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Old 10-05-2017, 03:09 AM   #44
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,794

Do you only have 40428 reads in the file? 48 threads seems like an overkill for this amount of reads. Can you use 4 and see if that helps? You can also delete the previous bbmap index files and force the program to create new ones using ref=.

Adding relative paths before the file names should not cause the program to crash. It never has for me.
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