Logging started at 21:38:49 on 29 May 2018
QIIME version: 1.9.1

qiime_config values:
blastmat_dir	/qiime_software/blast-2.2.22-release/data
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	/qiime_software/blast-2.2.22-release/bin/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,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
filter_samples_from_otu_table:min_count	500
plot_taxa_summary:labels	Phylum,Class,Order,Family,Genus,Species
plot_taxa_summary:chart_type	bar,area,pie
core_diversity_analyses:categories	Week

Input file md5 sums:
qiime_results/data_all/final_otu_map_all_tax.biom: 3d7e21445e4c0e3975a7d2e4ef355583
meta.txt: a72086c2ab21804761519933277da0c1
qiime_results/data_all/rep_set_all.tre: 631d0d2817797d9126557a2da43c607f

Executing commands.

# Generate BIOM table summary command 
biom summarize-table -i qiime_results/data_all/final_otu_map_all_tax.biom -o qiime_results/cd_all/biom_table_summary.txt 

Stdout:

Stderr:

# Filter low sequence count samples from table (minimum sequence count: 510) command 
filter_samples_from_otu_table.py -i qiime_results/data_all/final_otu_map_all_tax.biom -o qiime_results/cd_all/table_mc510.biom -n 510

Stdout:

Stderr:

# Rarify the OTU table to 510 sequences/sample command 
single_rarefaction.py -i qiime_results/cd_all/table_mc510.biom -o qiime_results/cd_all/table_even510.biom -d 510

Stdout:

Stderr:

Executing commands.

# Beta Diversity (abund_jaccard) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics abund_jaccard  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//abund_jaccard_table_even510.txt qiime_results/cd_all/bdiv_even510//abund_jaccard_dm.txt

Stdout:

Stderr:

# Principal coordinates (abund_jaccard) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//abund_jaccard_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.287984616061 and the largest is 8.79457371836.
  RuntimeWarning

# Make emperor plots, abund_jaccard) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//abund_jaccard_pc.txt -o qiime_results/cd_all/bdiv_even510//abund_jaccard_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_chisq) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_chisq  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_chisq_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_chisq_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_chisq) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_chisq_dm.txt -o qiime_results/cd_all/bdiv_even510//binary_chisq_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_chisq) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_chisq_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_chisq_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_chord) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_chord  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_chord_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_chord_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_chord) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_chord_dm.txt -o qiime_results/cd_all/bdiv_even510//binary_chord_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_chord) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_chord_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_chord_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_euclidean) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_euclidean  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_euclidean_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_euclidean_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_euclidean) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_euclidean_dm.txt -o qiime_results/cd_all/bdiv_even510//binary_euclidean_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_euclidean) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_euclidean_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_euclidean_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_hamming) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_hamming  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_hamming_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_hamming_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_hamming) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_hamming_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -2593.61187525 and the largest is 28711.3992101.
  RuntimeWarning

# Make emperor plots, binary_hamming) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_hamming_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_hamming_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_jaccard) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_jaccard  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_jaccard_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_jaccard_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_jaccard) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_jaccard_dm.txt -o qiime_results/cd_all/bdiv_even510//binary_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 -0.0255018730456 and the largest is 4.82399288448.
  RuntimeWarning

# Make emperor plots, binary_jaccard) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_jaccard_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_jaccard_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_lennon) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_lennon  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_lennon_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_lennon_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_lennon) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_lennon_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.789365543816 and the largest is 5.67544547958.
  RuntimeWarning

# Make emperor plots, binary_lennon) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_lennon_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_lennon_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_ochiai) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_ochiai  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_ochiai_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_ochiai_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_ochiai) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_ochiai_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.150762813157 and the largest is 5.4634248563.
  RuntimeWarning

# Make emperor plots, binary_ochiai) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_ochiai_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_ochiai_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_pearson) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_pearson  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_pearson_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_pearson) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_pearson_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.159906493877 and the largest is 5.84292788159.
  RuntimeWarning

# Make emperor plots, binary_pearson) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_pearson_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_pearson_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_sorensen_dice) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics binary_sorensen_dice  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//binary_sorensen_dice_table_even510.txt qiime_results/cd_all/bdiv_even510//binary_sorensen_dice_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_sorensen_dice) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//binary_sorensen_dice_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.133386842918 and the largest is 5.47857867357.
  RuntimeWarning

# Make emperor plots, binary_sorensen_dice) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//binary_sorensen_dice_pc.txt -o qiime_results/cd_all/bdiv_even510//binary_sorensen_dice_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics bray_curtis  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//bray_curtis_table_even510.txt qiime_results/cd_all/bdiv_even510//bray_curtis_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//bray_curtis_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.174938411875 and the largest is 7.61625778367.
  RuntimeWarning

# Make emperor plots, bray_curtis) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//bray_curtis_pc.txt -o qiime_results/cd_all/bdiv_even510//bray_curtis_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis_faith) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics bray_curtis_faith  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//bray_curtis_faith_table_even510.txt qiime_results/cd_all/bdiv_even510//bray_curtis_faith_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis_faith) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//bray_curtis_faith_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.174938411875 and the largest is 7.61625778367.
  RuntimeWarning

# Make emperor plots, bray_curtis_faith) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//bray_curtis_faith_pc.txt -o qiime_results/cd_all/bdiv_even510//bray_curtis_faith_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis_magurran) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics bray_curtis_magurran  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//bray_curtis_magurran_table_even510.txt qiime_results/cd_all/bdiv_even510//bray_curtis_magurran_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis_magurran) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//bray_curtis_magurran_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.174938411875 and the largest is 7.61625778367.
  RuntimeWarning

# Make emperor plots, bray_curtis_magurran) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//bray_curtis_magurran_pc.txt -o qiime_results/cd_all/bdiv_even510//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (canberra) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics canberra  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//canberra_table_even510.txt qiime_results/cd_all/bdiv_even510//canberra_dm.txt

Stdout:

Stderr:

# Principal coordinates (canberra) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//canberra_dm.txt -o qiime_results/cd_all/bdiv_even510//canberra_pc.txt 

Stdout:

Stderr:

# Make emperor plots, canberra) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//canberra_pc.txt -o qiime_results/cd_all/bdiv_even510//canberra_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (chisq) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics chisq  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//chisq_table_even510.txt qiime_results/cd_all/bdiv_even510//chisq_dm.txt

Stdout:

Stderr:

# Principal coordinates (chisq) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//chisq_dm.txt -o qiime_results/cd_all/bdiv_even510//chisq_pc.txt 

Stdout:

Stderr:

# Make emperor plots, chisq) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//chisq_pc.txt -o qiime_results/cd_all/bdiv_even510//chisq_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (chord) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics chord  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//chord_table_even510.txt qiime_results/cd_all/bdiv_even510//chord_dm.txt

Stdout:

Stderr:

# Principal coordinates (chord) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//chord_dm.txt -o qiime_results/cd_all/bdiv_even510//chord_pc.txt 

Stdout:

Stderr:

# Make emperor plots, chord) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//chord_pc.txt -o qiime_results/cd_all/bdiv_even510//chord_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (euclidean) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics euclidean  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//euclidean_table_even510.txt qiime_results/cd_all/bdiv_even510//euclidean_dm.txt

Stdout:

Stderr:

# Principal coordinates (euclidean) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//euclidean_dm.txt -o qiime_results/cd_all/bdiv_even510//euclidean_pc.txt 

Stdout:

Stderr:

# Make emperor plots, euclidean) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//euclidean_pc.txt -o qiime_results/cd_all/bdiv_even510//euclidean_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (gower) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics gower  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//gower_table_even510.txt qiime_results/cd_all/bdiv_even510//gower_dm.txt

Stdout:

Stderr:

# Principal coordinates (gower) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//gower_dm.txt -o qiime_results/cd_all/bdiv_even510//gower_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 -4690.76775639 and the largest is 13141.6159833.
  RuntimeWarning

# Make emperor plots, gower) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//gower_pc.txt -o qiime_results/cd_all/bdiv_even510//gower_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (hellinger) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics hellinger  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//hellinger_table_even510.txt qiime_results/cd_all/bdiv_even510//hellinger_dm.txt

Stdout:

Stderr:

# Principal coordinates (hellinger) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//hellinger_dm.txt -o qiime_results/cd_all/bdiv_even510//hellinger_pc.txt 

Stdout:

Stderr:

# Make emperor plots, hellinger) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//hellinger_pc.txt -o qiime_results/cd_all/bdiv_even510//hellinger_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (kulczynski) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics kulczynski  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//kulczynski_table_even510.txt qiime_results/cd_all/bdiv_even510//kulczynski_dm.txt

Stdout:

Stderr:

# Principal coordinates (kulczynski) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//kulczynski_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.174938411875 and the largest is 7.61625778367.
  RuntimeWarning

# Make emperor plots, kulczynski) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//kulczynski_pc.txt -o qiime_results/cd_all/bdiv_even510//kulczynski_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (manhattan) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics manhattan  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//manhattan_table_even510.txt qiime_results/cd_all/bdiv_even510//manhattan_dm.txt

Stdout:

Stderr:

# Principal coordinates (manhattan) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//manhattan_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -182005.923715 and the largest is 7923954.59813.
  RuntimeWarning

# Make emperor plots, manhattan) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//manhattan_pc.txt -o qiime_results/cd_all/bdiv_even510//manhattan_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (morisita_horn) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics morisita_horn  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//morisita_horn_table_even510.txt qiime_results/cd_all/bdiv_even510//morisita_horn_dm.txt

Stdout:

Stderr:

# Principal coordinates (morisita_horn) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//morisita_horn_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.469916765568 and the largest is 8.51487285797.
  RuntimeWarning

# Make emperor plots, morisita_horn) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//morisita_horn_pc.txt -o qiime_results/cd_all/bdiv_even510//morisita_horn_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (pearson) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics pearson  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//pearson_table_even510.txt qiime_results/cd_all/bdiv_even510//pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (pearson) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//pearson_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.556467951729 and the largest is 8.69381628326.
  RuntimeWarning

# Make emperor plots, pearson) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//pearson_pc.txt -o qiime_results/cd_all/bdiv_even510//pearson_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (soergel) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics soergel  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//soergel_table_even510.txt qiime_results/cd_all/bdiv_even510//soergel_dm.txt

Stdout:

Stderr:

# Principal coordinates (soergel) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//soergel_dm.txt -o qiime_results/cd_all/bdiv_even510//soergel_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 -0.0294530076217 and the largest is 6.63838904856.
  RuntimeWarning

# Make emperor plots, soergel) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//soergel_pc.txt -o qiime_results/cd_all/bdiv_even510//soergel_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (spearman_approx) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics spearman_approx  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//spearman_approx_table_even510.txt qiime_results/cd_all/bdiv_even510//spearman_approx_dm.txt

Stdout:

Stderr:

# Principal coordinates (spearman_approx) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//spearman_approx_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.0702080430944 and the largest is 0.209000012074.
  RuntimeWarning

# Make emperor plots, spearman_approx) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//spearman_approx_pc.txt -o qiime_results/cd_all/bdiv_even510//spearman_approx_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (specprof) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics specprof  -t qiime_results/data_all/rep_set_all.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_all/bdiv_even510//specprof_table_even510.txt qiime_results/cd_all/bdiv_even510//specprof_dm.txt

Stdout:

Stderr:

# Principal coordinates (specprof) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//specprof_dm.txt -o qiime_results/cd_all/bdiv_even510//specprof_pc.txt 

Stdout:

Stderr:

# Make emperor plots, specprof) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//specprof_pc.txt -o qiime_results/cd_all/bdiv_even510//specprof_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unifrac) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics unifrac  -t qiime_results/data_all/rep_set_all.tre 

Stdout:

Stderr:

# Rename distance matrix (unifrac) command 
mv qiime_results/cd_all/bdiv_even510//unifrac_table_even510.txt qiime_results/cd_all/bdiv_even510//unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unifrac) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//unifrac_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.0461479372976 and the largest is 3.6938962595.
  RuntimeWarning

# Make emperor plots, unifrac) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//unifrac_pc.txt -o qiime_results/cd_all/bdiv_even510//unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics unweighted_unifrac  -t qiime_results/data_all/rep_set_all.tre 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac) command 
mv qiime_results/cd_all/bdiv_even510//unweighted_unifrac_table_even510.txt qiime_results/cd_all/bdiv_even510//unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//unweighted_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.0461479372976 and the largest is 3.6938962595.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//unweighted_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even510//unweighted_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac_full_tree) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics unweighted_unifrac_full_tree  -t qiime_results/data_all/rep_set_all.tre 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac_full_tree) command 
mv qiime_results/cd_all/bdiv_even510//unweighted_unifrac_full_tree_table_even510.txt qiime_results/cd_all/bdiv_even510//unweighted_unifrac_full_tree_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac_full_tree) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.0135141080818 and the largest is 0.349870583835.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac_full_tree) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_all/bdiv_even510//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_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics weighted_normalized_unifrac  -t qiime_results/data_all/rep_set_all.tre 

Stdout:

Stderr:

# Rename distance matrix (weighted_normalized_unifrac) command 
mv qiime_results/cd_all/bdiv_even510//weighted_normalized_unifrac_table_even510.txt qiime_results/cd_all/bdiv_even510//weighted_normalized_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_normalized_unifrac) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.0978003655266 and the largest is 2.71551140767.
  RuntimeWarning

# Make emperor plots, weighted_normalized_unifrac) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even510//weighted_normalized_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (weighted_unifrac) command 
beta_diversity.py -i qiime_results/cd_all/table_even510.biom -o qiime_results/cd_all/bdiv_even510/ --metrics weighted_unifrac  -t qiime_results/data_all/rep_set_all.tre 

Stdout:

Stderr:

# Rename distance matrix (weighted_unifrac) command 
mv qiime_results/cd_all/bdiv_even510//weighted_unifrac_table_even510.txt qiime_results/cd_all/bdiv_even510//weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even510//weighted_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even510//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 -0.104801371189 and the largest is 3.0955249076.
  RuntimeWarning

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even510//weighted_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even510//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

Executing commands.

# Alpha rarefaction command 
multiple_rarefactions.py -i qiime_results/cd_all/table_mc510.biom -m 10 -x 510 -s 50 -o qiime_results/cd_all/arare_max510//rarefaction/ 

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
alpha_diversity.py -i qiime_results/cd_all/arare_max510//rarefaction/ -o qiime_results/cd_all/arare_max510//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,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree -t qiime_results/data_all/rep_set_all.tre

Stdout:

Stderr:

# Collate alpha command 
collate_alpha.py -i qiime_results/cd_all/arare_max510//alpha_div/ -o qiime_results/cd_all/arare_max510//alpha_div_collated/ 

Stdout:

Stderr:

# Removing intermediate files command 
rm -r qiime_results/cd_all/arare_max510//rarefaction/ qiime_results/cd_all/arare_max510//alpha_div/

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
make_rarefaction_plots.py -i qiime_results/cd_all/arare_max510//alpha_div_collated/ -m meta.txt -o qiime_results/cd_all/arare_max510//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_all/table_mc510.biom -o qiime_results/cd_all/taxa_plots/table_mc510_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i qiime_results/cd_all/taxa_plots/table_mc510_sorted.biom -o qiime_results/cd_all/taxa_plots/ --level 2,3,4,5,6,7

Stdout:

Stderr:

# Plot Taxonomy Summary command 
plot_taxa_summary.py -i qiime_results/cd_all/taxa_plots/table_mc510_sorted_L2.txt,qiime_results/cd_all/taxa_plots/table_mc510_sorted_L3.txt,qiime_results/cd_all/taxa_plots/table_mc510_sorted_L4.txt,qiime_results/cd_all/taxa_plots/table_mc510_sorted_L5.txt,qiime_results/cd_all/taxa_plots/table_mc510_sorted_L6.txt,qiime_results/cd_all/taxa_plots/table_mc510_sorted_L7.txt -o qiime_results/cd_all/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_all/table_mc510.biom

Stdout:

Stderr:

# Compress the rarefied BIOM table command 
gzip qiime_results/cd_all/table_even510.biom

Stdout:

Stderr:


Logging stopped at 21:59:36 on 29 May 2018
