Logging started at 14:37:16 on 30 Mar 2017
QIIME version: 1.9.0

qiime_config values:
pick_otus_reference_seqs_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference-0.1.3-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue	all.q
pynast_template_alignment_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference-0.1.3-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
cluster_jobs_fp	start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference-0.1.3-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue	friendlyq
jobs_to_start	1
denoiser_min_per_core	50
assign_taxonomy_id_to_taxonomy_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference-0.1.3-py2.7.egg/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/tmp/
blastall_fp	blastall
seconds_to_sleep	1

parameter file values:
beta_diversity:metrics	bray_curtis
parallel:jobs_to_start	1

Input file md5 sums:
NGTaxMerged_conv.biom: 8b5ea7c030bab548f5bebd92a641775d
mapping.txt: 0be22ae63c63013f229a947bcca9b560
combinedTree.tre: 9a8aed29f86090c767efc93442c8eb34

Executing commands.

# Beta Diversity (bray_curtis) command 
beta_diversity.py -i NGTaxMerged_conv.biom -o beta_div_NG_Tax_BrayCurtis --metrics bray_curtis  -t combinedTree.tre 

Stdout:

Stderr:

# Rename distance matrix (bray_curtis) command 
mv beta_div_NG_Tax_BrayCurtis/bray_curtis_NGTaxMerged_conv.txt beta_div_NG_Tax_BrayCurtis/bray_curtis_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis) command 
principal_coordinates.py -i beta_div_NG_Tax_BrayCurtis/bray_curtis_dm.txt -o beta_div_NG_Tax_BrayCurtis/bray_curtis_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/scikit_bio-0.2.3-py2.7-linux-x86_64.egg/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.047527186414 and the largest is 6.99367398369.
  RuntimeWarning

# Make emperor plots, bray_curtis) command 
make_emperor.py -i beta_div_NG_Tax_BrayCurtis/bray_curtis_pc.txt -o beta_div_NG_Tax_BrayCurtis/bray_curtis_emperor_pcoa_plot/ -m mapping.txt 

Stdout:

Stderr:


Logging stopped at 14:37:21 on 30 Mar 2017
