BSMAP v2.73
Start at: Wed Feb 12 17:22:20 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. 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: ++,-+
Single-end alignment(1 threads)
Input read file: /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/BiGo_Larvae/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq.gz (format: gzipped FASTQ)
Output file: bsmap_out.sam (format: SAM)
Thread #0: 50000 reads finished. 30 secs passed
Thread #0: 100000 reads finished. 35 secs passed
Thread #0: 150000 reads finished. 39 secs passed
Thread #0: 200000 reads finished. 44 secs passed
Thread #0: 250000 reads finished. 49 secs passed
Thread #0: 300000 reads finished. 53 secs passed
Thread #0: 350000 reads finished. 58 secs passed
Thread #0: 400000 reads finished. 62 secs passed
Thread #0: 450000 reads finished. 67 secs passed
Thread #0: 500000 reads finished. 72 secs passed
Thread #0: 550000 reads finished. 76 secs passed
Thread #0: 600000 reads finished. 81 secs passed
Thread #0: 650000 reads finished. 86 secs passed
Thread #0: 700000 reads finished. 90 secs passed
Thread #0: 750000 reads finished. 95 secs passed
Thread #0: 800000 reads finished. 100 secs passed
Thread #0: 850000 reads finished. 105 secs passed
Thread #0: 900000 reads finished. 109 secs passed
Thread #0: 950000 reads finished. 114 secs passed
Thread #0: 1000000 reads finished. 119 secs passed
Thread #0: 1050000 reads finished. 124 secs passed
Thread #0: 1100000 reads finished. 130 secs passed
Thread #0: 1150000 reads finished. 135 secs passed
Thread #0: 1200000 reads finished. 140 secs passed
Thread #0: 1250000 reads finished. 145 secs passed
Thread #0: 1300000 reads finished. 150 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. 177 secs passed
Thread #0: 1600000 reads finished. 182 secs passed
Thread #0: 1650000 reads finished. 186 secs passed
Thread #0: 1700000 reads finished. 191 secs passed
Thread #0: 1750000 reads finished. 196 secs passed
Thread #0: 1800000 reads finished. 201 secs passed
Thread #0: 1850000 reads finished. 206 secs passed
Thread #0: 1900000 reads finished. 211 secs passed
Thread #0: 1950000 reads finished. 216 secs passed
Thread #0: 2000000 reads finished. 221 secs passed
Thread #0: 2050000 reads finished. 226 secs passed
Thread #0: 2100000 reads finished. 231 secs passed
Thread #0: 2150000 reads finished. 236 secs passed
Thread #0: 2200000 reads finished. 241 secs passed
Thread #0: 2250000 reads finished. 245 secs passed
Thread #0: 2300000 reads finished. 250 secs passed
Thread #0: 2350000 reads finished. 255 secs passed
Thread #0: 2400000 reads finished. 260 secs passed
Thread #0: 2450000 reads finished. 265 secs passed
Thread #0: 2500000 reads finished. 270 secs passed
Thread #0: 2550000 reads finished. 275 secs passed
Thread #0: 2600000 reads finished. 280 secs passed
Thread #0: 2650000 reads finished. 284 secs passed
Thread #0: 2700000 reads finished. 289 secs passed
Thread #0: 2709822 reads finished. 290 secs passed
Total number of aligned reads: 1905030 (70%)
Done.
Finished at Wed Feb 12 17:27:10 2014
Total time consumed: 290 secs