BSMAP v2.73
Start at: Wed Feb 12 16:28:15 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. 24 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_CgF_TTAGGC_L007_R1.fastq.gz (format: gzipped FASTQ)
Output file: bsmap_out.sam (format: SAM)
Thread #0: 50000 reads finished. 29 secs passed
Thread #0: 100000 reads finished. 34 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. 54 secs passed
Thread #0: 323336 reads finished. 56 secs passed
Total number of aligned reads: 227701 (70%)
Done.
Finished at Wed Feb 12 16:29:11 2014
Total time consumed: 56 secs