BSMAP v2.74
Start at:  Thu Jan 25 07:47:07 2018

Input reference file: jelly-5k.fasta 	(format: FASTA)
Load in 66732 db seqs, total size 915450032 bp. 11 secs passed
total_kmers: 43046721
Create seed table. 42 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(8 threads)
Input read file: zr_1-sub001.fastq 	(format: FASTQ)
Output file: bsmap_out_jelly-5k.sam	 (format: SAM)
Thread #4: 	200000 reads finished. 313 secs passed
Thread #3: 	100000 reads finished. 313 secs passed
Thread #1: 	350000 reads finished. 315 secs passed
Thread #6: 	300000 reads finished. 318 secs passed
Thread #7: 	400000 reads finished. 318 secs passed
Thread #2: 	150000 reads finished. 319 secs passed
Thread #0: 	250000 reads finished. 322 secs passed
Thread #5: 	50000 reads finished. 322 secs passed
Thread #0: 	725000 reads finished. 445 secs passed
Thread #3: 	500000 reads finished. 536 secs passed
Thread #1: 	550000 reads finished. 537 secs passed
Thread #4: 	450000 reads finished. 539 secs passed
Thread #6: 	600000 reads finished. 540 secs passed
Thread #7: 	650000 reads finished. 540 secs passed
Thread #2: 	700000 reads finished. 540 secs passed
Total number of aligned reads: 33848 (4.7%)
Done.
Finished at Thu Jan 25 07:56:07 2018
Total time consumed:  540 secs