Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools'
Reference genome folder provided is ../data/	(absolute path is '/home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/)'
FastQ format assumed (by default)
Processing sequences up to read no. 10000 from the input file
Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4