BSMAP v2.74 Start at: Sun Mar 8 08:36:08 2015 Input reference file: /Volumes/web/halfshell/bu-data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 10 secs passed total_kmers: 43046721 Create seed table. 32 secs passed max number of mismatches: 10 max gap size: 3 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(16 threads) Input read file: /Volumes/web/halfshell/bu-data-genomic/tentacle/2112_lane1_NoIndex_L001_R1_002.fastq.gz (format: gzipped FASTQ) Output file: /Volumes/web/halfshell/humm/2112_Cv_LSU_bsmapout_Cg.sam (format: SAM) Thread #1: 50000 reads finished. 101 secs passed Thread #0: 100000 reads finished. 101 secs passed Thread #7: 200000 reads finished. 102 secs passed Thread #6: 250000 reads finished. 102 secs passed Thread #2: 150000 reads finished. 102 secs passed Thread #4: 300000 reads finished. 103 secs passed Thread #10: 350000 reads finished. 103 secs passed Thread #14: 450000 reads finished. 103 secs passed Thread #3: 400000 reads finished. 104 secs passed Thread #8: 600000 reads finished. 104 secs passed Thread #5: 700000 reads finished. 105 secs passed Thread #11: 550000 reads finished. 105 secs passed Thread #13: 500000 reads finished. 105 secs passed Thread #12: 650000 reads finished. 105 secs passed Thread #9: 800000 reads finished. 106 secs passed Thread #15: 750000 reads finished. 106 secs passed Thread #7: 950000 reads finished. 170 secs passed Thread #1: 850000 reads finished. 170 secs passed Thread #0: 900000 reads finished. 171 secs passed Thread #2: 1050000 reads finished. 171 secs passed Thread #6: 1000000 reads finished. 171 secs passed Thread #4: 1100000 reads finished. 172 secs passed Thread #10: 1150000 reads finished. 173 secs passed Thread #3: 1250000 reads finished. 174 secs passed Thread #14: 1200000 reads finished. 174 secs passed Thread #8: 1300000 reads finished. 174 secs passed Thread #11: 1400000 reads finished. 174 secs passed Thread #5: 1350000 reads finished. 175 secs passed Thread #13: 1450000 reads finished. 175 secs passed Thread #15: 1600000 reads finished. 175 secs passed Thread #9: 1550000 reads finished. 175 secs passed Thread #12: 1500000 reads finished. 176 secs passed Thread #7: 1650000 reads finished. 238 secs passed Thread #1: 1700000 reads finished. 239 secs passed Thread #0: 1750000 reads finished. 241 secs passed Thread #4: 1900000 reads finished. 241 secs passed Thread #2: 1800000 reads finished. 241 secs passed Thread #6: 1850000 reads finished. 241 secs passed Thread #14: 2050000 reads finished. 243 secs passed Thread #10: 1950000 reads finished. 243 secs passed Thread #8: 2100000 reads finished. 243 secs passed Thread #3: 2000000 reads finished. 244 secs passed Thread #11: 2150000 reads finished. 244 secs passed Thread #13: 2250000 reads finished. 244 secs passed Thread #5: 2200000 reads finished. 244 secs passed Thread #15: 2300000 reads finished. 245 secs passed Thread #12: 2400000 reads finished. 245 secs passed Thread #9: 2350000 reads finished. 245 secs passed Thread #7: 2450000 reads finished. 307 secs passed Thread #1: 2500000 reads finished. 307 secs passed Thread #0: 2550000 reads finished. 309 secs passed Thread #4: 2600000 reads finished. 309 secs passed Thread #2: 2650000 reads finished. 310 secs passed Thread #6: 2700000 reads finished. 310 secs passed Thread #8: 2850000 reads finished. 312 secs passed Thread #10: 2800000 reads finished. 312 secs passed Thread #14: 2750000 reads finished. 312 secs passed Thread #3: 2900000 reads finished. 312 secs passed Thread #11: 2950000 reads finished. 313 secs passed Thread #13: 3000000 reads finished. 313 secs passed Thread #15: 3100000 reads finished. 314 secs passed Thread #5: 3050000 reads finished. 314 secs passed Thread #12: 3150000 reads finished. 315 secs passed Thread #9: 3200000 reads finished. 315 secs passed Thread #7: 3250000 reads finished. 374 secs passed Thread #1: 3300000 reads finished. 376 secs passed Thread #0: 3350000 reads finished. 378 secs passed Thread #6: 3500000 reads finished. 378 secs passed Thread #4: 3400000 reads finished. 378 secs passed Thread #2: 3450000 reads finished. 378 secs passed Thread #8: 3550000 reads finished. 380 secs passed Thread #10: 3600000 reads finished. 380 secs passed Thread #14: 3650000 reads finished. 380 secs passed Thread #3: 3700000 reads finished. 380 secs passed Thread #13: 3800000 reads finished. 381 secs passed Thread #11: 3750000 reads finished. 381 secs passed Thread #15: 3850000 reads finished. 381 secs passed Thread #5: 3900000 reads finished. 382 secs passed Thread #12: 3950000 reads finished. 382 secs passed Thread #9: 4000000 reads finished. 383 secs passed Thread #1: 4100000 reads finished. 443 secs passed Thread #7: 4050000 reads finished. 444 secs passed Thread #6: 4200000 reads finished. 446 secs passed Thread #0: 4150000 reads finished. 446 secs passed Thread #2: 4300000 reads finished. 447 secs passed Thread #4: 4250000 reads finished. 448 secs passed Thread #10: 4400000 reads finished. 448 secs passed Thread #8: 4350000 reads finished. 448 secs passed Thread #3: 4500000 reads finished. 448 secs passed Thread #14: 4450000 reads finished. 449 secs passed Thread #13: 4550000 reads finished. 450 secs passed Thread #11: 4600000 reads finished. 453 secs passed Thread #12: 4750000 reads finished. 458 secs passed Thread #15: 4650000 reads finished. 458 secs passed Thread #9: 4800000 reads finished. 458 secs passed Thread #5: 4700000 reads finished. 460 secs passed Thread #7: 4900000 reads finished. 512 secs passed Thread #1: 4850000 reads finished. 512 secs passed Thread #6: 4950000 reads finished. 515 secs passed Thread #0: 5000000 reads finished. 515 secs passed Thread #4: 5100000 reads finished. 516 secs passed Thread #2: 5050000 reads finished. 516 secs passed Thread #10: 5150000 reads finished. 517 secs passed Thread #8: 5200000 reads finished. 518 secs passed Thread #3: 5250000 reads finished. 518 secs passed Thread #14: 5300000 reads finished. 518 secs passed Thread #13: 5350000 reads finished. 518 secs passed Thread #11: 5400000 reads finished. 522 secs passed Thread #15: 5500000 reads finished. 527 secs passed Thread #12: 5450000 reads finished. 527 secs passed Thread #9: 5550000 reads finished. 528 secs passed Thread #5: 5600000 reads finished. 529 secs passed Thread #1: 5700000 reads finished. 581 secs passed Thread #7: 5650000 reads finished. 582 secs passed Thread #6: 5750000 reads finished. 584 secs passed Thread #0: 5800000 reads finished. 584 secs passed Thread #4: 5850000 reads finished. 585 secs passed Thread #2: 5900000 reads finished. 585 secs passed Thread #10: 5950000 reads finished. 586 secs passed Thread #8: 6000000 reads finished. 586 secs passed Thread #14: 6100000 reads finished. 587 secs passed Thread #3: 6050000 reads finished. 587 secs passed Thread #13: 6150000 reads finished. 588 secs passed Thread #11: 6200000 reads finished. 590 secs passed Thread #15: 6250000 reads finished. 594 secs passed Thread #12: 6300000 reads finished. 595 secs passed Thread #9: 6350000 reads finished. 595 secs passed Thread #5: 6400000 reads finished. 597 secs passed Thread #1: 6450000 reads finished. 648 secs passed Thread #7: 6500000 reads finished. 650 secs passed Thread #6: 6550000 reads finished. 652 secs passed Thread #2: 6700000 reads finished. 652 secs passed Thread #0: 6600000 reads finished. 653 secs passed Thread #4: 6650000 reads finished. 653 secs passed Thread #10: 6750000 reads finished. 654 secs passed Thread #8: 6800000 reads finished. 654 secs passed Thread #14: 6850000 reads finished. 655 secs passed Thread #3: 6900000 reads finished. 656 secs passed Thread #13: 6950000 reads finished. 656 secs passed Thread #11: 7000000 reads finished. 658 secs passed Thread #12: 7100000 reads finished. 662 secs passed Thread #15: 7050000 reads finished. 662 secs passed Thread #9: 7150000 reads finished. 664 secs passed Thread #5: 7200000 reads finished. 665 secs passed Thread #1: 7250000 reads finished. 716 secs passed Thread #7: 7300000 reads finished. 718 secs passed Thread #2: 7400000 reads finished. 720 secs passed Thread #6: 7350000 reads finished. 720 secs passed Thread #0: 7450000 reads finished. 720 secs passed Thread #4: 7500000 reads finished. 721 secs passed Thread #10: 7550000 reads finished. 722 secs passed Thread #8: 7600000 reads finished. 722 secs passed Thread #14: 7650000 reads finished. 722 secs passed Thread #13: 7750000 reads finished. 724 secs passed Thread #3: 7700000 reads finished. 724 secs passed Thread #11: 7800000 reads finished. 726 secs passed Thread #12: 7850000 reads finished. 730 secs passed Thread #15: 7900000 reads finished. 730 secs passed Thread #9: 7950000 reads finished. 731 secs passed Thread #5: 8000000 reads finished. 732 secs passed Thread #1: 8050000 reads finished. 784 secs passed Thread #7: 8100000 reads finished. 785 secs passed Thread #2: 8150000 reads finished. 788 secs passed Thread #0: 8250000 reads finished. 788 secs passed Thread #6: 8200000 reads finished. 788 secs passed Thread #10: 8350000 reads finished. 789 secs passed Thread #4: 8300000 reads finished. 790 secs passed Thread #8: 8400000 reads finished. 790 secs passed Thread #14: 8450000 reads finished. 791 secs passed Thread #13: 8500000 reads finished. 795 secs passed Thread #3: 8550000 reads finished. 796 secs passed Thread #11: 8600000 reads finished. 796 secs passed Thread #15: 8700000 reads finished. 800 secs passed Thread #12: 8650000 reads finished. 800 secs passed Thread #9: 8750000 reads finished. 801 secs passed Thread #5: 8800000 reads finished. 804 secs passed Thread #1: 8850000 reads finished. 855 secs passed Thread #7: 8900000 reads finished. 857 secs passed Thread #2: 8950000 reads finished. 858 secs passed Thread #0: 9000000 reads finished. 858 secs passed Thread #6: 9050000 reads finished. 859 secs passed Thread #10: 9100000 reads finished. 861 secs passed Thread #4: 9150000 reads finished. 861 secs passed Thread #8: 9200000 reads finished. 862 secs passed Thread #14: 9250000 reads finished. 862 secs passed Thread #3: 9350000 reads finished. 866 secs passed Thread #13: 9300000 reads finished. 867 secs passed Thread #11: 9400000 reads finished. 867 secs passed Thread #15: 9450000 reads finished. 871 secs passed Thread #12: 9500000 reads finished. 871 secs passed Thread #9: 9550000 reads finished. 872 secs passed Thread #5: 9600000 reads finished. 875 secs passed Thread #1: 9650000 reads finished. 925 secs passed Thread #7: 9700000 reads finished. 928 secs passed Thread #2: 9750000 reads finished. 929 secs passed Thread #0: 9800000 reads finished. 929 secs passed Thread #6: 9850000 reads finished. 931 secs passed Thread #4: 9950000 reads finished. 932 secs passed Thread #10: 9900000 reads finished. 932 secs passed Thread #8: 10000000 reads finished. 933 secs passed Thread #14: 10050000 reads finished. 934 secs passed Thread #3: 10100000 reads finished. 936 secs passed Thread #13: 10150000 reads finished. 938 secs passed Thread #11: 10200000 reads finished. 939 secs passed Thread #12: 10300000 reads finished. 943 secs passed Thread #15: 10250000 reads finished. 943 secs passed Thread #9: 10350000 reads finished. 944 secs passed Thread #5: 10400000 reads finished. 947 secs passed Thread #1: 10450000 reads finished. 997 secs passed Thread #7: 10500000 reads finished. 999 secs passed Thread #2: 10550000 reads finished. 1001 secs passed Thread #0: 10600000 reads finished. 1001 secs passed Thread #6: 10650000 reads finished. 1002 secs passed Thread #10: 10750000 reads finished. 1003 secs passed Thread #14: 10850000 reads finished. 1003 secs passed Thread #4: 10700000 reads finished. 1003 secs passed Thread #8: 10800000 reads finished. 1004 secs passed Thread #3: 10900000 reads finished. 1006 secs passed Thread #13: 10950000 reads finished. 1008 secs passed Thread #11: 11000000 reads finished. 1008 secs passed Thread #15: 11100000 reads finished. 1013 secs passed Thread #12: 11050000 reads finished. 1013 secs passed Thread #9: 11150000 reads finished. 1014 secs passed Thread #5: 11200000 reads finished. 1016 secs passed Thread #1: 11250000 reads finished. 1066 secs passed Thread #7: 11300000 reads finished. 1069 secs passed Thread #2: 11350000 reads finished. 1070 secs passed Thread #0: 11400000 reads finished. 1071 secs passed Thread #6: 11450000 reads finished. 1072 secs passed Thread #10: 11500000 reads finished. 1073 secs passed Thread #4: 11600000 reads finished. 1073 secs passed Thread #14: 11550000 reads finished. 1073 secs passed Thread #8: 11650000 reads finished. 1074 secs passed Thread #3: 11700000 reads finished. 1076 secs passed Thread #11: 11800000 reads finished. 1078 secs passed Thread #13: 11750000 reads finished. 1079 secs passed Thread #15: 11850000 reads finished. 1082 secs passed Thread #12: 11900000 reads finished. 1083 secs passed Thread #9: 11950000 reads finished. 1085 secs passed Thread #5: 12000000 reads finished. 1086 secs passed Thread #1: 12050000 reads finished. 1137 secs passed Thread #7: 12100000 reads finished. 1139 secs passed Thread #0: 12200000 reads finished. 1140 secs passed Thread #6: 12250000 reads finished. 1140 secs passed Thread #2: 12150000 reads finished. 1141 secs passed Thread #10: 12300000 reads finished. 1142 secs passed Thread #4: 12350000 reads finished. 1143 secs passed Thread #8: 12450000 reads finished. 1144 secs passed Thread #14: 12400000 reads finished. 1144 secs passed Thread #3: 12500000 reads finished. 1146 secs passed Thread #13: 12600000 reads finished. 1148 secs passed Thread #11: 12550000 reads finished. 1149 secs passed Thread #15: 12650000 reads finished. 1153 secs passed Thread #12: 12700000 reads finished. 1154 secs passed Thread #9: 12750000 reads finished. 1154 secs passed Thread #5: 12800000 reads finished. 1156 secs passed Thread #1: 12850000 reads finished. 1207 secs passed Thread #7: 12900000 reads finished. 1209 secs passed Thread #0: 12950000 reads finished. 1210 secs passed Thread #6: 13000000 reads finished. 1210 secs passed Thread #2: 13050000 reads finished. 1211 secs passed Thread #10: 13100000 reads finished. 1212 secs passed Thread #4: 13150000 reads finished. 1214 secs passed Thread #8: 13200000 reads finished. 1214 secs passed Thread #14: 13250000 reads finished. 1214 secs passed Thread #3: 13300000 reads finished. 1216 secs passed Thread #13: 13350000 reads finished. 1218 secs passed Thread #11: 13400000 reads finished. 1218 secs passed Thread #15: 13450000 reads finished. 1220 secs passed Thread #9: 13550000 reads finished. 1222 secs passed Thread #12: 13500000 reads finished. 1222 secs passed Thread #5: 13600000 reads finished. 1225 secs passed Thread #1: 13650000 reads finished. 1275 secs passed Thread #7: 13700000 reads finished. 1277 secs passed Thread #0: 13750000 reads finished. 1278 secs passed Thread #6: 13800000 reads finished. 1278 secs passed Thread #2: 13850000 reads finished. 1280 secs passed Thread #10: 13900000 reads finished. 1280 secs passed Thread #4: 13950000 reads finished. 1281 secs passed Thread #8: 14000000 reads finished. 1283 secs passed Thread #14: 14050000 reads finished. 1284 secs passed Thread #3: 14100000 reads finished. 1286 secs passed Thread #13: 14150000 reads finished. 1286 secs passed Thread #11: 14200000 reads finished. 1287 secs passed Thread #15: 14250000 reads finished. 1288 secs passed Thread #9: 14300000 reads finished. 1290 secs passed Thread #12: 14350000 reads finished. 1290 secs passed Thread #5: 14400000 reads finished. 1293 secs passed Thread #1: 14450000 reads finished. 1344 secs passed Thread #7: 14500000 reads finished. 1346 secs passed Thread #0: 14550000 reads finished. 1348 secs passed Thread #6: 14600000 reads finished. 1348 secs passed Thread #2: 14650000 reads finished. 1349 secs passed Thread #4: 14750000 reads finished. 1350 secs passed Thread #10: 14700000 reads finished. 1350 secs passed Thread #8: 14800000 reads finished. 1352 secs passed Thread #3: 14900000 reads finished. 1353 secs passed Thread #14: 14850000 reads finished. 1354 secs passed Thread #13: 14950000 reads finished. 1355 secs passed Thread #11: 15000000 reads finished. 1356 secs passed Thread #15: 15050000 reads finished. 1357 secs passed Thread #12: 15150000 reads finished. 1359 secs passed Thread #9: 15100000 reads finished. 1359 secs passed Thread #5: 15200000 reads finished. 1362 secs passed Thread #1: 15250000 reads finished. 1412 secs passed Thread #7: 15300000 reads finished. 1415 secs passed Thread #2: 15450000 reads finished. 1416 secs passed Thread #6: 15400000 reads finished. 1416 secs passed Thread #0: 15350000 reads finished. 1417 secs passed Thread #4: 15500000 reads finished. 1417 secs passed Thread #10: 15550000 reads finished. 1418 secs passed Thread #8: 15600000 reads finished. 1419 secs passed Thread #3: 15650000 reads finished. 1420 secs passed Thread #13: 15750000 reads finished. 1421 secs passed Thread #14: 15700000 reads finished. 1422 secs passed Thread #15: 15850000 reads finished. 1422 secs passed Thread #11: 15800000 reads finished. 1422 secs passed Thread #12: 15900000 reads finished. 1423 secs passed Thread #9: 15950000 reads finished. 1424 secs passed Thread #5: 16000000 reads finished. 1426 secs passed Total number of aligned reads: 114857 (0.72%) Done. Finished at Sun Mar 8 08:59:54 2015 Total time consumed: 1426 secs