22997 secs passed Thread #1: 14100000 reads finished. 23034 secs passed Thread #2: 14150000 reads finished. 23166 secs passed Thread #3: 14200000 reads finished. 23185 secs passed Thread #7: 14374642 reads finished. 23214 secs passed Thread #6: 14250000 reads finished. 23226 secs passed Thread #4: 14300000 reads finished. 23268 secs passed Thread #0: 14350000 reads finished. 23272 secs passed Total number of aligned reads: 2434825 (17%) Done. Finished at Tue Mar 13 04:08:00 2018 Total time consumed: 23272 secs