assign_taxonomy on EC2

Goal: using qiime 1.7.0 on EC2 to assign taxonomy to soil OTUs.

Methods: This script was used by Ryan for the fracking project, and we used it again.

The file run_soil.sh:
#!/bin/bash

nohup echo "start time: $(date)"

nohup time \
parallel_assign_taxonomy_rdp.py \
-i /home/ubuntu/data/soil/pick_rep_set.fasta \
-O 8 \
--rdp_max_memory 4000 \
-o /home/ubuntu/data/soil/tax_assign_out/

nohup echo "end time: $(date)"

We then ran ./run_soil.sh & to use this script.

1.5 hours