BSMAP v2.74
Start at:  Fri Nov  3 10:20:24 2017

Input reference file: genomes/canu_sjw_01.fa 	(format: FASTA)
Load in 11246 db seqs, total size 132146852 bp. 1 secs passed
total_kmers: 43046721
Create seed table. 5 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(5 threads)
Input read file: zr_1-sub001.fastq 	(format: FASTQ)
Output file: analyses/bsmap_out_canu_sjw_01.sam	 (format: SAM)
Thread #1: 	50000 reads finished. 10 secs passed
Thread #2: 	100000 reads finished. 10 secs passed
Thread #3: 	150000 reads finished. 11 secs passed
Thread #0: 	200000 reads finished. 11 secs passed
Thread #4: 	250000 reads finished. 11 secs passed
Thread #2: 	350000 reads finished. 16 secs passed
Thread #1: 	300000 reads finished. 16 secs passed
Thread #3: 	400000 reads finished. 16 secs passed
Thread #0: 	450000 reads finished. 16 secs passed
Thread #4: 	500000 reads finished. 16 secs passed
Thread #4: 	725000 reads finished. 18 secs passed
Thread #2: 	550000 reads finished. 20 secs passed
Thread #1: 	600000 reads finished. 20 secs passed
Thread #3: 	650000 reads finished. 20 secs passed
Thread #0: 	700000 reads finished. 21 secs passed
Total number of aligned reads: 60126 (8.3%)
Done.
Finished at Fri Nov  3 10:20:45 2017
Total time consumed:  21 secs