BSMAP v2.73
Start at: Wed Feb 12 17:08:33 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. 17 secs passed
total_kmers: 43046721
Create seed table. 32 secs passed
max number of mismatches: read_length * 8% max gap size: 0
kmer cut-off ratio:5e-07
max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4
quality cutoff: 0 base quality char: '!'
min fragment size:28 max fragemt size:500
start from read #1 end at read #4294967295
additional alignment: T in reads => C in reference
mapping strand: ++,-+
Single-end alignment(1 threads)
Input read file: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/BiGo_Larvae/filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq.gz (format: gzipped FASTQ)
Output file: bsmap_out.sam (format: SAM)
Thread #0: 50000 reads finished. 37 secs passed
Thread #0: 100000 reads finished. 42 secs passed
Thread #0: 150000 reads finished. 46 secs passed
Thread #0: 200000 reads finished. 51 secs passed
Thread #0: 250000 reads finished. 56 secs passed
Thread #0: 300000 reads finished. 61 secs passed
Thread #0: 350000 reads finished. 65 secs passed
Thread #0: 400000 reads finished. 70 secs passed
Thread #0: 450000 reads finished. 75 secs passed
Thread #0: 500000 reads finished. 80 secs passed
Thread #0: 550000 reads finished. 85 secs passed
Thread #0: 600000 reads finished. 89 secs passed
Thread #0: 650000 reads finished. 94 secs passed
Thread #0: 700000 reads finished. 99 secs passed
Thread #0: 750000 reads finished. 104 secs passed
Thread #0: 800000 reads finished. 108 secs passed
Thread #0: 850000 reads finished. 113 secs passed
Thread #0: 900000 reads finished. 118 secs passed
Thread #0: 950000 reads finished. 122 secs passed
Thread #0: 1000000 reads finished. 127 secs passed
Thread #0: 1050000 reads finished. 132 secs passed
Thread #0: 1100000 reads finished. 136 secs passed
Thread #0: 1150000 reads finished. 141 secs passed
Thread #0: 1200000 reads finished. 146 secs passed
Thread #0: 1250000 reads finished. 150 secs passed
Thread #0: 1300000 reads finished. 155 secs passed
Thread #0: 1350000 reads finished. 160 secs passed
Thread #0: 1400000 reads finished. 164 secs passed
Thread #0: 1450000 reads finished. 169 secs passed
Thread #0: 1500000 reads finished. 174 secs passed
Thread #0: 1550000 reads finished. 178 secs passed
Thread #0: 1600000 reads finished. 183 secs passed
Thread #0: 1650000 reads finished. 188 secs passed
Thread #0: 1700000 reads finished. 194 secs passed
Thread #0: 1750000 reads finished. 199 secs passed
Thread #0: 1800000 reads finished. 204 secs passed
Thread #0: 1850000 reads finished. 209 secs passed
Thread #0: 1900000 reads finished. 214 secs passed
Thread #0: 1950000 reads finished. 219 secs passed
Thread #0: 2000000 reads finished. 224 secs passed
Thread #0: 2050000 reads finished. 228 secs passed
Thread #0: 2100000 reads finished. 233 secs passed
Thread #0: 2150000 reads finished. 238 secs passed
Thread #0: 2200000 reads finished. 243 secs passed
Thread #0: 2250000 reads finished. 248 secs passed
Thread #0: 2300000 reads finished. 252 secs passed
Thread #0: 2350000 reads finished. 257 secs passed
Thread #0: 2400000 reads finished. 262 secs passed
Thread #0: 2450000 reads finished. 267 secs passed
Thread #0: 2500000 reads finished. 272 secs passed
Thread #0: 2550000 reads finished. 277 secs passed
Thread #0: 2600000 reads finished. 281 secs passed
Thread #0: 2650000 reads finished. 286 secs passed
Thread #0: 2700000 reads finished. 292 secs passed
Thread #0: 2750000 reads finished. 297 secs passed
Thread #0: 2800000 reads finished. 302 secs passed
Thread #0: 2850000 reads finished. 307 secs passed
Thread #0: 2900000 reads finished. 312 secs passed
Thread #0: 2950000 reads finished. 317 secs passed
Thread #0: 3000000 reads finished. 321 secs passed
Thread #0: 3050000 reads finished. 326 secs passed
Thread #0: 3100000 reads finished. 331 secs passed
Thread #0: 3150000 reads finished. 336 secs passed
Thread #0: 3200000 reads finished. 341 secs passed
Thread #0: 3250000 reads finished. 346 secs passed
Thread #0: 3300000 reads finished. 350 secs passed
Thread #0: 3343987 reads finished. 355 secs passed
Total number of aligned reads: 2346435 (70%)
Done.
Finished at Wed Feb 12 17:14:28 2014
Total time consumed: 355 secs