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Old 01-24-2019, 12:46 PM   #661
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,015
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Have you verified that the $i variable is expanding correctly?

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
this will create a "ref" directory with all index files. Don't worry about what is in the directory (bbmap uses it own organization).

Then when you run use
Code:
path=dir_containing_ref_dir
in command line, instead of "ref=". This will avoid re-indexing the genome each time.

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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