BSMAP v2.74
Start at:  Thu Jan 25 06:11:16 2018

Input reference file: jelly.out.fasta 	(format: FASTA)
Load in 696946 db seqs, total size 1253001795 bp. 14 secs passed
total_kmers: 43046721
Create seed table. 59 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: bsmap_out_jelly.sam	 (format: SAM)
Thread #4: 	50000 reads finished. 1835 secs passed
Thread #0: 	100000 reads finished. 1853 secs passed
Thread #1: 	200000 reads finished. 1854 secs passed
Thread #3: 	150000 reads finished. 1854 secs passed
Thread #2: 	250000 reads finished. 1877 secs passed
Thread #4: 	300000 reads finished. 3579 secs passed
Thread #3: 	450000 reads finished. 3601 secs passed
Thread #0: 	350000 reads finished. 3603 secs passed
Thread #1: 	400000 reads finished. 3607 secs passed
Thread #2: 	500000 reads finished. 3649 secs passed
Thread #2: 	725000 reads finished. 4537 secs passed
Thread #4: 	550000 reads finished. 5180 secs passed
Thread #0: 	650000 reads finished. 5196 secs passed
Thread #3: 	600000 reads finished. 5196 secs passed
Thread #1: 	700000 reads finished. 5198 secs passed
Total number of aligned reads: 46486 (6.4%)
Done.
Finished at Thu Jan 25 07:37:54 2018
Total time consumed:  5198 secs