BSMAP v2.74
Start at: Tue Dec 2 14:03:03 2014
Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA)
Load in 7658 db seqs, total size 557717710 bp. 9 secs passed
total_kmers: 43046721
Create seed table. 25 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 (read_1): ++,-+
mapping strand (read_2): +-,--
Pair-end alignment(4 threads)
Input read file #1: mcf_M1_R1.fastq (format: FASTQ)
Input read file #2: mcf_M1_R2.fastq (format: FASTQ)
Output file: bsmap_out_M1.sam (format: SAM)
Thread #1: 100000 read pairs finished. 44 secs passed
Thread #3: 50000 read pairs finished. 45 secs passed
Thread #0: 150000 read pairs finished. 45 secs passed
Thread #2: 200000 read pairs finished. 46 secs passed
Thread #1: 250000 read pairs finished. 61 secs passed
Thread #3: 300000 read pairs finished. 62 secs passed
Thread #0: 350000 read pairs finished. 63 secs passed
Thread #2: 400000 read pairs finished. 64 secs passed
Thread #1: 450000 read pairs finished. 78 secs passed
Thread #3: 500000 read pairs finished. 79 secs passed
Thread #0: 550000 read pairs finished. 81 secs passed
Thread #2: 600000 read pairs finished. 81 secs passed
Thread #1: 650000 read pairs finished. 95 secs passed
Thread #3: 700000 read pairs finished. 97 secs passed
Thread #0: 750000 read pairs finished. 98 secs passed
Thread #2: 800000 read pairs finished. 99 secs passed
Thread #1: 850000 read pairs finished. 113 secs passed
Thread #3: 900000 read pairs finished. 114 secs passed
Thread #2: 1000000 read pairs finished. 116 secs passed
Thread #0: 950000 read pairs finished. 117 secs passed
Thread #1: 1050000 read pairs finished. 129 secs passed
Thread #3: 1100000 read pairs finished. 132 secs passed
Thread #2: 1150000 read pairs finished. 133 secs passed
Thread #0: 1200000 read pairs finished. 135 secs passed
Thread #1: 1250000 read pairs finished. 146 secs passed
Thread #3: 1300000 read pairs finished. 149 secs passed
Thread #2: 1350000 read pairs finished. 150 secs passed
Thread #0: 1400000 read pairs finished. 153 secs passed
Thread #1: 1450000 read pairs finished. 163 secs passed
Thread #3: 1500000 read pairs finished. 166 secs passed
Thread #2: 1550000 read pairs finished. 167 secs passed
Thread #0: 1600000 read pairs finished. 169 secs passed
Thread #1: 1650000 read pairs finished. 181 secs passed
Thread #3: 1700000 read pairs finished. 184 secs passed
Thread #2: 1750000 read pairs finished. 185 secs passed
Thread #0: 1800000 read pairs finished. 187 secs passed
Thread #1: 1850000 read pairs finished. 198 secs passed
Thread #3: 1900000 read pairs finished. 202 secs passed
Thread #2: 1950000 read pairs finished. 202 secs passed
Thread #0: 2000000 read pairs finished. 205 secs passed
Thread #1: 2050000 read pairs finished. 215 secs passed
Thread #3: 2100000 read pairs finished. 219 secs passed
Thread #2: 2150000 read pairs finished. 219 secs passed
Thread #0: 2200000 read pairs finished. 222 secs passed
Thread #1: 2250000 read pairs finished. 233 secs passed
Thread #2: 2350000 read pairs finished. 237 secs passed
Thread #3: 2300000 read pairs finished. 237 secs passed
Thread #0: 2400000 read pairs finished. 239 secs passed
Thread #1: 2450000 read pairs finished. 249 secs passed
Thread #3: 2550000 read pairs finished. 255 secs passed
Thread #2: 2500000 read pairs finished. 255 secs passed
Thread #0: 2600000 read pairs finished. 256 secs passed
Thread #1: 2650000 read pairs finished. 267 secs passed
Thread #3: 2700000 read pairs finished. 273 secs passed
Thread #2: 2750000 read pairs finished. 273 secs passed
Thread #0: 2800000 read pairs finished. 274 secs passed
Thread #1: 2850000 read pairs finished. 284 secs passed
Thread #2: 2950000 read pairs finished. 291 secs passed
Thread #3: 2900000 read pairs finished. 291 secs passed
Thread #0: 3000000 read pairs finished. 291 secs passed
Thread #1: 3050000 read pairs finished. 301 secs passed
Thread #2: 3100000 read pairs finished. 308 secs passed
Thread #3: 3150000 read pairs finished. 309 secs passed
Thread #0: 3200000 read pairs finished. 309 secs passed
Thread #1: 3250000 read pairs finished. 318 secs passed
Thread #2: 3300000 read pairs finished. 325 secs passed
Thread #3: 3350000 read pairs finished. 326 secs passed
Thread #0: 3400000 read pairs finished. 326 secs passed
Thread #1: 3450000 read pairs finished. 334 secs passed
Thread #2: 3500000 read pairs finished. 342 secs passed
Thread #3: 3550000 read pairs finished. 344 secs passed
Thread #0: 3600000 read pairs finished. 345 secs passed
Thread #1: 3650000 read pairs finished. 353 secs passed
Thread #2: 3700000 read pairs finished. 360 secs passed
Thread #3: 3750000 read pairs finished. 362 secs passed
Thread #0: 3800000 read pairs finished. 362 secs passed
Thread #1: 3850000 read pairs finished. 370 secs passed
Thread #2: 3900000 read pairs finished. 377 secs passed
Thread #3: 3950000 read pairs finished. 379 secs passed
Thread #0: 4000000 read pairs finished. 379 secs passed
Thread #1: 4050000 read pairs finished. 388 secs passed
Thread #2: 4100000 read pairs finished. 394 secs passed
Thread #3: 4150000 read pairs finished. 396 secs passed
Thread #0: 4200000 read pairs finished. 396 secs passed
Thread #1: 4250000 read pairs finished. 405 secs passed
Thread #2: 4300000 read pairs finished. 412 secs passed
Thread #3: 4350000 read pairs finished. 413 secs passed
Thread #0: 4400000 read pairs finished. 414 secs passed
Thread #1: 4450000 read pairs finished. 423 secs passed
Thread #2: 4500000 read pairs finished. 429 secs passed
Thread #3: 4550000 read pairs finished. 430 secs passed
Thread #0: 4600000 read pairs finished. 432 secs passed
Thread #1: 4650000 read pairs finished. 440 secs passed
Thread #2: 4700000 read pairs finished. 446 secs passed
Thread #3: 4750000 read pairs finished. 448 secs passed
Thread #0: 4800000 read pairs finished. 449 secs passed
Thread #1: 4850000 read pairs finished. 457 secs passed
Thread #2: 4900000 read pairs finished. 464 secs passed
Thread #3: 4950000 read pairs finished. 465 secs passed
Thread #0: 5000000 read pairs finished. 466 secs passed
Thread #1: 5050000 read pairs finished. 474 secs passed
Thread #2: 5100000 read pairs finished. 480 secs passed
Thread #3: 5150000 read pairs finished. 482 secs passed
Thread #0: 5200000 read pairs finished. 483 secs passed
Thread #1: 5250000 read pairs finished. 491 secs passed
Thread #2: 5300000 read pairs finished. 499 secs passed
Thread #3: 5350000 read pairs finished. 499 secs passed
Thread #0: 5400000 read pairs finished. 500 secs passed
Thread #1: 5450000 read pairs finished. 508 secs passed
Thread #2: 5500000 read pairs finished. 516 secs passed
Thread #3: 5550000 read pairs finished. 517 secs passed
Thread #0: 5600000 read pairs finished. 518 secs passed
Thread #1: 5650000 read pairs finished. 526 secs passed
Thread #2: 5700000 read pairs finished. 533 secs passed
Thread #3: 5750000 read pairs finished. 534 secs passed
Thread #0: 5800000 read pairs finished. 535 secs passed
Thread #1: 5850000 read pairs finished. 543 secs passed
Thread #2: 5900000 read pairs finished. 552 secs passed
Thread #3: 5950000 read pairs finished. 553 secs passed
Thread #0: 6000000 read pairs finished. 554 secs passed
Thread #1: 6050000 read pairs finished. 561 secs passed
Thread #2: 6100000 read pairs finished. 569 secs passed
Thread #3: 6150000 read pairs finished. 570 secs passed
Thread #0: 6200000 read pairs finished. 571 secs passed
Thread #1: 6250000 read pairs finished. 579 secs passed
Thread #2: 6300000 read pairs finished. 588 secs passed
Thread #3: 6350000 read pairs finished. 588 secs passed
Thread #0: 6400000 read pairs finished. 589 secs passed
Thread #1: 6450000 read pairs finished. 597 secs passed
Thread #2: 6500000 read pairs finished. 605 secs passed
Thread #3: 6550000 read pairs finished. 606 secs passed
Thread #0: 6600000 read pairs finished. 606 secs passed
Thread #1: 6650000 read pairs finished. 614 secs passed
Thread #2: 6700000 read pairs finished. 623 secs passed
Thread #3: 6750000 read pairs finished. 623 secs passed
Thread #0: 6800000 read pairs finished. 624 secs passed
Thread #1: 6850000 read pairs finished. 631 secs passed
Thread #2: 6900000 read pairs finished. 640 secs passed
Thread #3: 6950000 read pairs finished. 641 secs passed
Thread #0: 7000000 read pairs finished. 641 secs passed
Thread #1: 7050000 read pairs finished. 649 secs passed
Thread #2: 7100000 read pairs finished. 657 secs passed
Thread #3: 7150000 read pairs finished. 659 secs passed
Thread #0: 7200000 read pairs finished. 659 secs passed
Thread #1: 7250000 read pairs finished. 666 secs passed
Thread #2: 7300000 read pairs finished. 674 secs passed
Thread #3: 7350000 read pairs finished. 676 secs passed
Thread #0: 7400000 read pairs finished. 677 secs passed
Thread #1: 7450000 read pairs finished. 683 secs passed
Thread #2: 7500000 read pairs finished. 692 secs passed
Thread #3: 7550000 read pairs finished. 693 secs passed
Thread #0: 7600000 read pairs finished. 694 secs passed
Thread #1: 7650000 read pairs finished. 699 secs passed
Thread #2: 7700000 read pairs finished. 709 secs passed
Thread #3: 7750000 read pairs finished. 710 secs passed
Thread #0: 7800000 read pairs finished. 711 secs passed
Thread #1: 7850000 read pairs finished. 717 secs passed
Thread #1: 8023643 read pairs finished. 725 secs passed
Thread #2: 7900000 read pairs finished. 726 secs passed
Thread #3: 7950000 read pairs finished. 726 secs passed
Thread #0: 8000000 read pairs finished. 727 secs passed
Total number of aligned reads:
pairs: 3982551 (50%)
single a: 1489442 (19%)
single b: 1430646 (18%)
Done.
Finished at Tue Dec 2 14:15:10 2014
Total time consumed: 727 secs
BSMAP v2.74
Start at: Tue Dec 2 14:15:11 2014
Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA)
Load in 7658 db seqs, total size 557717710 bp. 9 secs passed
total_kmers: 43046721
Create seed table. 25 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 (read_1): ++,-+
mapping strand (read_2): +-,--
Pair-end alignment(4 threads)
Input read file #1: mcf_T1D3_R1.fastq (format: FASTQ)
Input read file #2: mcf_T1D3_R2.fastq (format: FASTQ)
Output file: bsmap_out_T1D3.sam (format: SAM)
Thread #3: 50000 read pairs finished. 39 secs passed
Thread #0: 100000 read pairs finished. 39 secs passed
Thread #1: 150000 read pairs finished. 40 secs passed
Thread #2: 200000 read pairs finished. 40 secs passed
Thread #3: 250000 read pairs finished. 54 secs passed
Thread #0: 300000 read pairs finished. 54 secs passed
Thread #1: 350000 read pairs finished. 55 secs passed
Thread #2: 400000 read pairs finished. 55 secs passed
Thread #3: 450000 read pairs finished. 68 secs passed
Thread #0: 500000 read pairs finished. 68 secs passed
Thread #2: 600000 read pairs finished. 69 secs passed
Thread #1: 550000 read pairs finished. 69 secs passed
Thread #3: 650000 read pairs finished. 82 secs passed
Thread #0: 700000 read pairs finished. 83 secs passed
Thread #2: 750000 read pairs finished. 83 secs passed
Thread #1: 800000 read pairs finished. 83 secs passed
Thread #3: 850000 read pairs finished. 96 secs passed
Thread #0: 900000 read pairs finished. 97 secs passed
Thread #2: 950000 read pairs finished. 97 secs passed
Thread #1: 1000000 read pairs finished. 98 secs passed
Thread #3: 1050000 read pairs finished. 110 secs passed
Thread #0: 1100000 read pairs finished. 111 secs passed
Thread #2: 1150000 read pairs finished. 111 secs passed
Thread #1: 1200000 read pairs finished. 111 secs passed
Thread #3: 1250000 read pairs finished. 124 secs passed
Thread #0: 1300000 read pairs finished. 125 secs passed
Thread #2: 1350000 read pairs finished. 125 secs passed
Thread #1: 1400000 read pairs finished. 126 secs passed
Thread #3: 1450000 read pairs finished. 137 secs passed
Thread #0: 1500000 read pairs finished. 139 secs passed
Thread #2: 1550000 read pairs finished. 140 secs passed
Thread #1: 1600000 read pairs finished. 140 secs passed
Thread #3: 1650000 read pairs finished. 151 secs passed
Thread #0: 1700000 read pairs finished. 153 secs passed
Thread #2: 1750000 read pairs finished. 154 secs passed
Thread #1: 1800000 read pairs finished. 154 secs passed
Thread #3: 1850000 read pairs finished. 165 secs passed
Thread #0: 1900000 read pairs finished. 168 secs passed
Thread #2: 1950000 read pairs finished. 168 secs passed
Thread #1: 2000000 read pairs finished. 168 secs passed
Thread #3: 2050000 read pairs finished. 179 secs passed
Thread #2: 2150000 read pairs finished. 182 secs passed
Thread #0: 2100000 read pairs finished. 182 secs passed
Thread #1: 2200000 read pairs finished. 182 secs passed
Thread #3: 2250000 read pairs finished. 192 secs passed
Thread #2: 2300000 read pairs finished. 195 secs passed
Thread #1: 2400000 read pairs finished. 196 secs passed
Thread #0: 2350000 read pairs finished. 196 secs passed
Thread #3: 2450000 read pairs finished. 205 secs passed
Thread #2: 2500000 read pairs finished. 209 secs passed
Thread #1: 2550000 read pairs finished. 210 secs passed
Thread #0: 2600000 read pairs finished. 210 secs passed
Thread #3: 2650000 read pairs finished. 218 secs passed
Thread #2: 2700000 read pairs finished. 223 secs passed
Thread #1: 2750000 read pairs finished. 223 secs passed
Thread #0: 2800000 read pairs finished. 224 secs passed
Thread #3: 2850000 read pairs finished. 231 secs passed
Thread #2: 2900000 read pairs finished. 236 secs passed
Thread #1: 2950000 read pairs finished. 237 secs passed
Thread #0: 3000000 read pairs finished. 238 secs passed
Thread #3: 3050000 read pairs finished. 244 secs passed
Thread #2: 3100000 read pairs finished. 250 secs passed
Thread #1: 3150000 read pairs finished. 251 secs passed
Thread #0: 3200000 read pairs finished. 251 secs passed
Thread #3: 3250000 read pairs finished. 258 secs passed
Thread #2: 3300000 read pairs finished. 263 secs passed
Thread #1: 3350000 read pairs finished. 264 secs passed
Thread #0: 3400000 read pairs finished. 265 secs passed
Thread #3: 3450000 read pairs finished. 271 secs passed
Thread #2: 3500000 read pairs finished. 277 secs passed
Thread #1: 3550000 read pairs finished. 278 secs passed
Thread #0: 3600000 read pairs finished. 279 secs passed
Thread #3: 3650000 read pairs finished. 286 secs passed
Thread #2: 3700000 read pairs finished. 291 secs passed
Thread #1: 3750000 read pairs finished. 291 secs passed
Thread #0: 3800000 read pairs finished. 292 secs passed
Thread #3: 3850000 read pairs finished. 299 secs passed
Thread #2: 3900000 read pairs finished. 304 secs passed
Thread #1: 3950000 read pairs finished. 305 secs passed
Thread #0: 4000000 read pairs finished. 306 secs passed
Thread #3: 4050000 read pairs finished. 314 secs passed
Thread #2: 4100000 read pairs finished. 319 secs passed
Thread #1: 4150000 read pairs finished. 320 secs passed
Thread #0: 4200000 read pairs finished. 321 secs passed
Thread #3: 4250000 read pairs finished. 329 secs passed
Thread #2: 4300000 read pairs finished. 333 secs passed
Thread #1: 4350000 read pairs finished. 333 secs passed
Thread #0: 4400000 read pairs finished. 334 secs passed
Thread #3: 4450000 read pairs finished. 342 secs passed
Thread #2: 4500000 read pairs finished. 347 secs passed
Thread #1: 4550000 read pairs finished. 348 secs passed
Thread #0: 4600000 read pairs finished. 348 secs passed
Thread #3: 4650000 read pairs finished. 357 secs passed
Thread #2: 4700000 read pairs finished. 361 secs passed
Thread #1: 4750000 read pairs finished. 361 secs passed
Thread #0: 4800000 read pairs finished. 362 secs passed
Thread #3: 4850000 read pairs finished. 371 secs passed
Thread #2: 4900000 read pairs finished. 375 secs passed
Thread #3: 5016400 read pairs finished. 375 secs passed
Thread #1: 4950000 read pairs finished. 376 secs passed
Thread #0: 5000000 read pairs finished. 376 secs passed
Total number of aligned reads:
pairs: 2717832 (54%)
single a: 1117376 (22%)
single b: 1178713 (23%)
Done.
Finished at Tue Dec 2 14:21:27 2014
Total time consumed: 376 secs
BSMAP v2.74
Start at: Tue Dec 2 14:21:28 2014
Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA)
Load in 7658 db seqs, total size 557717710 bp. 8 secs passed
total_kmers: 43046721
Create seed table. 25 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 (read_1): ++,-+
mapping strand (read_2): +-,--
Pair-end alignment(4 threads)
Input read file #1: mcf_T1D5_R1.fastq (format: FASTQ)
Input read file #2: mcf_T1D5_R2.fastq (format: FASTQ)
Output file: bsmap_out_T1D5.sam (format: SAM)
Thread #0: 50000 read pairs finished. 43 secs passed
Thread #1: 150000 read pairs finished. 43 secs passed
Thread #2: 100000 read pairs finished. 44 secs passed
Thread #3: 200000 read pairs finished. 44 secs passed
Thread #0: 250000 read pairs finished. 60 secs passed
Thread #1: 300000 read pairs finished. 61 secs passed
Thread #2: 350000 read pairs finished. 62 secs passed
Thread #3: 400000 read pairs finished. 63 secs passed
Thread #0: 450000 read pairs finished. 77 secs passed
Thread #1: 500000 read pairs finished. 78 secs passed
Thread #2: 550000 read pairs finished. 80 secs passed
Thread #3: 600000 read pairs finished. 80 secs passed
Thread #0: 650000 read pairs finished. 94 secs passed
Thread #1: 700000 read pairs finished. 96 secs passed
Thread #2: 750000 read pairs finished. 98 secs passed
Thread #3: 800000 read pairs finished. 99 secs passed
Thread #0: 850000 read pairs finished. 112 secs passed
Thread #1: 900000 read pairs finished. 114 secs passed
Thread #2: 950000 read pairs finished. 116 secs passed
Thread #3: 1000000 read pairs finished. 117 secs passed
Thread #0: 1050000 read pairs finished. 129 secs passed
Thread #1: 1100000 read pairs finished. 131 secs passed
Thread #2: 1150000 read pairs finished. 133 secs passed
Thread #3: 1200000 read pairs finished. 134 secs passed
Thread #0: 1250000 read pairs finished. 146 secs passed
Thread #1: 1300000 read pairs finished. 147 secs passed
Thread #2: 1350000 read pairs finished. 150 secs passed
Thread #3: 1400000 read pairs finished. 152 secs passed
Thread #0: 1450000 read pairs finished. 163 secs passed
Thread #1: 1500000 read pairs finished. 164 secs passed
Thread #2: 1550000 read pairs finished. 167 secs passed
Thread #3: 1600000 read pairs finished. 168 secs passed
Thread #0: 1650000 read pairs finished. 179 secs passed
Thread #1: 1700000 read pairs finished. 182 secs passed
Thread #2: 1750000 read pairs finished. 184 secs passed
Thread #3: 1800000 read pairs finished. 185 secs passed
Thread #0: 1850000 read pairs finished. 196 secs passed
Thread #1: 1900000 read pairs finished. 199 secs passed
Thread #2: 1950000 read pairs finished. 201 secs passed
Thread #3: 2000000 read pairs finished. 202 secs passed
Thread #0: 2050000 read pairs finished. 213 secs passed
Thread #1: 2100000 read pairs finished. 216 secs passed
Thread #2: 2150000 read pairs finished. 218 secs passed
Thread #3: 2200000 read pairs finished. 219 secs passed
Thread #0: 2250000 read pairs finished. 229 secs passed
Thread #1: 2300000 read pairs finished. 233 secs passed
Thread #2: 2350000 read pairs finished. 235 secs passed
Thread #3: 2400000 read pairs finished. 236 secs passed
Thread #0: 2450000 read pairs finished. 246 secs passed
Thread #1: 2500000 read pairs finished. 250 secs passed
Thread #2: 2550000 read pairs finished. 252 secs passed
Thread #3: 2600000 read pairs finished. 253 secs passed
Thread #0: 2650000 read pairs finished. 262 secs passed
Thread #1: 2700000 read pairs finished. 267 secs passed
Thread #2: 2750000 read pairs finished. 268 secs passed
Thread #3: 2800000 read pairs finished. 269 secs passed
Thread #0: 2850000 read pairs finished. 279 secs passed
Thread #1: 2900000 read pairs finished. 284 secs passed
Thread #2: 2950000 read pairs finished. 285 secs passed
Thread #3: 3000000 read pairs finished. 287 secs passed
Thread #0: 3050000 read pairs finished. 296 secs passed
Thread #1: 3100000 read pairs finished. 301 secs passed
Thread #2: 3150000 read pairs finished. 303 secs passed
Thread #3: 3200000 read pairs finished. 304 secs passed
Thread #0: 3250000 read pairs finished. 313 secs passed
Thread #1: 3300000 read pairs finished. 318 secs passed
Thread #2: 3350000 read pairs finished. 320 secs passed
Thread #3: 3400000 read pairs finished. 321 secs passed
Thread #0: 3450000 read pairs finished. 330 secs passed
Thread #1: 3500000 read pairs finished. 335 secs passed
Thread #2: 3550000 read pairs finished. 337 secs passed
Thread #3: 3600000 read pairs finished. 338 secs passed
Thread #0: 3650000 read pairs finished. 348 secs passed
Thread #1: 3700000 read pairs finished. 352 secs passed
Thread #2: 3750000 read pairs finished. 355 secs passed
Thread #3: 3800000 read pairs finished. 355 secs passed
Thread #0: 3850000 read pairs finished. 364 secs passed
Thread #1: 3900000 read pairs finished. 369 secs passed
Thread #2: 3950000 read pairs finished. 371 secs passed
Thread #3: 4000000 read pairs finished. 374 secs passed
Thread #0: 4050000 read pairs finished. 382 secs passed
Thread #1: 4100000 read pairs finished. 386 secs passed
Thread #2: 4150000 read pairs finished. 388 secs passed
Thread #3: 4200000 read pairs finished. 391 secs passed
Thread #0: 4250000 read pairs finished. 399 secs passed
Thread #1: 4300000 read pairs finished. 403 secs passed
Thread #2: 4350000 read pairs finished. 405 secs passed
Thread #3: 4400000 read pairs finished. 408 secs passed
Thread #0: 4450000 read pairs finished. 416 secs passed
Thread #1: 4500000 read pairs finished. 419 secs passed
Thread #2: 4550000 read pairs finished. 422 secs passed
Thread #3: 4600000 read pairs finished. 424 secs passed
Thread #0: 4650000 read pairs finished. 433 secs passed
Thread #1: 4700000 read pairs finished. 436 secs passed
Thread #2: 4750000 read pairs finished. 439 secs passed
Thread #3: 4800000 read pairs finished. 441 secs passed
Thread #0: 4850000 read pairs finished. 450 secs passed
Thread #1: 4900000 read pairs finished. 454 secs passed
Thread #2: 4950000 read pairs finished. 456 secs passed
Thread #3: 5000000 read pairs finished. 458 secs passed
Thread #0: 5050000 read pairs finished. 467 secs passed
Thread #1: 5100000 read pairs finished. 471 secs passed
Thread #2: 5150000 read pairs finished. 474 secs passed
Thread #3: 5200000 read pairs finished. 475 secs passed
Thread #0: 5250000 read pairs finished. 483 secs passed
Thread #1: 5300000 read pairs finished. 488 secs passed
Thread #2: 5350000 read pairs finished. 491 secs passed
Thread #3: 5400000 read pairs finished. 492 secs passed
Thread #0: 5450000 read pairs finished. 500 secs passed
Thread #1: 5500000 read pairs finished. 505 secs passed
Thread #2: 5550000 read pairs finished. 509 secs passed
Thread #3: 5600000 read pairs finished. 510 secs passed
Thread #0: 5650000 read pairs finished. 517 secs passed
Thread #1: 5700000 read pairs finished. 522 secs passed
Thread #2: 5750000 read pairs finished. 527 secs passed
Thread #3: 5800000 read pairs finished. 527 secs passed
Thread #0: 5850000 read pairs finished. 534 secs passed
Thread #1: 5900000 read pairs finished. 539 secs passed
Thread #3: 6000000 read pairs finished. 545 secs passed
Thread #2: 5950000 read pairs finished. 545 secs passed
Thread #0: 6050000 read pairs finished. 550 secs passed
Thread #2: 6179274 read pairs finished. 554 secs passed
Thread #1: 6100000 read pairs finished. 554 secs passed
Thread #3: 6150000 read pairs finished. 558 secs passed
Total number of aligned reads:
pairs: 2725017 (44%)
single a: 1704213 (28%)
single b: 1415455 (23%)
Done.
Finished at Tue Dec 2 14:30:46 2014
Total time consumed: 558 secs
BSMAP v2.74
Start at: Tue Dec 2 14:30:47 2014
Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA)
Load in 7658 db seqs, total size 557717710 bp. 9 secs passed
total_kmers: 43046721
Create seed table. 26 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 (read_1): ++,-+
mapping strand (read_2): +-,--
Pair-end alignment(4 threads)
Input read file #1: mcf_M3_R1.fastq (format: FASTQ)
Input read file #2: mcf_M3_R2.fastq (format: FASTQ)
Output file: bsmap_out_M3.sam (format: SAM)
Thread #1: 50000 read pairs finished. 41 secs passed
Thread #2: 100000 read pairs finished. 41 secs passed
Thread #0: 200000 read pairs finished. 42 secs passed
Thread #3: 150000 read pairs finished. 42 secs passed
Thread #1: 250000 read pairs finished. 55 secs passed
Thread #2: 300000 read pairs finished. 57 secs passed
Thread #0: 350000 read pairs finished. 57 secs passed
Thread #3: 400000 read pairs finished. 58 secs passed
Thread #1: 450000 read pairs finished. 71 secs passed
Thread #2: 500000 read pairs finished. 72 secs passed
Thread #0: 550000 read pairs finished. 72 secs passed
Thread #3: 600000 read pairs finished. 73 secs passed
Thread #1: 650000 read pairs finished. 85 secs passed
Thread #2: 700000 read pairs finished. 87 secs passed
Thread #0: 750000 read pairs finished. 88 secs passed
Thread #3: 800000 read pairs finished. 89 secs passed
Thread #1: 850000 read pairs finished. 101 secs passed
Thread #2: 900000 read pairs finished. 103 secs passed
Thread #0: 950000 read pairs finished. 103 secs passed
Thread #3: 1000000 read pairs finished. 104 secs passed
Thread #1: 1050000 read pairs finished. 116 secs passed
Thread #2: 1100000 read pairs finished. 118 secs passed
Thread #0: 1150000 read pairs finished. 118 secs passed
Thread #3: 1200000 read pairs finished. 119 secs passed
Thread #1: 1250000 read pairs finished. 131 secs passed
Thread #2: 1300000 read pairs finished. 133 secs passed
Thread #0: 1350000 read pairs finished. 133 secs passed
Thread #3: 1400000 read pairs finished. 134 secs passed
Thread #1: 1450000 read pairs finished. 146 secs passed
Thread #2: 1500000 read pairs finished. 148 secs passed
Thread #0: 1550000 read pairs finished. 149 secs passed
Thread #3: 1600000 read pairs finished. 150 secs passed
Thread #1: 1650000 read pairs finished. 160 secs passed
Thread #2: 1700000 read pairs finished. 164 secs passed
Thread #0: 1750000 read pairs finished. 164 secs passed
Thread #3: 1800000 read pairs finished. 165 secs passed
Thread #1: 1850000 read pairs finished. 176 secs passed
Thread #2: 1900000 read pairs finished. 179 secs passed
Thread #0: 1950000 read pairs finished. 179 secs passed
Thread #3: 2000000 read pairs finished. 181 secs passed
Thread #1: 2050000 read pairs finished. 191 secs passed
Thread #2: 2100000 read pairs finished. 194 secs passed
Thread #0: 2150000 read pairs finished. 195 secs passed
Thread #3: 2200000 read pairs finished. 196 secs passed
Thread #1: 2250000 read pairs finished. 205 secs passed
Thread #2: 2300000 read pairs finished. 209 secs passed
Thread #0: 2350000 read pairs finished. 210 secs passed
Thread #3: 2400000 read pairs finished. 211 secs passed
Thread #1: 2450000 read pairs finished. 220 secs passed
Thread #2: 2500000 read pairs finished. 225 secs passed
Thread #0: 2550000 read pairs finished. 226 secs passed
Thread #3: 2600000 read pairs finished. 227 secs passed
Thread #1: 2650000 read pairs finished. 236 secs passed
Thread #2: 2700000 read pairs finished. 240 secs passed
Thread #0: 2750000 read pairs finished. 241 secs passed
Thread #3: 2800000 read pairs finished. 242 secs passed
Thread #1: 2850000 read pairs finished. 251 secs passed
Thread #2: 2900000 read pairs finished. 255 secs passed
Thread #0: 2950000 read pairs finished. 256 secs passed
Thread #3: 3000000 read pairs finished. 257 secs passed
Thread #1: 3050000 read pairs finished. 265 secs passed
Thread #2: 3100000 read pairs finished. 271 secs passed
Thread #0: 3150000 read pairs finished. 271 secs passed
Thread #3: 3200000 read pairs finished. 272 secs passed
Thread #1: 3250000 read pairs finished. 280 secs passed
Thread #2: 3300000 read pairs finished. 285 secs passed
Thread #0: 3350000 read pairs finished. 286 secs passed
Thread #3: 3400000 read pairs finished. 289 secs passed
Thread #1: 3450000 read pairs finished. 297 secs passed
Thread #2: 3500000 read pairs finished. 301 secs passed
Thread #0: 3550000 read pairs finished. 302 secs passed
Thread #3: 3600000 read pairs finished. 304 secs passed
Thread #1: 3650000 read pairs finished. 312 secs passed
Thread #2: 3700000 read pairs finished. 317 secs passed
Thread #0: 3750000 read pairs finished. 317 secs passed
Thread #3: 3800000 read pairs finished. 319 secs passed
Thread #1: 3850000 read pairs finished. 327 secs passed
Thread #2: 3900000 read pairs finished. 332 secs passed
Thread #0: 3950000 read pairs finished. 332 secs passed
Thread #3: 4000000 read pairs finished. 334 secs passed
Thread #1: 4050000 read pairs finished. 342 secs passed
Thread #2: 4100000 read pairs finished. 346 secs passed
Thread #0: 4150000 read pairs finished. 347 secs passed
Thread #3: 4200000 read pairs finished. 349 secs passed
Thread #1: 4250000 read pairs finished. 358 secs passed
Thread #2: 4300000 read pairs finished. 361 secs passed
Thread #0: 4350000 read pairs finished. 363 secs passed
Thread #3: 4400000 read pairs finished. 365 secs passed
Thread #1: 4450000 read pairs finished. 373 secs passed
Thread #2: 4500000 read pairs finished. 376 secs passed
Thread #0: 4550000 read pairs finished. 378 secs passed
Thread #3: 4600000 read pairs finished. 380 secs passed
Thread #1: 4650000 read pairs finished. 388 secs passed
Thread #2: 4700000 read pairs finished. 391 secs passed
Thread #0: 4750000 read pairs finished. 393 secs passed
Thread #3: 4800000 read pairs finished. 395 secs passed
Thread #1: 4850000 read pairs finished. 403 secs passed
Thread #2: 4900000 read pairs finished. 406 secs passed
Thread #0: 4950000 read pairs finished. 408 secs passed
Thread #3: 5000000 read pairs finished. 410 secs passed
Thread #1: 5050000 read pairs finished. 417 secs passed
Thread #2: 5100000 read pairs finished. 421 secs passed
Thread #0: 5150000 read pairs finished. 423 secs passed
Thread #3: 5200000 read pairs finished. 426 secs passed
Thread #1: 5250000 read pairs finished. 433 secs passed
Thread #2: 5300000 read pairs finished. 436 secs passed
Thread #0: 5350000 read pairs finished. 438 secs passed
Thread #3: 5400000 read pairs finished. 442 secs passed
Thread #1: 5450000 read pairs finished. 448 secs passed
Thread #2: 5500000 read pairs finished. 451 secs passed
Thread #0: 5550000 read pairs finished. 453 secs passed
Thread #3: 5600000 read pairs finished. 457 secs passed
Thread #1: 5650000 read pairs finished. 463 secs passed
Thread #2: 5700000 read pairs finished. 466 secs passed
Thread #0: 5750000 read pairs finished. 468 secs passed
Thread #3: 5800000 read pairs finished. 472 secs passed
Thread #1: 5850000 read pairs finished. 478 secs passed
Thread #2: 5900000 read pairs finished. 481 secs passed
Thread #0: 5950000 read pairs finished. 483 secs passed
Thread #3: 6000000 read pairs finished. 487 secs passed
Thread #1: 6050000 read pairs finished. 492 secs passed
Thread #2: 6100000 read pairs finished. 498 secs passed
Thread #0: 6150000 read pairs finished. 500 secs passed
Thread #3: 6200000 read pairs finished. 502 secs passed
Thread #1: 6250000 read pairs finished. 508 secs passed
Thread #2: 6300000 read pairs finished. 513 secs passed
Thread #0: 6350000 read pairs finished. 515 secs passed
Thread #3: 6400000 read pairs finished. 518 secs passed
Thread #1: 6450000 read pairs finished. 523 secs passed
Thread #2: 6500000 read pairs finished. 528 secs passed
Thread #0: 6550000 read pairs finished. 530 secs passed
Thread #3: 6600000 read pairs finished. 533 secs passed
Thread #1: 6650000 read pairs finished. 538 secs passed
Thread #2: 6700000 read pairs finished. 543 secs passed
Thread #0: 6750000 read pairs finished. 545 secs passed
Thread #3: 6800000 read pairs finished. 548 secs passed
Thread #1: 6850000 read pairs finished. 553 secs passed
Thread #2: 6900000 read pairs finished. 558 secs passed
Thread #0: 6950000 read pairs finished. 561 secs passed
Thread #3: 7000000 read pairs finished. 564 secs passed
Thread #1: 7050000 read pairs finished. 568 secs passed
Thread #2: 7100000 read pairs finished. 573 secs passed
Thread #0: 7150000 read pairs finished. 576 secs passed
Thread #3: 7200000 read pairs finished. 579 secs passed
Thread #1: 7250000 read pairs finished. 583 secs passed
Thread #2: 7300000 read pairs finished. 589 secs passed
Thread #0: 7350000 read pairs finished. 591 secs passed
Thread #3: 7400000 read pairs finished. 594 secs passed
Thread #1: 7450000 read pairs finished. 598 secs passed
Thread #2: 7500000 read pairs finished. 604 secs passed
Thread #0: 7550000 read pairs finished. 606 secs passed
Thread #3: 7600000 read pairs finished. 609 secs passed
Thread #1: 7650000 read pairs finished. 613 secs passed
Thread #2: 7700000 read pairs finished. 618 secs passed
Thread #0: 7750000 read pairs finished. 621 secs passed
Thread #2: 7867124 read pairs finished. 623 secs passed
Thread #3: 7800000 read pairs finished. 624 secs passed
Thread #1: 7850000 read pairs finished. 626 secs passed
Total number of aligned reads:
pairs: 4545285 (58%)
single a: 1331429 (17%)
single b: 1233410 (16%)
Done.
Finished at Tue Dec 2 14:41:13 2014
Total time consumed: 626 secs
BSMAP v2.74
Start at: Tue Dec 2 14:41:14 2014
Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA)
Load in 7658 db seqs, total size 557717710 bp. 9 secs passed
total_kmers: 43046721
Create seed table. 25 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 (read_1): ++,-+
mapping strand (read_2): +-,--
Pair-end alignment(4 threads)
Input read file #1: mcf_T3D3_R1.fastq (format: FASTQ)
Input read file #2: mcf_T3D3_R2.fastq (format: FASTQ)
Output file: bsmap_out_T3D3.sam (format: SAM)
Thread #0: 50000 read pairs finished. 41 secs passed
Thread #3: 100000 read pairs finished. 41 secs passed
Thread #2: 150000 read pairs finished. 42 secs passed
Thread #1: 200000 read pairs finished. 42 secs passed
Thread #0: 250000 read pairs finished. 57 secs passed
Thread #3: 300000 read pairs finished. 57 secs passed
Thread #2: 350000 read pairs finished. 58 secs passed
Thread #1: 400000 read pairs finished. 58 secs passed
Thread #0: 450000 read pairs finished. 72 secs passed
Thread #3: 500000 read pairs finished. 73 secs passed
Thread #2: 550000 read pairs finished. 73 secs passed
Thread #1: 600000 read pairs finished. 74 secs passed
Thread #0: 650000 read pairs finished. 87 secs passed
Thread #3: 700000 read pairs finished. 88 secs passed
Thread #2: 750000 read pairs finished. 89 secs passed
Thread #1: 800000 read pairs finished. 90 secs passed
Thread #0: 850000 read pairs finished. 103 secs passed
Thread #3: 900000 read pairs finished. 103 secs passed
Thread #2: 950000 read pairs finished. 104 secs passed
Thread #1: 1000000 read pairs finished. 105 secs passed
Thread #0: 1050000 read pairs finished. 119 secs passed
Thread #3: 1100000 read pairs finished. 119 secs passed
Thread #2: 1150000 read pairs finished. 120 secs passed
Thread #1: 1200000 read pairs finished. 121 secs passed
Thread #0: 1250000 read pairs finished. 134 secs passed
Thread #3: 1300000 read pairs finished. 135 secs passed
Thread #2: 1350000 read pairs finished. 135 secs passed
Thread #1: 1400000 read pairs finished. 136 secs passed
Thread #0: 1450000 read pairs finished. 149 secs passed
Thread #3: 1500000 read pairs finished. 151 secs passed
Thread #2: 1550000 read pairs finished. 152 secs passed
Thread #1: 1600000 read pairs finished. 152 secs passed
Thread #0: 1650000 read pairs finished. 165 secs passed
Thread #3: 1700000 read pairs finished. 167 secs passed
Thread #2: 1750000 read pairs finished. 167 secs passed
Thread #1: 1800000 read pairs finished. 168 secs passed
Thread #0: 1850000 read pairs finished. 181 secs passed
Thread #3: 1900000 read pairs finished. 182 secs passed
Thread #2: 1950000 read pairs finished. 183 secs passed
Thread #1: 2000000 read pairs finished. 184 secs passed
Thread #0: 2050000 read pairs finished. 196 secs passed
Thread #3: 2100000 read pairs finished. 198 secs passed
Thread #2: 2150000 read pairs finished. 198 secs passed
Thread #1: 2200000 read pairs finished. 199 secs passed
Thread #0: 2250000 read pairs finished. 212 secs passed
Thread #3: 2300000 read pairs finished. 213 secs passed
Thread #2: 2350000 read pairs finished. 214 secs passed
Thread #1: 2400000 read pairs finished. 215 secs passed
Thread #0: 2450000 read pairs finished. 229 secs passed
Thread #3: 2500000 read pairs finished. 230 secs passed
Thread #2: 2550000 read pairs finished. 230 secs passed
Thread #1: 2600000 read pairs finished. 231 secs passed
Thread #0: 2650000 read pairs finished. 245 secs passed
Thread #3: 2700000 read pairs finished. 246 secs passed
Thread #2: 2750000 read pairs finished. 247 secs passed
Thread #1: 2800000 read pairs finished. 247 secs passed
Thread #0: 2850000 read pairs finished. 260 secs passed
Thread #3: 2900000 read pairs finished. 262 secs passed
Thread #2: 2950000 read pairs finished. 263 secs passed
Thread #1: 3000000 read pairs finished. 263 secs passed
Thread #0: 3050000 read pairs finished. 275 secs passed
Thread #3: 3100000 read pairs finished. 277 secs passed
Thread #2: 3150000 read pairs finished. 278 secs passed
Thread #1: 3200000 read pairs finished. 279 secs passed
Thread #0: 3250000 read pairs finished. 291 secs passed
Thread #3: 3300000 read pairs finished. 293 secs passed
Thread #2: 3350000 read pairs finished. 294 secs passed
Thread #1: 3400000 read pairs finished. 294 secs passed
Thread #0: 3450000 read pairs finished. 306 secs passed
Thread #3: 3500000 read pairs finished. 309 secs passed
Thread #2: 3550000 read pairs finished. 310 secs passed
Thread #1: 3600000 read pairs finished. 310 secs passed
Thread #0: 3650000 read pairs finished. 322 secs passed
Thread #3: 3700000 read pairs finished. 324 secs passed
Thread #2: 3750000 read pairs finished. 325 secs passed
Thread #1: 3800000 read pairs finished. 326 secs passed
Thread #0: 3850000 read pairs finished. 337 secs passed
Thread #3: 3900000 read pairs finished. 339 secs passed
Thread #2: 3950000 read pairs finished. 341 secs passed
Thread #1: 4000000 read pairs finished. 341 secs passed
Thread #0: 4050000 read pairs finished. 353 secs passed
Thread #3: 4100000 read pairs finished. 355 secs passed
Thread #2: 4150000 read pairs finished. 356 secs passed
Thread #1: 4200000 read pairs finished. 356 secs passed
Thread #0: 4250000 read pairs finished. 369 secs passed
Thread #3: 4300000 read pairs finished. 371 secs passed
Thread #2: 4350000 read pairs finished. 372 secs passed
Thread #1: 4400000 read pairs finished. 372 secs passed
Thread #0: 4450000 read pairs finished. 385 secs passed
Thread #3: 4500000 read pairs finished. 386 secs passed
Thread #2: 4550000 read pairs finished. 388 secs passed
Thread #1: 4600000 read pairs finished. 388 secs passed
Thread #0: 4650000 read pairs finished. 400 secs passed
Thread #3: 4700000 read pairs finished. 401 secs passed
Thread #2: 4750000 read pairs finished. 404 secs passed
Thread #1: 4800000 read pairs finished. 404 secs passed
Thread #0: 4850000 read pairs finished. 415 secs passed
Thread #3: 4900000 read pairs finished. 416 secs passed
Thread #2: 4950000 read pairs finished. 419 secs passed
Thread #1: 5000000 read pairs finished. 420 secs passed
Thread #0: 5050000 read pairs finished. 431 secs passed
Thread #3: 5100000 read pairs finished. 432 secs passed
Thread #2: 5150000 read pairs finished. 435 secs passed
Thread #1: 5200000 read pairs finished. 435 secs passed
Thread #0: 5250000 read pairs finished. 448 secs passed
Thread #3: 5300000 read pairs finished. 449 secs passed
Thread #1: 5400000 read pairs finished. 451 secs passed
Thread #2: 5350000 read pairs finished. 452 secs passed
Thread #0: 5450000 read pairs finished. 464 secs passed
Thread #3: 5500000 read pairs finished. 464 secs passed
Thread #1: 5550000 read pairs finished. 467 secs passed
Thread #2: 5600000 read pairs finished. 468 secs passed
Thread #0: 5650000 read pairs finished. 479 secs passed
Thread #3: 5700000 read pairs finished. 480 secs passed
Thread #1: 5750000 read pairs finished. 483 secs passed
Thread #2: 5800000 read pairs finished. 484 secs passed
Thread #0: 5850000 read pairs finished. 494 secs passed
Thread #3: 5900000 read pairs finished. 495 secs passed
Thread #1: 5950000 read pairs finished. 499 secs passed
Thread #2: 6000000 read pairs finished. 500 secs passed
Thread #0: 6050000 read pairs finished. 510 secs passed
Thread #3: 6100000 read pairs finished. 510 secs passed
Thread #1: 6150000 read pairs finished. 515 secs passed
Thread #2: 6200000 read pairs finished. 516 secs passed
Thread #0: 6250000 read pairs finished. 525 secs passed
Thread #3: 6300000 read pairs finished. 526 secs passed
Thread #1: 6350000 read pairs finished. 531 secs passed
Thread #2: 6400000 read pairs finished. 532 secs passed
Thread #0: 6450000 read pairs finished. 541 secs passed
Thread #3: 6500000 read pairs finished. 542 secs passed
Thread #1: 6550000 read pairs finished. 547 secs passed
Thread #2: 6600000 read pairs finished. 548 secs passed
Thread #0: 6650000 read pairs finished. 557 secs passed
Thread #3: 6700000 read pairs finished. 557 secs passed
Thread #1: 6750000 read pairs finished. 562 secs passed
Thread #2: 6800000 read pairs finished. 563 secs passed
Thread #0: 6850000 read pairs finished. 572 secs passed
Thread #3: 6900000 read pairs finished. 572 secs passed
Thread #1: 6950000 read pairs finished. 578 secs passed
Thread #2: 7000000 read pairs finished. 579 secs passed
Thread #1: 7109789 read pairs finished. 580 secs passed
Thread #0: 7050000 read pairs finished. 585 secs passed
Thread #3: 7100000 read pairs finished. 585 secs passed
Total number of aligned reads:
pairs: 4047152 (57%)
single a: 1332491 (19%)
single b: 1205102 (17%)
Done.
Finished at Tue Dec 2 14:50:59 2014
Total time consumed: 585 secs
BSMAP v2.74
Start at: Tue Dec 2 14:51:00 2014
Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA)
Load in 7658 db seqs, total size 557717710 bp. 9 secs passed
total_kmers: 43046721
Create seed table. 25 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 (read_1): ++,-+
mapping strand (read_2): +-,--
Pair-end alignment(4 threads)
Input read file #1: mcf_T3D5_R1.fastq (format: FASTQ)
Input read file #2: mcf_T3D5_R2.fastq (format: FASTQ)
Output file: bsmap_out_T3D5.sam (format: SAM)
Thread #1: 50000 read pairs finished. 41 secs passed
Thread #2: 100000 read pairs finished. 42 secs passed
Thread #0: 150000 read pairs finished. 42 secs passed
Thread #3: 200000 read pairs finished. 42 secs passed
Thread #1: 250000 read pairs finished. 57 secs passed
Thread #2: 300000 read pairs finished. 58 secs passed
Thread #0: 350000 read pairs finished. 58 secs passed
Thread #3: 400000 read pairs finished. 59 secs passed
Thread #1: 450000 read pairs finished. 72 secs passed
Thread #2: 500000 read pairs finished. 73 secs passed
Thread #0: 550000 read pairs finished. 74 secs passed
Thread #3: 600000 read pairs finished. 75 secs passed
Thread #1: 650000 read pairs finished. 87 secs passed
Thread #2: 700000 read pairs finished. 88 secs passed
Thread #0: 750000 read pairs finished. 90 secs passed
Thread #3: 800000 read pairs finished. 90 secs passed
Thread #1: 850000 read pairs finished. 102 secs passed
Thread #2: 900000 read pairs finished. 103 secs passed
Thread #0: 950000 read pairs finished. 105 secs passed
Thread #3: 1000000 read pairs finished. 106 secs passed
Thread #1: 1050000 read pairs finished. 118 secs passed
Thread #2: 1100000 read pairs finished. 118 secs passed
Thread #0: 1150000 read pairs finished. 120 secs passed
Thread #3: 1200000 read pairs finished. 121 secs passed
Thread #1: 1250000 read pairs finished. 134 secs passed
Thread #2: 1300000 read pairs finished. 134 secs passed
Thread #0: 1350000 read pairs finished. 136 secs passed
Thread #3: 1400000 read pairs finished. 136 secs passed
Thread #1: 1450000 read pairs finished. 150 secs passed
Thread #2: 1500000 read pairs finished. 151 secs passed
Thread #0: 1550000 read pairs finished. 151 secs passed
Thread #3: 1600000 read pairs finished. 152 secs passed
Thread #1: 1650000 read pairs finished. 166 secs passed
Thread #2: 1700000 read pairs finished. 166 secs passed
Thread #0: 1750000 read pairs finished. 167 secs passed
Thread #3: 1800000 read pairs finished. 168 secs passed
Thread #1: 1850000 read pairs finished. 181 secs passed
Thread #2: 1900000 read pairs finished. 182 secs passed
Thread #0: 1950000 read pairs finished. 182 secs passed
Thread #3: 2000000 read pairs finished. 183 secs passed
Thread #1: 2050000 read pairs finished. 197 secs passed
Thread #2: 2100000 read pairs finished. 197 secs passed
Thread #0: 2150000 read pairs finished. 198 secs passed
Thread #3: 2200000 read pairs finished. 199 secs passed
Thread #1: 2250000 read pairs finished. 212 secs passed
Thread #2: 2300000 read pairs finished. 213 secs passed
Thread #0: 2350000 read pairs finished. 214 secs passed
Thread #3: 2400000 read pairs finished. 214 secs passed
Thread #1: 2450000 read pairs finished. 228 secs passed
Thread #2: 2500000 read pairs finished. 229 secs passed
Thread #0: 2550000 read pairs finished. 229 secs passed
Thread #3: 2600000 read pairs finished. 230 secs passed
Thread #1: 2650000 read pairs finished. 244 secs passed
Thread #2: 2700000 read pairs finished. 244 secs passed
Thread #0: 2750000 read pairs finished. 244 secs passed
Thread #3: 2800000 read pairs finished. 245 secs passed
Thread #1: 2850000 read pairs finished. 260 secs passed
Thread #0: 2950000 read pairs finished. 261 secs passed
Thread #2: 2900000 read pairs finished. 261 secs passed
Thread #3: 3000000 read pairs finished. 261 secs passed
Thread #1: 3050000 read pairs finished. 275 secs passed
Thread #0: 3100000 read pairs finished. 276 secs passed
Thread #2: 3150000 read pairs finished. 277 secs passed
Thread #3: 3200000 read pairs finished. 278 secs passed
Thread #1: 3250000 read pairs finished. 291 secs passed
Thread #0: 3300000 read pairs finished. 291 secs passed
Thread #2: 3350000 read pairs finished. 292 secs passed
Thread #3: 3400000 read pairs finished. 293 secs passed
Thread #1: 3450000 read pairs finished. 306 secs passed
Thread #0: 3500000 read pairs finished. 306 secs passed
Thread #2: 3550000 read pairs finished. 308 secs passed
Thread #3: 3600000 read pairs finished. 310 secs passed
Thread #0: 3700000 read pairs finished. 322 secs passed
Thread #1: 3650000 read pairs finished. 323 secs passed
Thread #2: 3750000 read pairs finished. 323 secs passed
Thread #3: 3800000 read pairs finished. 325 secs passed
Thread #0: 3850000 read pairs finished. 338 secs passed
Thread #2: 3950000 read pairs finished. 338 secs passed
Thread #1: 3900000 read pairs finished. 339 secs passed
Thread #3: 4000000 read pairs finished. 339 secs passed
Thread #0: 4050000 read pairs finished. 352 secs passed
Thread #2: 4100000 read pairs finished. 353 secs passed
Thread #1: 4150000 read pairs finished. 354 secs passed
Thread #3: 4200000 read pairs finished. 355 secs passed
Thread #0: 4250000 read pairs finished. 367 secs passed
Thread #2: 4300000 read pairs finished. 369 secs passed
Thread #1: 4350000 read pairs finished. 370 secs passed
Thread #3: 4400000 read pairs finished. 371 secs passed
Thread #0: 4450000 read pairs finished. 382 secs passed
Thread #2: 4500000 read pairs finished. 384 secs passed
Thread #1: 4550000 read pairs finished. 386 secs passed
Thread #3: 4600000 read pairs finished. 386 secs passed
Thread #0: 4650000 read pairs finished. 397 secs passed
Thread #2: 4700000 read pairs finished. 399 secs passed
Thread #1: 4750000 read pairs finished. 401 secs passed
Thread #3: 4800000 read pairs finished. 402 secs passed
Thread #0: 4850000 read pairs finished. 412 secs passed
Thread #2: 4900000 read pairs finished. 414 secs passed
Thread #1: 4950000 read pairs finished. 417 secs passed
Thread #3: 5000000 read pairs finished. 418 secs passed
Thread #0: 5050000 read pairs finished. 427 secs passed
Thread #2: 5100000 read pairs finished. 429 secs passed
Thread #1: 5150000 read pairs finished. 433 secs passed
Thread #3: 5200000 read pairs finished. 433 secs passed
Thread #0: 5250000 read pairs finished. 442 secs passed
Thread #2: 5300000 read pairs finished. 444 secs passed
Thread #1: 5350000 read pairs finished. 448 secs passed
Thread #3: 5400000 read pairs finished. 449 secs passed
Thread #0: 5450000 read pairs finished. 457 secs passed
Thread #2: 5500000 read pairs finished. 458 secs passed
Thread #1: 5550000 read pairs finished. 464 secs passed
Thread #3: 5600000 read pairs finished. 464 secs passed
Thread #0: 5650000 read pairs finished. 472 secs passed
Thread #2: 5700000 read pairs finished. 475 secs passed
Thread #1: 5750000 read pairs finished. 481 secs passed
Thread #3: 5800000 read pairs finished. 482 secs passed
Thread #0: 5850000 read pairs finished. 487 secs passed
Thread #2: 5900000 read pairs finished. 490 secs passed
Thread #3: 6000000 read pairs finished. 497 secs passed
Thread #1: 5950000 read pairs finished. 498 secs passed
Thread #0: 6050000 read pairs finished. 503 secs passed
Thread #2: 6100000 read pairs finished. 505 secs passed
Thread #3: 6150000 read pairs finished. 512 secs passed
Thread #1: 6200000 read pairs finished. 513 secs passed
Thread #0: 6250000 read pairs finished. 518 secs passed
Thread #2: 6300000 read pairs finished. 520 secs passed
Thread #3: 6350000 read pairs finished. 527 secs passed
Thread #1: 6400000 read pairs finished. 529 secs passed
Thread #0: 6450000 read pairs finished. 534 secs passed
Thread #2: 6500000 read pairs finished. 536 secs passed
Thread #3: 6550000 read pairs finished. 542 secs passed
Thread #1: 6600000 read pairs finished. 545 secs passed
Thread #0: 6650000 read pairs finished. 549 secs passed
Thread #2: 6700000 read pairs finished. 551 secs passed
Thread #3: 6750000 read pairs finished. 557 secs passed
Thread #1: 6800000 read pairs finished. 560 secs passed
Thread #0: 6850000 read pairs finished. 564 secs passed
Thread #2: 6900000 read pairs finished. 566 secs passed
Thread #3: 6950000 read pairs finished. 572 secs passed
Thread #1: 7000000 read pairs finished. 575 secs passed
Thread #0: 7050000 read pairs finished. 579 secs passed
Thread #3: 7125800 read pairs finished. 579 secs passed
Thread #2: 7100000 read pairs finished. 580 secs passed
Total number of aligned reads:
pairs: 4092568 (57%)
single a: 1250715 (18%)
single b: 1133306 (16%)
Done.
Finished at Tue Dec 2 15:00:40 2014
Total time consumed: 580 secs