BSMAP v2.73
Start at: Wed Feb 12 17:32:09 2014
Input reference file: /Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa (format: FASTA)
Load in 7658 db seqs, total size 557717710 bp. 10 secs passed
total_kmers: 43046721
Create seed table. 27 secs passed
max number of mismatches: read_length * 8% max gap size: 0
kmer cut-off ratio:5e-07
max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4
quality cutoff: 0 base quality char: '!'
min fragment size:28 max fragemt size:500
start from read #1 end at read #4294967295
additional alignment: T in reads => C in reference
mapping strand: ++,-+
Single-end alignment(1 threads)
Input read file: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/BiGo_Larvae/filtered_BS_CgLarv_T3D5_CAGATC_L007_R1.fastq.gz (format: gzipped FASTQ)
Output file: bsmap_out.sam (format: SAM)
Thread #0: 50000 reads finished. 32 secs passed
Thread #0: 100000 reads finished. 37 secs passed
Thread #0: 150000 reads finished. 42 secs passed
Thread #0: 200000 reads finished. 47 secs passed
Thread #0: 250000 reads finished. 52 secs passed
Thread #0: 300000 reads finished. 57 secs passed
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Thread #0: 500000 reads finished. 77 secs passed
Thread #0: 550000 reads finished. 82 secs passed
Thread #0: 600000 reads finished. 87 secs passed
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Thread #0: 1000000 reads finished. 125 secs passed
Thread #0: 1050000 reads finished. 129 secs passed
Thread #0: 1100000 reads finished. 134 secs passed
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Thread #0: 1300000 reads finished. 153 secs passed
Thread #0: 1350000 reads finished. 157 secs passed
Thread #0: 1400000 reads finished. 162 secs passed
Thread #0: 1450000 reads finished. 167 secs passed
Thread #0: 1500000 reads finished. 172 secs passed
Thread #0: 1550000 reads finished. 178 secs passed
Thread #0: 1600000 reads finished. 185 secs passed
Thread #0: 1650000 reads finished. 190 secs passed
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Thread #0: 1850000 reads finished. 210 secs passed
Thread #0: 1900000 reads finished. 215 secs passed
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Thread #0: 2100000 reads finished. 235 secs passed
Thread #0: 2150000 reads finished. 240 secs passed
Thread #0: 2200000 reads finished. 245 secs passed
Thread #0: 2250000 reads finished. 250 secs passed
Thread #0: 2300000 reads finished. 255 secs passed
Thread #0: 2350000 reads finished. 260 secs passed
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Thread #0: 2450000 reads finished. 270 secs passed
Thread #0: 2500000 reads finished. 275 secs passed
Thread #0: 2550000 reads finished. 280 secs passed
Thread #0: 2600000 reads finished. 285 secs passed
Thread #0: 2650000 reads finished. 291 secs passed
Thread #0: 2700000 reads finished. 296 secs passed
Thread #0: 2750000 reads finished. 302 secs passed
Thread #0: 2800000 reads finished. 309 secs passed
Thread #0: 2850000 reads finished. 316 secs passed
Thread #0: 2900000 reads finished. 321 secs passed
Thread #0: 2950000 reads finished. 327 secs passed
Thread #0: 3000000 reads finished. 332 secs passed
Thread #0: 3050000 reads finished. 338 secs passed
Thread #0: 3100000 reads finished. 344 secs passed
Thread #0: 3150000 reads finished. 349 secs passed
Thread #0: 3200000 reads finished. 354 secs passed
Thread #0: 3250000 reads finished. 360 secs passed
Thread #0: 3300000 reads finished. 366 secs passed
Thread #0: 3350000 reads finished. 371 secs passed
Thread #0: 3400000 reads finished. 377 secs passed
Thread #0: 3450000 reads finished. 382 secs passed
Thread #0: 3500000 reads finished. 388 secs passed
Thread #0: 3550000 reads finished. 393 secs passed
Thread #0: 3600000 reads finished. 399 secs passed
Thread #0: 3650000 reads finished. 404 secs passed
Thread #0: 3700000 reads finished. 410 secs passed
Thread #0: 3750000 reads finished. 415 secs passed
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Thread #0: 3850000 reads finished. 426 secs passed
Thread #0: 3900000 reads finished. 431 secs passed
Thread #0: 3950000 reads finished. 436 secs passed
Thread #0: 4000000 reads finished. 441 secs passed
Thread #0: 4050000 reads finished. 447 secs passed
Thread #0: 4100000 reads finished. 452 secs passed
Thread #0: 4150000 reads finished. 457 secs passed
Thread #0: 4200000 reads finished. 462 secs passed
Thread #0: 4250000 reads finished. 467 secs passed
Thread #0: 4300000 reads finished. 473 secs passed
Thread #0: 4350000 reads finished. 478 secs passed
Thread #0: 4400000 reads finished. 483 secs passed
Thread #0: 4421486 reads finished. 485 secs passed
Total number of aligned reads: 3227635 (73%)
Done.
Finished at Wed Feb 12 17:40:15 2014
Total time consumed: 486 secs