$ ./bs3-align -1 B213-036-pool_S6_L001_R1_001.fastq -2 B213-036-pool_S6_L001_R2_001.fastq -o B213-036 -f sam -g reference_genome/genome.fa -d reference_genome/

     BS-Seeker3 beta

Welcome to SNAP version 1.0.0.

Loading index from directory... 0s.  60856842 bases, seed size 20
Aligning.
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns  %Pairs    Reads/s   Time in Aligner (s)
398,926        0 (0.00%)              0 (0.00%)              398,926 (100.00%)      0 (0.00%)              0.00%     60,979    7                   
(None, None)


	BS-seeker3 Result

	Final Alignment Report
================================================

Number of reads in total: 398926
Number of unique-hits reads (before post-filtering): 0.0
Number of reads mapped after post-filtering 0.0

Alignment Time: 9.74573802948secs

	Final Cytosine Report
================================================

Total Number of Cytosines: 0.0
Total Number of Cs in CpG context: 0.0
Total Number of Cs in CHG context: 0.0
Total Number of Cs in CHH context: 0.0

Rate of Methylation
 mCG  0.000%
 mCHG  0.000%
 mCHH  0.000%



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