./bsmap -a /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/web/cnidarian/Cgigas_Mitochondria_genome.fasta -o /Volumes/web/cnidarian/BSMAP_output_PE_ Mitochondria_A.sam -p 8