Logging started at 12:03:34 on 10 Jun 2016
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp	/usr/local/lib/python2.7/dist-packages/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/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/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/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/tmp/
blastall_fp	blastall
seconds_to_sleep	1

parameter file values:
alpha_diversity:metrics	berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,michaelis_menten_fit,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree
beta_diversity:metrics	abund_jaccard,binary_chisq,binary_chord,binary_euclidean,binary_hamming,binary_jaccard,binary_lennon,binary_ochiai,binary_pearson,binary_sorensen_dice,bray_curtis,bray_curtis_faith,bray_curtis_magurran,canberra,chisq,chord,euclidean,gower,hellinger,kulczynski,manhattan,morisita_horn,pearson,soergel,spearman_approx,specprof,unifrac,unweighted_unifrac,unweighted_unifrac_full_tree,weighted_normalized_unifrac,weighted_unifrac
summarize_taxa:level	2,3,4,5,6,7
parallel:jobs_to_start	1
plot_taxa_summary:labels	Phylum,Class,Order,Family,Genus,Species
plot_taxa_summary:chart_type	bar,area,pie
core_diversity_analyses:categories	status

Input file md5 sums:
qiime_results/data_mc50/final_otu_map_mc50_tax.biom: 4b58d798885fa253bf539b2b2469978c
meta.txt: 4a8c1aac4ce74f349e5b94ef6b7c078c
qiime_results/data_mc50/rep_set_mc50.tre: a23474dcef0bd6724f08eba9e9a3e094

Executing commands.

# Generate BIOM table summary command 
biom summarize-table -i qiime_results/data_mc50/final_otu_map_mc50_tax.biom -o qiime_results/cd_mc50/biom_table_summary.txt 

Stdout:

Stderr:

# Filter low sequence count samples from table (minimum sequence count: 859) command 
filter_samples_from_otu_table.py -i qiime_results/data_mc50/final_otu_map_mc50_tax.biom -o qiime_results/cd_mc50/table_mc859.biom -n 859

Stdout:

Stderr:

# Rarify the OTU table to 859 sequences/sample command 
single_rarefaction.py -i qiime_results/cd_mc50/table_mc859.biom -o qiime_results/cd_mc50/table_even859.biom -d 859

Stdout:

Stderr:

Executing commands.

# Beta Diversity (abund_jaccard) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics abund_jaccard  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (abund_jaccard) command 
mv qiime_results/cd_mc50/bdiv_even859//abund_jaccard_table_even859.txt qiime_results/cd_mc50/bdiv_even859//abund_jaccard_dm.txt

Stdout:

Stderr:

# Principal coordinates (abund_jaccard) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//abund_jaccard_dm.txt -o qiime_results/cd_mc50/bdiv_even859//abund_jaccard_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.22613038952 and the largest is 0.853561839675.
  RuntimeWarning

# Make emperor plots, abund_jaccard) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//abund_jaccard_pc.txt -o qiime_results/cd_mc50/bdiv_even859//abund_jaccard_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_chisq) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_chisq  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_chisq) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_chisq_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_chisq_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_chisq) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_chisq_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_chisq_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_chisq) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_chisq_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_chisq_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_chord) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_chord  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_chord) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_chord_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_chord_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_chord) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_chord_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_chord_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_chord) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_chord_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_chord_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_euclidean) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_euclidean  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_euclidean) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_euclidean_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_euclidean_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_euclidean) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_euclidean_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_euclidean_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_euclidean) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_euclidean_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_euclidean_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_hamming) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_hamming  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_hamming) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_hamming_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_hamming_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_hamming) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_hamming_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_hamming_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -375.94349676 and the largest is 3600.38944412.
  RuntimeWarning

# Make emperor plots, binary_hamming) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_hamming_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_hamming_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_jaccard) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_jaccard  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_jaccard) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_jaccard_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_jaccard_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_jaccard) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_jaccard_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_jaccard_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_jaccard) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_jaccard_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_jaccard_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_lennon) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_lennon  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_lennon) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_lennon_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_lennon_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_lennon) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_lennon_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_lennon_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.170269512583 and the largest is 0.374458727821.
  RuntimeWarning

# Make emperor plots, binary_lennon) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_lennon_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_lennon_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_ochiai) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_ochiai  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_ochiai) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_ochiai_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_ochiai_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_ochiai) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_ochiai_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_ochiai_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0350431784638 and the largest is 0.395574315314.
  RuntimeWarning

# Make emperor plots, binary_ochiai) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_ochiai_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_ochiai_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_pearson) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_pearson  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_pearson) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_pearson_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_pearson) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_pearson_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_pearson_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.115044488053 and the largest is 1.17804374062.
  RuntimeWarning

# Make emperor plots, binary_pearson) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_pearson_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_pearson_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_sorensen_dice) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics binary_sorensen_dice  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (binary_sorensen_dice) command 
mv qiime_results/cd_mc50/bdiv_even859//binary_sorensen_dice_table_even859.txt qiime_results/cd_mc50/bdiv_even859//binary_sorensen_dice_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_sorensen_dice) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//binary_sorensen_dice_dm.txt -o qiime_results/cd_mc50/bdiv_even859//binary_sorensen_dice_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0347839787412 and the largest is 0.397885607113.
  RuntimeWarning

# Make emperor plots, binary_sorensen_dice) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//binary_sorensen_dice_pc.txt -o qiime_results/cd_mc50/bdiv_even859//binary_sorensen_dice_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics bray_curtis  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (bray_curtis) command 
mv qiime_results/cd_mc50/bdiv_even859//bray_curtis_table_even859.txt qiime_results/cd_mc50/bdiv_even859//bray_curtis_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//bray_curtis_dm.txt -o qiime_results/cd_mc50/bdiv_even859//bray_curtis_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0123240542902 and the largest is 1.21700032452.
  RuntimeWarning

# Make emperor plots, bray_curtis) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//bray_curtis_pc.txt -o qiime_results/cd_mc50/bdiv_even859//bray_curtis_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis_faith) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics bray_curtis_faith  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (bray_curtis_faith) command 
mv qiime_results/cd_mc50/bdiv_even859//bray_curtis_faith_table_even859.txt qiime_results/cd_mc50/bdiv_even859//bray_curtis_faith_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis_faith) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//bray_curtis_faith_dm.txt -o qiime_results/cd_mc50/bdiv_even859//bray_curtis_faith_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0123240542902 and the largest is 1.21700032452.
  RuntimeWarning

# Make emperor plots, bray_curtis_faith) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//bray_curtis_faith_pc.txt -o qiime_results/cd_mc50/bdiv_even859//bray_curtis_faith_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis_magurran) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics bray_curtis_magurran  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (bray_curtis_magurran) command 
mv qiime_results/cd_mc50/bdiv_even859//bray_curtis_magurran_table_even859.txt qiime_results/cd_mc50/bdiv_even859//bray_curtis_magurran_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis_magurran) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//bray_curtis_magurran_dm.txt -o qiime_results/cd_mc50/bdiv_even859//bray_curtis_magurran_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0123240542902 and the largest is 1.21700032452.
  RuntimeWarning

# Make emperor plots, bray_curtis_magurran) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//bray_curtis_magurran_pc.txt -o qiime_results/cd_mc50/bdiv_even859//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (canberra) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics canberra  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (canberra) command 
mv qiime_results/cd_mc50/bdiv_even859//canberra_table_even859.txt qiime_results/cd_mc50/bdiv_even859//canberra_dm.txt

Stdout:

Stderr:

# Principal coordinates (canberra) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//canberra_dm.txt -o qiime_results/cd_mc50/bdiv_even859//canberra_pc.txt 

Stdout:

Stderr:

# Make emperor plots, canberra) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//canberra_pc.txt -o qiime_results/cd_mc50/bdiv_even859//canberra_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (chisq) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics chisq  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (chisq) command 
mv qiime_results/cd_mc50/bdiv_even859//chisq_table_even859.txt qiime_results/cd_mc50/bdiv_even859//chisq_dm.txt

Stdout:

Stderr:

# Principal coordinates (chisq) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//chisq_dm.txt -o qiime_results/cd_mc50/bdiv_even859//chisq_pc.txt 

Stdout:

Stderr:

# Make emperor plots, chisq) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//chisq_pc.txt -o qiime_results/cd_mc50/bdiv_even859//chisq_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (chord) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics chord  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (chord) command 
mv qiime_results/cd_mc50/bdiv_even859//chord_table_even859.txt qiime_results/cd_mc50/bdiv_even859//chord_dm.txt

Stdout:

Stderr:

# Principal coordinates (chord) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//chord_dm.txt -o qiime_results/cd_mc50/bdiv_even859//chord_pc.txt 

Stdout:

Stderr:

# Make emperor plots, chord) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//chord_pc.txt -o qiime_results/cd_mc50/bdiv_even859//chord_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (euclidean) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics euclidean  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (euclidean) command 
mv qiime_results/cd_mc50/bdiv_even859//euclidean_table_even859.txt qiime_results/cd_mc50/bdiv_even859//euclidean_dm.txt

Stdout:

Stderr:

# Principal coordinates (euclidean) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//euclidean_dm.txt -o qiime_results/cd_mc50/bdiv_even859//euclidean_pc.txt 

Stdout:

Stderr:

# Make emperor plots, euclidean) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//euclidean_pc.txt -o qiime_results/cd_mc50/bdiv_even859//euclidean_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (gower) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics gower  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (gower) command 
mv qiime_results/cd_mc50/bdiv_even859//gower_table_even859.txt qiime_results/cd_mc50/bdiv_even859//gower_dm.txt

Stdout:

Stderr:

# Principal coordinates (gower) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//gower_dm.txt -o qiime_results/cd_mc50/bdiv_even859//gower_pc.txt 

Stdout:

Stderr:

# Make emperor plots, gower) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//gower_pc.txt -o qiime_results/cd_mc50/bdiv_even859//gower_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (hellinger) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics hellinger  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (hellinger) command 
mv qiime_results/cd_mc50/bdiv_even859//hellinger_table_even859.txt qiime_results/cd_mc50/bdiv_even859//hellinger_dm.txt

Stdout:

Stderr:

# Principal coordinates (hellinger) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//hellinger_dm.txt -o qiime_results/cd_mc50/bdiv_even859//hellinger_pc.txt 

Stdout:

Stderr:

# Make emperor plots, hellinger) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//hellinger_pc.txt -o qiime_results/cd_mc50/bdiv_even859//hellinger_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (kulczynski) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics kulczynski  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (kulczynski) command 
mv qiime_results/cd_mc50/bdiv_even859//kulczynski_table_even859.txt qiime_results/cd_mc50/bdiv_even859//kulczynski_dm.txt

Stdout:

Stderr:

# Principal coordinates (kulczynski) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//kulczynski_dm.txt -o qiime_results/cd_mc50/bdiv_even859//kulczynski_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0123240542902 and the largest is 1.21700032452.
  RuntimeWarning

# Make emperor plots, kulczynski) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//kulczynski_pc.txt -o qiime_results/cd_mc50/bdiv_even859//kulczynski_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (manhattan) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics manhattan  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (manhattan) command 
mv qiime_results/cd_mc50/bdiv_even859//manhattan_table_even859.txt qiime_results/cd_mc50/bdiv_even859//manhattan_dm.txt

Stdout:

Stderr:

# Principal coordinates (manhattan) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//manhattan_dm.txt -o qiime_results/cd_mc50/bdiv_even859//manhattan_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -36374.7420156 and the largest is 3592005.66584.
  RuntimeWarning

# Make emperor plots, manhattan) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//manhattan_pc.txt -o qiime_results/cd_mc50/bdiv_even859//manhattan_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (morisita_horn) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics morisita_horn  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (morisita_horn) command 
mv qiime_results/cd_mc50/bdiv_even859//morisita_horn_table_even859.txt qiime_results/cd_mc50/bdiv_even859//morisita_horn_dm.txt

Stdout:

Stderr:

# Principal coordinates (morisita_horn) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//morisita_horn_dm.txt -o qiime_results/cd_mc50/bdiv_even859//morisita_horn_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.129683420384 and the largest is 1.56735392272.
  RuntimeWarning

# Make emperor plots, morisita_horn) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//morisita_horn_pc.txt -o qiime_results/cd_mc50/bdiv_even859//morisita_horn_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (pearson) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics pearson  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (pearson) command 
mv qiime_results/cd_mc50/bdiv_even859//pearson_table_even859.txt qiime_results/cd_mc50/bdiv_even859//pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (pearson) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//pearson_dm.txt -o qiime_results/cd_mc50/bdiv_even859//pearson_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.166221691856 and the largest is 1.89498506457.
  RuntimeWarning

# Make emperor plots, pearson) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//pearson_pc.txt -o qiime_results/cd_mc50/bdiv_even859//pearson_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (soergel) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics soergel  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (soergel) command 
mv qiime_results/cd_mc50/bdiv_even859//soergel_table_even859.txt qiime_results/cd_mc50/bdiv_even859//soergel_dm.txt

Stdout:

Stderr:

# Principal coordinates (soergel) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//soergel_dm.txt -o qiime_results/cd_mc50/bdiv_even859//soergel_pc.txt 

Stdout:

Stderr:

# Make emperor plots, soergel) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//soergel_pc.txt -o qiime_results/cd_mc50/bdiv_even859//soergel_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (spearman_approx) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics spearman_approx  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (spearman_approx) command 
mv qiime_results/cd_mc50/bdiv_even859//spearman_approx_table_even859.txt qiime_results/cd_mc50/bdiv_even859//spearman_approx_dm.txt

Stdout:

Stderr:

# Principal coordinates (spearman_approx) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//spearman_approx_dm.txt -o qiime_results/cd_mc50/bdiv_even859//spearman_approx_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.082900183942 and the largest is 0.839263079918.
  RuntimeWarning

# Make emperor plots, spearman_approx) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//spearman_approx_pc.txt -o qiime_results/cd_mc50/bdiv_even859//spearman_approx_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (specprof) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics specprof  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (specprof) command 
mv qiime_results/cd_mc50/bdiv_even859//specprof_table_even859.txt qiime_results/cd_mc50/bdiv_even859//specprof_dm.txt

Stdout:

Stderr:

# Principal coordinates (specprof) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//specprof_dm.txt -o qiime_results/cd_mc50/bdiv_even859//specprof_pc.txt 

Stdout:

Stderr:

# Make emperor plots, specprof) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//specprof_pc.txt -o qiime_results/cd_mc50/bdiv_even859//specprof_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unifrac) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics unifrac  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:

# Rename distance matrix (unifrac) command 
mv qiime_results/cd_mc50/bdiv_even859//unifrac_table_even859.txt qiime_results/cd_mc50/bdiv_even859//unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unifrac) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//unifrac_dm.txt -o qiime_results/cd_mc50/bdiv_even859//unifrac_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0118697970892 and the largest is 0.23803374978.
  RuntimeWarning

# Make emperor plots, unifrac) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//unifrac_pc.txt -o qiime_results/cd_mc50/bdiv_even859//unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics unweighted_unifrac  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac) command 
mv qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_table_even859.txt qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_dm.txt -o qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0118697970892 and the largest is 0.23803374978.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_pc.txt -o qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac_full_tree) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics unweighted_unifrac_full_tree  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac_full_tree) command 
mv qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_full_tree_table_even859.txt qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_full_tree_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac_full_tree) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_full_tree_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0166012366457 and the largest is 0.1540203338.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac_full_tree) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_mc50/bdiv_even859//unweighted_unifrac_full_tree_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (weighted_normalized_unifrac) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics weighted_normalized_unifrac  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:

# Rename distance matrix (weighted_normalized_unifrac) command 
mv qiime_results/cd_mc50/bdiv_even859//weighted_normalized_unifrac_table_even859.txt qiime_results/cd_mc50/bdiv_even859//weighted_normalized_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_normalized_unifrac) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_mc50/bdiv_even859//weighted_normalized_unifrac_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0142489749905 and the largest is 0.600310485605.
  RuntimeWarning

# Make emperor plots, weighted_normalized_unifrac) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_mc50/bdiv_even859//weighted_normalized_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (weighted_unifrac) command 
beta_diversity.py -i qiime_results/cd_mc50/table_even859.biom -o qiime_results/cd_mc50/bdiv_even859/ --metrics weighted_unifrac  -t qiime_results/data_mc50/rep_set_mc50.tre 

Stdout:

Stderr:

# Rename distance matrix (weighted_unifrac) command 
mv qiime_results/cd_mc50/bdiv_even859//weighted_unifrac_table_even859.txt qiime_results/cd_mc50/bdiv_even859//weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
principal_coordinates.py -i qiime_results/cd_mc50/bdiv_even859//weighted_unifrac_dm.txt -o qiime_results/cd_mc50/bdiv_even859//weighted_unifrac_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/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 -0.0409040099746 and the largest is 1.28989423681.
  RuntimeWarning

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i qiime_results/cd_mc50/bdiv_even859//weighted_unifrac_pc.txt -o qiime_results/cd_mc50/bdiv_even859//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

Executing commands.

# Alpha rarefaction command 
multiple_rarefactions.py -i qiime_results/cd_mc50/table_mc859.biom -m 10 -x 859 -s 84 -o qiime_results/cd_mc50/arare_max859//rarefaction/ 

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
alpha_diversity.py -i qiime_results/cd_mc50/arare_max859//rarefaction/ -o qiime_results/cd_mc50/arare_max859//alpha_div/ --metrics berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,michaelis_menten_fit,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree -t qiime_results/data_mc50/rep_set_mc50.tre

Stdout:

Stderr:

# Collate alpha command 
collate_alpha.py -i qiime_results/cd_mc50/arare_max859//alpha_div/ -o qiime_results/cd_mc50/arare_max859//alpha_div_collated/ 

Stdout:

Stderr:

# Removing intermediate files command 
rm -r qiime_results/cd_mc50/arare_max859//rarefaction/ qiime_results/cd_mc50/arare_max859//alpha_div/

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
make_rarefaction_plots.py -i qiime_results/cd_mc50/arare_max859//alpha_div_collated/ -m meta.txt -o qiime_results/cd_mc50/arare_max859//alpha_rarefaction_plots/ 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/matplotlib/axes/_base.py:2809: UserWarning: Attempting to set identical bottom==top results
in singular transformations; automatically expanding.
bottom=0, top=0
  'bottom=%s, top=%s') % (bottom, top))

Skipping compare_alpha_diversity.py as no categories were provided.

Executing commands.

# Sort OTU Table command 
sort_otu_table.py -i qiime_results/cd_mc50/table_mc859.biom -o qiime_results/cd_mc50/taxa_plots/table_mc859_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i qiime_results/cd_mc50/taxa_plots/table_mc859_sorted.biom -o qiime_results/cd_mc50/taxa_plots/ --level 2,3,4,5,6,7

Stdout:

Stderr:

# Plot Taxonomy Summary command 
plot_taxa_summary.py -i qiime_results/cd_mc50/taxa_plots/table_mc859_sorted_L2.txt,qiime_results/cd_mc50/taxa_plots/table_mc859_sorted_L3.txt,qiime_results/cd_mc50/taxa_plots/table_mc859_sorted_L4.txt,qiime_results/cd_mc50/taxa_plots/table_mc859_sorted_L5.txt,qiime_results/cd_mc50/taxa_plots/table_mc859_sorted_L6.txt,qiime_results/cd_mc50/taxa_plots/table_mc859_sorted_L7.txt -o qiime_results/cd_mc50/taxa_plots//taxa_summary_plots/ --labels Phylum,Class,Order,Family,Genus,Species --chart_type bar,area,pie

Stdout:

Stderr:

Executing commands.

# Compress the filtered BIOM table command 
gzip qiime_results/cd_mc50/table_mc859.biom

Stdout:

Stderr:

# Compress the rarefied BIOM table command 
gzip qiime_results/cd_mc50/table_even859.biom

Stdout:

Stderr:


Logging stopped at 12:11:33 on 10 Jun 2016
