If you have multiple files to align you should first create an index by doing
Code:
bbmap.sh ref=/users/chutfilz/data/chutfilz/Dm3_Index/dm3.fa
Then when you run use
Code:
path=dir_containing_ref_dir
If you are using a job scheduler then you should submit each alignment job separately (not the way you have the loop setup, which I assume is submitted as a single job?)
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