Quick Reference for running QIIME on Amazon AWS


QIIME 1.7.0 (release) AMI:

To mount an EBS volume:

mkdir ~/data
sudo mount /dev/xvdf ~/data
sudo chown ubuntu ~/data
sudo chgrp ubuntu ~/data


Quick Guide to Common Commands

Assigning Taxonomy to 18S sequences via RDP:

parallel_assign_taxonomy_rdp.py -i /Users/hol
st99_F04NF1.fasta -o /Users/hollybik/Downloads/Clustered_OTUdata/QIIME/Uclust99
_PrimerF04andNF1/rdp_assigned_tax_30Apr14 -T --jobs_to_start 2 --reference_seqs
_fp /macqiime/silva_111/eukaryotes_only/rep_set_euks/99_Silva_111_rep_set_euk.f
asta --id_to_taxonomy_fp /macqiime/silva_111/eukaryotes_only/taxonomy_euks/99_S
ilva_111_taxa_map_RDP_7_levels_euks.txt --confidence 0.7

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