BSMAP v2.73
Start at: Thu Feb 13 09:19:12 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. 28 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_CgM3/filtered_BS_CgM3_GATCAG_L004_R1.fastq.gz (format: gzipped FASTQ)
Output file: bsmap_out.sam (format: SAM)
Thread #0: 50000 reads finished. 33 secs passed
Thread #0: 100000 reads finished. 38 secs passed
Thread #0: 150000 reads finished. 43 secs passed
Thread #0: 200000 reads finished. 48 secs passed
Thread #0: 250000 reads finished. 53 secs passed
Thread #0: 300000 reads finished. 58 secs passed
Thread #0: 350000 reads finished. 63 secs passed
Thread #0: 400000 reads finished. 68 secs passed
Thread #0: 450000 reads finished. 73 secs passed
Thread #0: 500000 reads finished. 78 secs passed
Thread #0: 550000 reads finished. 83 secs passed
Thread #0: 600000 reads finished. 88 secs passed
Thread #0: 650000 reads finished. 93 secs passed
Thread #0: 700000 reads finished. 98 secs passed
Thread #0: 750000 reads finished. 103 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. 123 secs passed
Thread #0: 1000000 reads finished. 128 secs passed
Thread #0: 1050000 reads finished. 134 secs passed
Thread #0: 1100000 reads finished. 139 secs passed
Thread #0: 1150000 reads finished. 144 secs passed
Thread #0: 1200000 reads finished. 149 secs passed
Thread #0: 1250000 reads finished. 154 secs passed
Thread #0: 1300000 reads finished. 159 secs passed
Thread #0: 1350000 reads finished. 163 secs passed
Thread #0: 1400000 reads finished. 168 secs passed
Thread #0: 1450000 reads finished. 173 secs passed
Thread #0: 1500000 reads finished. 178 secs passed
Thread #0: 1550000 reads finished. 185 secs passed
Thread #0: 1600000 reads finished. 190 secs passed
Thread #0: 1650000 reads finished. 195 secs passed
Thread #0: 1700000 reads finished. 200 secs passed
Thread #0: 1750000 reads finished. 205 secs passed
Thread #0: 1800000 reads finished. 210 secs passed
Thread #0: 1850000 reads finished. 215 secs passed
Thread #0: 1900000 reads finished. 220 secs passed
Thread #0: 1950000 reads finished. 225 secs passed
Thread #0: 2000000 reads finished. 230 secs passed
Thread #0: 2050000 reads finished. 235 secs passed
Thread #0: 2100000 reads finished. 239 secs passed
Thread #0: 2150000 reads finished. 244 secs passed
Thread #0: 2200000 reads finished. 249 secs passed
Thread #0: 2250000 reads finished. 254 secs passed
Thread #0: 2300000 reads finished. 259 secs passed
Thread #0: 2350000 reads finished. 263 secs passed
Thread #0: 2400000 reads finished. 268 secs passed
Thread #0: 2450000 reads finished. 273 secs passed
Thread #0: 2500000 reads finished. 278 secs passed
Thread #0: 2550000 reads finished. 283 secs passed
Thread #0: 2551374 reads finished. 283 secs passed
Total number of aligned reads: 1784682 (70%)
Done.
Finished at Thu Feb 13 09:23:55 2014
Total time consumed: 283 secs