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Old 01-24-2019, 01:03 PM   #662
chutfilz
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Location: Providence, RI

Join Date: Jan 2019
Posts: 3
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Wow! Thanks for the fast reply. I've pared down my job to just one set of directly-called, paired files to eliminate the possibility of a malfunctioning $i.

Code:
bbmap.sh ref=/users/chutfilz/data/chutfilz/Dm3_Index/dm3.fa in=PoolCH-1_R1_001_val_1.fa.gz in2=PoolCH-1_R2_001_val_2.fa.gz out=PoolCH-1.sam
The ref assignment was my first argument of the previous command as well, and I've retained it in this run (deleted the previous 'ref' folder first, from the previous failed run).

No use in posting the error I received - it's exactly the same as before!
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