BSMAP v2.74
Start at:  Thu Jan 25 07:42:05 2018

Input reference file: jelly-10k.fasta 	(format: FASTA)
Load in 35320 db seqs, total size 691523275 bp. 7 secs passed
total_kmers: 43046721
Create seed table. 33 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-10k.sam	 (format: SAM)
Thread #4: 	50000 reads finished. 180 secs passed
Thread #2: 	200000 reads finished. 181 secs passed
Thread #5: 	250000 reads finished. 182 secs passed
Thread #3: 	100000 reads finished. 182 secs passed
Thread #0: 	350000 reads finished. 182 secs passed
Thread #1: 	150000 reads finished. 183 secs passed
Thread #6: 	400000 reads finished. 183 secs passed
Thread #7: 	300000 reads finished. 184 secs passed
Thread #6: 	725000 reads finished. 249 secs passed
Thread #2: 	500000 reads finished. 300 secs passed
Thread #4: 	450000 reads finished. 300 secs passed
Thread #5: 	550000 reads finished. 301 secs passed
Thread #0: 	650000 reads finished. 301 secs passed
Thread #3: 	600000 reads finished. 301 secs passed
Thread #1: 	700000 reads finished. 301 secs passed
Total number of aligned reads: 34616 (4.8%)
Done.
Finished at Thu Jan 25 07:47:06 2018
Total time consumed:  301 secs