Logging started at 11:16:21 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_mc10/final_otu_map_mc10_tax.biom: ac88e1385357043d8c7742c30cf8831e
meta.txt: 13073d4a61ad0a90ce6a6e480a1cbaad
qiime_results/data_mc10/rep_set_mc10.tre: feb40308d6ea930dc42060b23a2876a2

Executing commands.

# Generate BIOM table summary command 
biom summarize-table -i qiime_results/data_mc10/final_otu_map_mc10_tax.biom -o qiime_results/cd_mc10/biom_table_summary.txt 

Stdout:

Stderr:

# Filter low sequence count samples from table (minimum sequence count: 4179) command 
filter_samples_from_otu_table.py -i qiime_results/data_mc10/final_otu_map_mc10_tax.biom -o qiime_results/cd_mc10/table_mc4179.biom -n 4179

Stdout:

Stderr:

# Rarify the OTU table to 4179 sequences/sample command 
single_rarefaction.py -i qiime_results/cd_mc10/table_mc4179.biom -o qiime_results/cd_mc10/table_even4179.biom -d 4179

Stdout:

Stderr:

Executing commands.

# Beta Diversity (abund_jaccard) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics abund_jaccard  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//abund_jaccard_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//abund_jaccard_dm.txt

Stdout:

Stderr:

# Principal coordinates (abund_jaccard) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//abund_jaccard_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.744731683735 and the largest is 2.28581493828.
  RuntimeWarning

# Make emperor plots, abund_jaccard) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//abund_jaccard_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//abund_jaccard_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_chisq) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_chisq  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_chisq_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_chisq_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_chisq) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_chisq_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_chisq_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_chisq) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_chisq_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_chisq_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_chord) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_chord  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_chord_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_chord_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_chord) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_chord_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_chord_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_chord) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_chord_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_chord_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_euclidean) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_euclidean  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_euclidean_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_euclidean_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_euclidean) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_euclidean_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_euclidean_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_euclidean) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_euclidean_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_euclidean_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_hamming) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_hamming  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_hamming_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_hamming_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_hamming) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_hamming_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -1884.69319211 and the largest is 57201.2204934.
  RuntimeWarning

# Make emperor plots, binary_hamming) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_hamming_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_hamming_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_jaccard) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_jaccard  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_jaccard_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_jaccard_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_jaccard) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_jaccard_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_jaccard_pc.txt 

Stdout:

Stderr:

# Make emperor plots, binary_jaccard) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_jaccard_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_jaccard_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_lennon) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_lennon  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_lennon_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_lennon_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_lennon) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_lennon_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -1.10117750072 and the largest is 1.39735452866.
  RuntimeWarning

# Make emperor plots, binary_lennon) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_lennon_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_lennon_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_ochiai) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_ochiai  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_ochiai_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_ochiai_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_ochiai) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_ochiai_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0363164802106 and the largest is 1.35458670503.
  RuntimeWarning

# Make emperor plots, binary_ochiai) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_ochiai_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_ochiai_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_pearson) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_pearson  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_pearson_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_pearson) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_pearson_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0471252232574 and the largest is 1.84436363079.
  RuntimeWarning

# Make emperor plots, binary_pearson) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_pearson_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_pearson_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (binary_sorensen_dice) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics binary_sorensen_dice  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//binary_sorensen_dice_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//binary_sorensen_dice_dm.txt

Stdout:

Stderr:

# Principal coordinates (binary_sorensen_dice) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//binary_sorensen_dice_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.030837490661 and the largest is 1.648435202.
  RuntimeWarning

# Make emperor plots, binary_sorensen_dice) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//binary_sorensen_dice_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//binary_sorensen_dice_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics bray_curtis  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//bray_curtis_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//bray_curtis_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//bray_curtis_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0749017760961 and the largest is 2.05021483443.
  RuntimeWarning

# Make emperor plots, bray_curtis) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//bray_curtis_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//bray_curtis_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis_faith) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics bray_curtis_faith  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//bray_curtis_faith_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//bray_curtis_faith_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis_faith) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//bray_curtis_faith_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0749017760961 and the largest is 2.05021483443.
  RuntimeWarning

# Make emperor plots, bray_curtis_faith) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//bray_curtis_faith_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//bray_curtis_faith_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis_magurran) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics bray_curtis_magurran  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//bray_curtis_magurran_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//bray_curtis_magurran_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis_magurran) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//bray_curtis_magurran_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0749017760961 and the largest is 2.05021483443.
  RuntimeWarning

# Make emperor plots, bray_curtis_magurran) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//bray_curtis_magurran_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (canberra) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics canberra  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//canberra_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//canberra_dm.txt

Stdout:

Stderr:

# Principal coordinates (canberra) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//canberra_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//canberra_pc.txt 

Stdout:

Stderr:

# Make emperor plots, canberra) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//canberra_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//canberra_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (chisq) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics chisq  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//chisq_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//chisq_dm.txt

Stdout:

Stderr:

# Principal coordinates (chisq) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//chisq_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//chisq_pc.txt 

Stdout:

Stderr:

# Make emperor plots, chisq) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//chisq_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//chisq_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (chord) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics chord  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//chord_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//chord_dm.txt

Stdout:

Stderr:

# Principal coordinates (chord) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//chord_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//chord_pc.txt 

Stdout:

Stderr:

# Make emperor plots, chord) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//chord_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//chord_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (euclidean) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics euclidean  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//euclidean_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//euclidean_dm.txt

Stdout:

Stderr:

# Principal coordinates (euclidean) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//euclidean_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//euclidean_pc.txt 

Stdout:

Stderr:

# Make emperor plots, euclidean) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//euclidean_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//euclidean_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (gower) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics gower  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//gower_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//gower_dm.txt

Stdout:

Stderr:

# Principal coordinates (gower) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//gower_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -3140.66532631 and the largest is 9370.45721156.
  RuntimeWarning

# Make emperor plots, gower) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//gower_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//gower_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (hellinger) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics hellinger  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//hellinger_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//hellinger_dm.txt

Stdout:

Stderr:

# Principal coordinates (hellinger) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//hellinger_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//hellinger_pc.txt 

Stdout:

Stderr:

# Make emperor plots, hellinger) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//hellinger_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//hellinger_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (kulczynski) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics kulczynski  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//kulczynski_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//kulczynski_dm.txt

Stdout:

Stderr:

# Principal coordinates (kulczynski) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//kulczynski_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0749017760961 and the largest is 2.05021483443.
  RuntimeWarning

# Make emperor plots, kulczynski) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//kulczynski_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//kulczynski_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (manhattan) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics manhattan  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//manhattan_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//manhattan_dm.txt

Stdout:

Stderr:

# Principal coordinates (manhattan) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//manhattan_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -5232350.75488 and the largest is 143220143.709.
  RuntimeWarning

# Make emperor plots, manhattan) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//manhattan_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//manhattan_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (morisita_horn) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics morisita_horn  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//morisita_horn_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//morisita_horn_dm.txt

Stdout:

Stderr:

# Principal coordinates (morisita_horn) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//morisita_horn_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.287997482264 and the largest is 2.96938362006.
  RuntimeWarning

# Make emperor plots, morisita_horn) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//morisita_horn_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//morisita_horn_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (pearson) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics pearson  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//pearson_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (pearson) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//pearson_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.350081675187 and the largest is 3.21481887167.
  RuntimeWarning

# Make emperor plots, pearson) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//pearson_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//pearson_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (soergel) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics soergel  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//soergel_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//soergel_dm.txt

Stdout:

Stderr:

# Principal coordinates (soergel) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//soergel_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//soergel_pc.txt 

Stdout:

Stderr:

# Make emperor plots, soergel) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//soergel_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//soergel_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (spearman_approx) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics spearman_approx  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//spearman_approx_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//spearman_approx_dm.txt

Stdout:

Stderr:

# Principal coordinates (spearman_approx) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//spearman_approx_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0521954400912 and the largest is 0.381401355768.
  RuntimeWarning

# Make emperor plots, spearman_approx) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//spearman_approx_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//spearman_approx_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (specprof) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics specprof  -t qiime_results/data_mc10/rep_set_mc10.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_mc10/bdiv_even4179//specprof_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//specprof_dm.txt

Stdout:

Stderr:

# Principal coordinates (specprof) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//specprof_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//specprof_pc.txt 

Stdout:

Stderr:

# Make emperor plots, specprof) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//specprof_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//specprof_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unifrac) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics unifrac  -t qiime_results/data_mc10/rep_set_mc10.tre 

Stdout:

Stderr:

# Rename distance matrix (unifrac) command 
mv qiime_results/cd_mc10/bdiv_even4179//unifrac_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unifrac) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.012452535916 and the largest is 1.65900997075.
  RuntimeWarning

# Make emperor plots, unifrac) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics unweighted_unifrac  -t qiime_results/data_mc10/rep_set_mc10.tre 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac) command 
mv qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.012452535916 and the largest is 1.65900997075.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac_full_tree) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics unweighted_unifrac_full_tree  -t qiime_results/data_mc10/rep_set_mc10.tre 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac_full_tree) command 
mv qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_full_tree_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_full_tree_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac_full_tree) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0224666829773 and the largest is 0.516372989668.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac_full_tree) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//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_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics weighted_normalized_unifrac  -t qiime_results/data_mc10/rep_set_mc10.tre 

Stdout:

Stderr:

# Rename distance matrix (weighted_normalized_unifrac) command 
mv qiime_results/cd_mc10/bdiv_even4179//weighted_normalized_unifrac_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//weighted_normalized_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_normalized_unifrac) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.0462165691571 and the largest is 1.25271609814.
  RuntimeWarning

# Make emperor plots, weighted_normalized_unifrac) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//weighted_normalized_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

# Beta Diversity (weighted_unifrac) command 
beta_diversity.py -i qiime_results/cd_mc10/table_even4179.biom -o qiime_results/cd_mc10/bdiv_even4179/ --metrics weighted_unifrac  -t qiime_results/data_mc10/rep_set_mc10.tre 

Stdout:

Stderr:

# Rename distance matrix (weighted_unifrac) command 
mv qiime_results/cd_mc10/bdiv_even4179//weighted_unifrac_table_even4179.txt qiime_results/cd_mc10/bdiv_even4179//weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even4179//weighted_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even4179//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 -0.056351391152 and the largest is 1.59883369442.
  RuntimeWarning

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i qiime_results/cd_mc10/bdiv_even4179//weighted_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even4179//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt 

Stdout:

Stderr:

Executing commands.

# Alpha rarefaction command 
multiple_rarefactions.py -i qiime_results/cd_mc10/table_mc4179.biom -m 10 -x 4179 -s 416 -o qiime_results/cd_mc10/arare_max4179//rarefaction/ 

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
alpha_diversity.py -i qiime_results/cd_mc10/arare_max4179//rarefaction/ -o qiime_results/cd_mc10/arare_max4179//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_mc10/rep_set_mc10.tre

Stdout:

Stderr:

# Collate alpha command 
collate_alpha.py -i qiime_results/cd_mc10/arare_max4179//alpha_div/ -o qiime_results/cd_mc10/arare_max4179//alpha_div_collated/ 

Stdout:

Stderr:

# Removing intermediate files command 
rm -r qiime_results/cd_mc10/arare_max4179//rarefaction/ qiime_results/cd_mc10/arare_max4179//alpha_div/

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
make_rarefaction_plots.py -i qiime_results/cd_mc10/arare_max4179//alpha_div_collated/ -m meta.txt -o qiime_results/cd_mc10/arare_max4179//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_mc10/table_mc4179.biom -o qiime_results/cd_mc10/taxa_plots/table_mc4179_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i qiime_results/cd_mc10/taxa_plots/table_mc4179_sorted.biom -o qiime_results/cd_mc10/taxa_plots/ --level 2,3,4,5,6,7

Stdout:

Stderr:

# Plot Taxonomy Summary command 
plot_taxa_summary.py -i qiime_results/cd_mc10/taxa_plots/table_mc4179_sorted_L2.txt,qiime_results/cd_mc10/taxa_plots/table_mc4179_sorted_L3.txt,qiime_results/cd_mc10/taxa_plots/table_mc4179_sorted_L4.txt,qiime_results/cd_mc10/taxa_plots/table_mc4179_sorted_L5.txt,qiime_results/cd_mc10/taxa_plots/table_mc4179_sorted_L6.txt,qiime_results/cd_mc10/taxa_plots/table_mc4179_sorted_L7.txt -o qiime_results/cd_mc10/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_mc10/table_mc4179.biom

Stdout:

Stderr:

# Compress the rarefied BIOM table command 
gzip qiime_results/cd_mc10/table_even4179.biom

Stdout:

Stderr:


Logging stopped at 11:29:38 on 13 Dec 2016
