I'm running bwa-meth in the cloud and have therefore no control over the timestamps of the .fa and related files. That is, the converted the .fa file via bwameth.py index-mem2, uploaded them in the correct order (that is, uploading the .fa file first) and still I have the problem that bwa-meth.py complains that

the modification time on the generated c2t files is newer than on the .fa file

Post-hoc manipulation of timestamps via touch is also unsuccessful. Would it be possible to disable checking the modification timestamps or have a flag for this?