BSMAP v2.73
Start at: Wed Feb 12 17:34:46 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. 9 secs passed
total_kmers: 43046721
Create seed table. 29 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/FCC39EM/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L004_R1.fastq.gz (format: gzipped FASTQ)
Output file: bsmap_out.sam (format: SAM)
Thread #0: 50000 reads finished. 34 secs passed
Thread #0: 100000 reads finished. 39 secs passed
Thread #0: 150000 reads finished. 44 secs passed
Thread #0: 200000 reads finished. 49 secs passed
Thread #0: 250000 reads finished. 54 secs passed
Thread #0: 300000 reads finished. 59 secs passed
Thread #0: 350000 reads finished. 64 secs passed
Thread #0: 400000 reads finished. 69 secs passed
Thread #0: 450000 reads finished. 74 secs passed
Thread #0: 500000 reads finished. 79 secs passed
Thread #0: 550000 reads finished. 84 secs passed
Thread #0: 600000 reads finished. 89 secs passed
Thread #0: 650000 reads finished. 94 secs passed
Thread #0: 700000 reads finished. 100 secs passed
Thread #0: 750000 reads finished. 105 secs passed
Thread #0: 800000 reads finished. 110 secs passed
Thread #0: 850000 reads finished. 115 secs passed
Thread #0: 900000 reads finished. 120 secs passed
Thread #0: 950000 reads finished. 126 secs passed
Thread #0: 1000000 reads finished. 131 secs passed
Thread #0: 1050000 reads finished. 137 secs passed
Thread #0: 1100000 reads finished. 143 secs passed
Thread #0: 1150000 reads finished. 150 secs passed
Thread #0: 1200000 reads finished. 156 secs passed
Thread #0: 1250000 reads finished. 162 secs passed
Thread #0: 1300000 reads finished. 168 secs passed
Thread #0: 1350000 reads finished. 174 secs passed
Thread #0: 1400000 reads finished. 179 secs passed
Thread #0: 1450000 reads finished. 185 secs passed
Thread #0: 1500000 reads finished. 190 secs passed
Thread #0: 1550000 reads finished. 196 secs passed
Thread #0: 1600000 reads finished. 201 secs passed
Thread #0: 1650000 reads finished. 207 secs passed
Thread #0: 1700000 reads finished. 213 secs passed
Thread #0: 1750000 reads finished. 218 secs passed
Thread #0: 1800000 reads finished. 224 secs passed
Thread #0: 1850000 reads finished. 229 secs passed
Thread #0: 1900000 reads finished. 235 secs passed
Thread #0: 1950000 reads finished. 240 secs passed
Thread #0: 2000000 reads finished. 246 secs passed
Thread #0: 2050000 reads finished. 251 secs passed
Thread #0: 2100000 reads finished. 256 secs passed
Thread #0: 2150000 reads finished. 261 secs passed
Thread #0: 2200000 reads finished. 266 secs passed
Thread #0: 2250000 reads finished. 272 secs passed
Thread #0: 2300000 reads finished. 278 secs passed
Thread #0: 2350000 reads finished. 283 secs passed
Thread #0: 2400000 reads finished. 288 secs passed
Thread #0: 2450000 reads finished. 293 secs passed
Thread #0: 2500000 reads finished. 298 secs passed
Thread #0: 2550000 reads finished. 304 secs passed
Thread #0: 2600000 reads finished. 309 secs passed
Thread #0: 2650000 reads finished. 314 secs passed
Thread #0: 2700000 reads finished. 320 secs passed
Thread #0: 2750000 reads finished. 325 secs passed
Thread #0: 2800000 reads finished. 330 secs passed
Thread #0: 2850000 reads finished. 336 secs passed
Thread #0: 2900000 reads finished. 341 secs passed
Thread #0: 2929159 reads finished. 344 secs passed
Total number of aligned reads: 2048300 (70%)
Done.
Finished at Wed Feb 12 17:40:30 2014
Total time consumed: 344 secs