BSMAP v2.73
Start at: Wed Feb 12 17:40:33 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. 10 secs passed
total_kmers: 43046721
Create seed table. 34 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_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R1.fastq.gz (format: gzipped FASTQ)
Output file: bsmap_out.sam (format: SAM)
Thread #0: 50000 reads finished. 40 secs passed
Thread #0: 100000 reads finished. 45 secs passed
Thread #0: 150000 reads finished. 50 secs passed
Thread #0: 200000 reads finished. 55 secs passed
Thread #0: 250000 reads finished. 60 secs passed
Thread #0: 300000 reads finished. 65 secs passed
Thread #0: 350000 reads finished. 70 secs passed
Thread #0: 400000 reads finished. 75 secs passed
Thread #0: 450000 reads finished. 79 secs passed
Thread #0: 500000 reads finished. 84 secs passed
Thread #0: 550000 reads finished. 89 secs passed
Thread #0: 600000 reads finished. 94 secs passed
Thread #0: 650000 reads finished. 98 secs passed
Thread #0: 700000 reads finished. 103 secs passed
Thread #0: 750000 reads finished. 108 secs passed
Thread #0: 800000 reads finished. 113 secs passed
Thread #0: 850000 reads finished. 118 secs passed
Thread #0: 900000 reads finished. 123 secs passed
Thread #0: 950000 reads finished. 128 secs passed
Thread #0: 1000000 reads finished. 133 secs passed
Thread #0: 1050000 reads finished. 138 secs passed
Thread #0: 1100000 reads finished. 143 secs passed
Thread #0: 1150000 reads finished. 148 secs passed
Thread #0: 1200000 reads finished. 153 secs passed
Thread #0: 1250000 reads finished. 157 secs passed
Thread #0: 1300000 reads finished. 162 secs passed
Thread #0: 1350000 reads finished. 167 secs passed
Thread #0: 1400000 reads finished. 172 secs passed
Thread #0: 1450000 reads finished. 179 secs passed
Thread #0: 1500000 reads finished. 183 secs passed
Thread #0: 1542983 reads finished. 189 secs passed
Total number of aligned reads: 1061500 (69%)
Done.
Finished at Wed Feb 12 17:43:42 2014
Total time consumed: 189 secs