find: ‘/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/*_R1_001_val_1.fq.gz’: No such file or directory
basename: missing operand
Try 'basename --help' for more information.
find: ‘*.bam’: No such file or directory
basename: missing operand
Try 'basename --help' for more information.

 *** Bismark methylation extractor version v0.22.3 ***

Trying to determine the type of mapping from the SAM header line of file *deduplicated.bam

[FATAL ERROR]:	File >>*deduplicated.bam<< did not exist. Please re-specify file names and try again...