These commands can be run from this directory once bwa-meth is installed

1. Index The Reference.
2. Align the Reads.

# rm ref.fa.bwameth.* 
bwameth.py index ref.fa
bwameth.py --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz -t 12 | samtools view -b - > bwa-meth.bam

Then check the alignments:

samtools flagstat bwa-meth.bam

92791 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
92723 + 0 mapped (99.93%:nan%)
92791 + 0 paired in sequencing
46399 + 0 read1
46392 + 0 read2
92276 + 0 properly paired (99.44%:nan%)
92652 + 0 with itself and mate mapped
71 + 0 singletons (0.08%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

From here, it is recommended to use PileOMeth for extraction and tabulation of the methylation.