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2

This is an error from bwa saying that it can't find your input files: Here's a checklist: Check that you have no whitespace after your \ newline breaks. I.e. \ is the very last character Check that you have no whitespace in any path names Quote your variables: $REF_PATH -> "$REF_PATH" Use set -x at the top of your bash script to debug. In ...


3

This option has been added in 0.7.16a, see https://github.com/lh3/bwa/releases, so consider updating.


3

Your link with those command line options is 1 year old. Looks like that version of bwa is 6 years old. You probably should update.


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