ARIBA run with this command:
/home/ubuntu/git/ariba/scripts/ariba_test prepareref -f refdata_query_prepareref.in.fa -m refdata_query_prepareref.in.tsv refdata_query_prepareref
from this directory: /home/ubuntu/git/ariba/ariba/tests/data

ARIBA version: local

External dependencies:
bcftools	1.3	/home/ubuntu/bin/bcftools
bowtie2	2.2.9	/home/ubuntu/bin/bowtie2
cdhit	4.6	/home/ubuntu/bin/cd-hit-est
gapfiller	v1-11_Final	/home/ubuntu/bin/GapFiller_v1-11_linux-x86_64/GapFiller.pl
nucmer	3.1	/usr/bin/nucmer
r	3.2.3	/usr/bin/Rscript
samtools	1.3	/home/ubuntu/bin/samtools
spades	3.8.2	python2 /home/ubuntu/bin/spades.py
sspace	Basic_v2.0_linux	/home/ubuntu/bin/SSPACE-BASIC-2.0_linux-x86_64/SSPACE_Basic_v2.0.pl

External dependencies OK: True

Python version:
3.5.1+ (default, Mar 30 2016, 22:46:26)
[GCC 5.3.1 20160330]

Python packages:
ariba	local	/home/ubuntu/git/ariba/scripts/ariba/__init__.py
pyfastaq	3.12.1	/home/ubuntu/.local/lib/python3.5/site-packages/pyfastaq/__init__.py
pymummer	0.7.1	/home/ubuntu/.local/lib/python3.5/site-packages/pymummer/__init__.py
pysam	0.9.1	/home/ubuntu/.local/lib/python3.5/site-packages/pysam/__init__.py

Python packages OK: True

Everything looks OK: True
