Logging started at 10:54:04 on 13 Dec 2016
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	3000
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_all/final_otu_map_all_tax.biom: 674bad527ef4c133077a3cfff5b8a4a2
meta.txt: 13073d4a61ad0a90ce6a6e480a1cbaad
qiime_results/data_all/rep_set_all.tre: 134fc1aabb14266341051c996daaca49

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: 4254) command 
filter_samples_from_otu_table.py -i qiime_results/data_all/final_otu_map_all_tax.biom -o qiime_results/cd_all/table_mc4254.biom -n 4254

Stdout:

Stderr:

# Rarify the OTU table to 4254 sequences/sample command 
single_rarefaction.py -i qiime_results/cd_all/table_mc4254.biom -o qiime_results/cd_all/table_even4254.biom -d 4254

Stdout:

Stderr:

Executing commands.

# Beta Diversity (abund_jaccard) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//abund_jaccard_table_even4254.txt qiime_results/cd_all/bdiv_even4254//abund_jaccard_dm.txt

Stdout:

Stderr:

# Principal coordinates (abund_jaccard) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//abund_jaccard_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.747591095584 and the largest is 2.2159374855.
  RuntimeWarning

# Make emperor plots, abund_jaccard) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//abund_jaccard_pc.txt -o qiime_results/cd_all/bdiv_even4254//abund_jaccard_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_chisq) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_chisq_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_chisq_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_chisq) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_chisq_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_chisq_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_chisq) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_chisq_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_chisq_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_chord) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_chord_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_chord_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_chord) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_chord_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_chord_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_chord) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_chord_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_chord_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_euclidean) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_euclidean_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_euclidean_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_euclidean) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_euclidean_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_euclidean_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_euclidean) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_euclidean_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_euclidean_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_hamming) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_hamming_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_hamming_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_hamming) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_hamming_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -4233.42847164 and the largest is 74214.770203.
  RuntimeWarning

# Make emperor plots, binary_hamming) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_hamming_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_hamming_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_jaccard) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_jaccard_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_jaccard_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_jaccard) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_jaccard_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_jaccard_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_jaccard) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_jaccard_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_jaccard_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_lennon) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_lennon_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_lennon_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_lennon) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_lennon_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -1.04505774424 and the largest is 1.37596741922.
  RuntimeWarning

# Make emperor plots, binary_lennon) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_lennon_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_lennon_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_ochiai) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_ochiai_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_ochiai_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_ochiai) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_ochiai_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.00632596342932 and the largest is 1.34965972779.
  RuntimeWarning

# Make emperor plots, binary_ochiai) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_ochiai_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_ochiai_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_pearson) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_pearson_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_pearson) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_pearson_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.0063297096301 and the largest is 1.61310915882.
  RuntimeWarning

# Make emperor plots, binary_pearson) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_pearson_pc.txt -o qiime_results/cd_all/bdiv_even4254//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_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//binary_sorensen_dice_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_sorensen_dice) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.000645544950963 and the largest is 1.63724948402.
  RuntimeWarning

# Make emperor plots, binary_sorensen_dice) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_pc.txt -o qiime_results/cd_all/bdiv_even4254//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_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//bray_curtis_table_even4254.txt qiime_results/cd_all/bdiv_even4254//bray_curtis_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.066790750884 and the largest is 2.02524057377.
  RuntimeWarning

# Make emperor plots, bray_curtis) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_pc.txt -o qiime_results/cd_all/bdiv_even4254//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_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//bray_curtis_faith_table_even4254.txt qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis_faith) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.066790750884 and the largest is 2.02524057377.
  RuntimeWarning

# Make emperor plots, bray_curtis_faith) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_pc.txt -o qiime_results/cd_all/bdiv_even4254//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_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//bray_curtis_magurran_table_even4254.txt qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis_magurran) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.066790750884 and the largest is 2.02524057377.
  RuntimeWarning

# Make emperor plots, bray_curtis_magurran) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_pc.txt -o qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (canberra) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//canberra_table_even4254.txt qiime_results/cd_all/bdiv_even4254//canberra_dm.txt

Stdout:

Stderr:

# Principal coordinates (canberra) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//canberra_dm.txt -o qiime_results/cd_all/bdiv_even4254//canberra_pc.txt 

Stdout:

Stderr:

# Make emperor plots, canberra) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//canberra_pc.txt -o qiime_results/cd_all/bdiv_even4254//canberra_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (chisq) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//chisq_table_even4254.txt qiime_results/cd_all/bdiv_even4254//chisq_dm.txt

Stdout:

Stderr:

# Principal coordinates (chisq) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//chisq_dm.txt -o qiime_results/cd_all/bdiv_even4254//chisq_pc.txt 

Stdout:

Stderr:

# Make emperor plots, chisq) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//chisq_pc.txt -o qiime_results/cd_all/bdiv_even4254//chisq_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (chord) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//chord_table_even4254.txt qiime_results/cd_all/bdiv_even4254//chord_dm.txt

Stdout:

Stderr:

# Principal coordinates (chord) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//chord_dm.txt -o qiime_results/cd_all/bdiv_even4254//chord_pc.txt 

Stdout:

Stderr:

# Make emperor plots, chord) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//chord_pc.txt -o qiime_results/cd_all/bdiv_even4254//chord_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (euclidean) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//euclidean_table_even4254.txt qiime_results/cd_all/bdiv_even4254//euclidean_dm.txt

Stdout:

Stderr:

# Principal coordinates (euclidean) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//euclidean_dm.txt -o qiime_results/cd_all/bdiv_even4254//euclidean_pc.txt 

Stdout:

Stderr:

# Make emperor plots, euclidean) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//euclidean_pc.txt -o qiime_results/cd_all/bdiv_even4254//euclidean_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (gower) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//gower_table_even4254.txt qiime_results/cd_all/bdiv_even4254//gower_dm.txt

Stdout:

Stderr:

# Principal coordinates (gower) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//gower_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -8083.67511708 and the largest is 14903.8009369.
  RuntimeWarning

# Make emperor plots, gower) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//gower_pc.txt -o qiime_results/cd_all/bdiv_even4254//gower_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (hellinger) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//hellinger_table_even4254.txt qiime_results/cd_all/bdiv_even4254//hellinger_dm.txt

Stdout:

Stderr:

# Principal coordinates (hellinger) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//hellinger_dm.txt -o qiime_results/cd_all/bdiv_even4254//hellinger_pc.txt 

Stdout:

Stderr:

# Make emperor plots, hellinger) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//hellinger_pc.txt -o qiime_results/cd_all/bdiv_even4254//hellinger_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (kulczynski) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//kulczynski_table_even4254.txt qiime_results/cd_all/bdiv_even4254//kulczynski_dm.txt

Stdout:

Stderr:

# Principal coordinates (kulczynski) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//kulczynski_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.066790750884 and the largest is 2.02524057377.
  RuntimeWarning

# Make emperor plots, kulczynski) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//kulczynski_pc.txt -o qiime_results/cd_all/bdiv_even4254//kulczynski_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (manhattan) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//manhattan_table_even4254.txt qiime_results/cd_all/bdiv_even4254//manhattan_dm.txt

Stdout:

Stderr:

# Principal coordinates (manhattan) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//manhattan_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -4834719.56809 and the largest is 146599193.788.
  RuntimeWarning

# Make emperor plots, manhattan) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//manhattan_pc.txt -o qiime_results/cd_all/bdiv_even4254//manhattan_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (morisita_horn) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//morisita_horn_table_even4254.txt qiime_results/cd_all/bdiv_even4254//morisita_horn_dm.txt

Stdout:

Stderr:

# Principal coordinates (morisita_horn) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//morisita_horn_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.284603321963 and the largest is 2.93891375593.
  RuntimeWarning

# Make emperor plots, morisita_horn) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//morisita_horn_pc.txt -o qiime_results/cd_all/bdiv_even4254//morisita_horn_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (pearson) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//pearson_table_even4254.txt qiime_results/cd_all/bdiv_even4254//pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (pearson) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//pearson_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.346676769024 and the largest is 3.14750373244.
  RuntimeWarning

# Make emperor plots, pearson) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//pearson_pc.txt -o qiime_results/cd_all/bdiv_even4254//pearson_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (soergel) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//soergel_table_even4254.txt qiime_results/cd_all/bdiv_even4254//soergel_dm.txt

Stdout:

Stderr:

# Principal coordinates (soergel) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//soergel_dm.txt -o qiime_results/cd_all/bdiv_even4254//soergel_pc.txt 

Stdout:

Stderr:

# Make emperor plots, soergel) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//soergel_pc.txt -o qiime_results/cd_all/bdiv_even4254//soergel_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (spearman_approx) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//spearman_approx_table_even4254.txt qiime_results/cd_all/bdiv_even4254//spearman_approx_dm.txt

Stdout:

Stderr:

# Principal coordinates (spearman_approx) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//spearman_approx_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.0227359222732 and the largest is 0.15189171353.
  RuntimeWarning

# Make emperor plots, spearman_approx) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//spearman_approx_pc.txt -o qiime_results/cd_all/bdiv_even4254//spearman_approx_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (specprof) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//specprof_table_even4254.txt qiime_results/cd_all/bdiv_even4254//specprof_dm.txt

Stdout:

Stderr:

# Principal coordinates (specprof) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//specprof_dm.txt -o qiime_results/cd_all/bdiv_even4254//specprof_pc.txt 

Stdout:

Stderr:

# Make emperor plots, specprof) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//specprof_pc.txt -o qiime_results/cd_all/bdiv_even4254//specprof_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unifrac) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics unifrac  -t qiime_results/data_all/rep_set_all.tre 

Stdout:

Stderr:

# Rename distance matrix (unifrac) command 
mv qiime_results/cd_all/bdiv_even4254//unifrac_table_even4254.txt qiime_results/cd_all/bdiv_even4254//unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unifrac) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//unifrac_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.00064077718732 and the largest is 1.77095884051.
  RuntimeWarning

# Make emperor plots, unifrac) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//unifrac_pc.txt -o qiime_results/cd_all/bdiv_even4254//unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//unweighted_unifrac_table_even4254.txt qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.00064077718732 and the largest is 1.77095884051.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even4254//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_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//unweighted_unifrac_full_tree_table_even4254.txt qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac_full_tree) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.0131511095181 and the largest is 0.356185881689.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac_full_tree) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_all/bdiv_even4254//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_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//weighted_normalized_unifrac_table_even4254.txt qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_normalized_unifrac) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.0461890329583 and the largest is 1.28976320534.
  RuntimeWarning

# Make emperor plots, weighted_normalized_unifrac) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even4254//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_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --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_even4254//weighted_unifrac_table_even4254.txt qiime_results/cd_all/bdiv_even4254//weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//weighted_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even4254//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 -0.0601973759946 and the largest is 2.12089734225.
  RuntimeWarning

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i qiime_results/cd_all/bdiv_even4254//weighted_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even4254//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

Executing commands.

# Alpha rarefaction command 
multiple_rarefactions.py -i qiime_results/cd_all/table_mc4254.biom -m 10 -x 4254 -s 424 -o qiime_results/cd_all/arare_max4254//rarefaction/ 

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
alpha_diversity.py -i qiime_results/cd_all/arare_max4254//rarefaction/ -o qiime_results/cd_all/arare_max4254//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_max4254//alpha_div/ -o qiime_results/cd_all/arare_max4254//alpha_div_collated/ 

Stdout:

Stderr:

# Removing intermediate files command 
rm -r qiime_results/cd_all/arare_max4254//rarefaction/ qiime_results/cd_all/arare_max4254//alpha_div/

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
make_rarefaction_plots.py -i qiime_results/cd_all/arare_max4254//alpha_div_collated/ -m meta.txt -o qiime_results/cd_all/arare_max4254//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_mc4254.biom -o qiime_results/cd_all/taxa_plots/table_mc4254_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i qiime_results/cd_all/taxa_plots/table_mc4254_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_mc4254_sorted_L2.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L3.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L4.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L5.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L6.txt,qiime_results/cd_all/taxa_plots/table_mc4254_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_mc4254.biom

Stdout:

Stderr:

# Compress the rarefied BIOM table command 
gzip qiime_results/cd_all/table_even4254.biom

Stdout:

Stderr:


Logging stopped at 11:11:28 on 13 Dec 2016
