Logging started at 11:51:11 on 10 Jun 2016 QIIME version: 1.9.1 qiime_config values: pick_otus_reference_seqs_fp /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta sc_queue all.q pynast_template_alignment_fp /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta cluster_jobs_fp start_parallel_jobs.py assign_taxonomy_reference_seqs_fp /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta torque_queue friendlyq jobs_to_start 1 denoiser_min_per_core 50 assign_taxonomy_id_to_taxonomy_fp /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt temp_dir /tmp/ blastall_fp blastall seconds_to_sleep 1 parameter file values: alpha_diversity:metrics berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,michaelis_menten_fit,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree beta_diversity:metrics abund_jaccard,binary_chisq,binary_chord,binary_euclidean,binary_hamming,binary_jaccard,binary_lennon,binary_ochiai,binary_pearson,binary_sorensen_dice,bray_curtis,bray_curtis_faith,bray_curtis_magurran,canberra,chisq,chord,euclidean,gower,hellinger,kulczynski,manhattan,morisita_horn,pearson,soergel,spearman_approx,specprof,unifrac,unweighted_unifrac,unweighted_unifrac_full_tree,weighted_normalized_unifrac,weighted_unifrac summarize_taxa:level 2,3,4,5,6,7 parallel:jobs_to_start 1 plot_taxa_summary:labels Phylum,Class,Order,Family,Genus,Species plot_taxa_summary:chart_type bar,area,pie core_diversity_analyses:categories status Input file md5 sums: qiime_results/data_mc10/final_otu_map_mc10_tax.biom: 32728d4ec53237afadc2c53a0bb025db meta.txt: 4a8c1aac4ce74f349e5b94ef6b7c078c qiime_results/data_mc10/rep_set_mc10.tre: 012d2e9640c1dc9bdf2ab86f42a77f0e 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: 963) command filter_samples_from_otu_table.py -i qiime_results/data_mc10/final_otu_map_mc10_tax.biom -o qiime_results/cd_mc10/table_mc963.biom -n 963 Stdout: Stderr: # Rarify the OTU table to 963 sequences/sample command single_rarefaction.py -i qiime_results/cd_mc10/table_mc963.biom -o qiime_results/cd_mc10/table_even963.biom -d 963 Stdout: Stderr: Executing commands. # Beta Diversity (abund_jaccard) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//abund_jaccard_table_even963.txt qiime_results/cd_mc10/bdiv_even963//abund_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (abund_jaccard) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//abund_jaccard_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.102445356939 and the largest is 0.72548985688. RuntimeWarning # Make emperor plots, abund_jaccard) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//abund_jaccard_pc.txt -o qiime_results/cd_mc10/bdiv_even963//abund_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chisq) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_chisq_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_chisq_dm.txt Stdout: Stderr: # Principal coordinates (binary_chisq) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_chisq_dm.txt -o qiime_results/cd_mc10/bdiv_even963//binary_chisq_pc.txt Stdout: Stderr: # Make emperor plots, binary_chisq) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_chisq_pc.txt -o qiime_results/cd_mc10/bdiv_even963//binary_chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chord) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_chord_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_chord_dm.txt Stdout: Stderr: # Principal coordinates (binary_chord) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_chord_dm.txt -o qiime_results/cd_mc10/bdiv_even963//binary_chord_pc.txt Stdout: Stderr: # Make emperor plots, binary_chord) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_chord_pc.txt -o qiime_results/cd_mc10/bdiv_even963//binary_chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_euclidean) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_euclidean_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_euclidean_dm.txt Stdout: Stderr: # Principal coordinates (binary_euclidean) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_euclidean_dm.txt -o qiime_results/cd_mc10/bdiv_even963//binary_euclidean_pc.txt Stdout: Stderr: # Make emperor plots, binary_euclidean) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_euclidean_pc.txt -o qiime_results/cd_mc10/bdiv_even963//binary_euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_hamming) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_hamming_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_hamming_dm.txt Stdout: Stderr: # Principal coordinates (binary_hamming) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_hamming_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -135.921672507 and the largest is 10397.5746497. RuntimeWarning # Make emperor plots, binary_hamming) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_hamming_pc.txt -o qiime_results/cd_mc10/bdiv_even963//binary_hamming_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_jaccard) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_jaccard_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (binary_jaccard) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_jaccard_dm.txt -o qiime_results/cd_mc10/bdiv_even963//binary_jaccard_pc.txt Stdout: Stderr: # Make emperor plots, binary_jaccard) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_jaccard_pc.txt -o qiime_results/cd_mc10/bdiv_even963//binary_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_lennon) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_lennon_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_lennon_dm.txt Stdout: Stderr: # Principal coordinates (binary_lennon) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_lennon_dm.txt -o qiime_results/cd_mc10/bdiv_even963//binary_lennon_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.160525617131 and the largest is 0.471252196179. RuntimeWarning # Make emperor plots, binary_lennon) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_lennon_pc.txt -o qiime_results/cd_mc10/bdiv_even963//binary_lennon_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_ochiai) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_ochiai_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_ochiai_dm.txt Stdout: Stderr: # Principal coordinates (binary_ochiai) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_ochiai_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.00241148253367 and the largest is 0.532447890468. RuntimeWarning # Make emperor plots, binary_ochiai) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_ochiai_pc.txt -o qiime_results/cd_mc10/bdiv_even963//binary_ochiai_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_pearson) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_pearson_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_pearson_dm.txt Stdout: Stderr: # Principal coordinates (binary_pearson) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_pearson_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.00608454152605 and the largest is 0.947512693951. RuntimeWarning # Make emperor plots, binary_pearson) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_pearson_pc.txt -o qiime_results/cd_mc10/bdiv_even963//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_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//binary_sorensen_dice_table_even963.txt qiime_results/cd_mc10/bdiv_even963//binary_sorensen_dice_dm.txt Stdout: Stderr: # Principal coordinates (binary_sorensen_dice) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//binary_sorensen_dice_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.00248548029831 and the largest is 0.549454239504. RuntimeWarning # Make emperor plots, binary_sorensen_dice) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//binary_sorensen_dice_pc.txt -o qiime_results/cd_mc10/bdiv_even963//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_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//bray_curtis_table_even963.txt qiime_results/cd_mc10/bdiv_even963//bray_curtis_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//bray_curtis_dm.txt -o qiime_results/cd_mc10/bdiv_even963//bray_curtis_pc.txt Stdout: Stderr: # Make emperor plots, bray_curtis) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//bray_curtis_pc.txt -o qiime_results/cd_mc10/bdiv_even963//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_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//bray_curtis_faith_table_even963.txt qiime_results/cd_mc10/bdiv_even963//bray_curtis_faith_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_faith) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//bray_curtis_faith_dm.txt -o qiime_results/cd_mc10/bdiv_even963//bray_curtis_faith_pc.txt Stdout: Stderr: # Make emperor plots, bray_curtis_faith) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//bray_curtis_faith_pc.txt -o qiime_results/cd_mc10/bdiv_even963//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_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//bray_curtis_magurran_table_even963.txt qiime_results/cd_mc10/bdiv_even963//bray_curtis_magurran_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_magurran) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//bray_curtis_magurran_dm.txt -o qiime_results/cd_mc10/bdiv_even963//bray_curtis_magurran_pc.txt Stdout: Stderr: # Make emperor plots, bray_curtis_magurran) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//bray_curtis_magurran_pc.txt -o qiime_results/cd_mc10/bdiv_even963//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (canberra) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//canberra_table_even963.txt qiime_results/cd_mc10/bdiv_even963//canberra_dm.txt Stdout: Stderr: # Principal coordinates (canberra) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//canberra_dm.txt -o qiime_results/cd_mc10/bdiv_even963//canberra_pc.txt Stdout: Stderr: # Make emperor plots, canberra) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//canberra_pc.txt -o qiime_results/cd_mc10/bdiv_even963//canberra_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chisq) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//chisq_table_even963.txt qiime_results/cd_mc10/bdiv_even963//chisq_dm.txt Stdout: Stderr: # Principal coordinates (chisq) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//chisq_dm.txt -o qiime_results/cd_mc10/bdiv_even963//chisq_pc.txt Stdout: Stderr: # Make emperor plots, chisq) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//chisq_pc.txt -o qiime_results/cd_mc10/bdiv_even963//chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chord) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//chord_table_even963.txt qiime_results/cd_mc10/bdiv_even963//chord_dm.txt Stdout: Stderr: # Principal coordinates (chord) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//chord_dm.txt -o qiime_results/cd_mc10/bdiv_even963//chord_pc.txt Stdout: Stderr: # Make emperor plots, chord) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//chord_pc.txt -o qiime_results/cd_mc10/bdiv_even963//chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (euclidean) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//euclidean_table_even963.txt qiime_results/cd_mc10/bdiv_even963//euclidean_dm.txt Stdout: Stderr: # Principal coordinates (euclidean) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//euclidean_dm.txt -o qiime_results/cd_mc10/bdiv_even963//euclidean_pc.txt Stdout: Stderr: # Make emperor plots, euclidean) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//euclidean_pc.txt -o qiime_results/cd_mc10/bdiv_even963//euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (gower) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//gower_table_even963.txt qiime_results/cd_mc10/bdiv_even963//gower_dm.txt Stdout: Stderr: # Principal coordinates (gower) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//gower_dm.txt -o qiime_results/cd_mc10/bdiv_even963//gower_pc.txt Stdout: Stderr: # Make emperor plots, gower) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//gower_pc.txt -o qiime_results/cd_mc10/bdiv_even963//gower_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (hellinger) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//hellinger_table_even963.txt qiime_results/cd_mc10/bdiv_even963//hellinger_dm.txt Stdout: Stderr: # Principal coordinates (hellinger) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//hellinger_dm.txt -o qiime_results/cd_mc10/bdiv_even963//hellinger_pc.txt Stdout: Stderr: # Make emperor plots, hellinger) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//hellinger_pc.txt -o qiime_results/cd_mc10/bdiv_even963//hellinger_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (kulczynski) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//kulczynski_table_even963.txt qiime_results/cd_mc10/bdiv_even963//kulczynski_dm.txt Stdout: Stderr: # Principal coordinates (kulczynski) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//kulczynski_dm.txt -o qiime_results/cd_mc10/bdiv_even963//kulczynski_pc.txt Stdout: Stderr: # Make emperor plots, kulczynski) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//kulczynski_pc.txt -o qiime_results/cd_mc10/bdiv_even963//kulczynski_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (manhattan) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//manhattan_table_even963.txt qiime_results/cd_mc10/bdiv_even963//manhattan_dm.txt Stdout: Stderr: # Principal coordinates (manhattan) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//manhattan_dm.txt -o qiime_results/cd_mc10/bdiv_even963//manhattan_pc.txt Stdout: Stderr: # Make emperor plots, manhattan) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//manhattan_pc.txt -o qiime_results/cd_mc10/bdiv_even963//manhattan_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (morisita_horn) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//morisita_horn_table_even963.txt qiime_results/cd_mc10/bdiv_even963//morisita_horn_dm.txt Stdout: Stderr: # Principal coordinates (morisita_horn) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//morisita_horn_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.137234871442 and the largest is 1.59074108143. RuntimeWarning # Make emperor plots, morisita_horn) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//morisita_horn_pc.txt -o qiime_results/cd_mc10/bdiv_even963//morisita_horn_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (pearson) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//pearson_table_even963.txt qiime_results/cd_mc10/bdiv_even963//pearson_dm.txt Stdout: Stderr: # Principal coordinates (pearson) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//pearson_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.155310019337 and the largest is 1.72155219778. RuntimeWarning # Make emperor plots, pearson) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//pearson_pc.txt -o qiime_results/cd_mc10/bdiv_even963//pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (soergel) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//soergel_table_even963.txt qiime_results/cd_mc10/bdiv_even963//soergel_dm.txt Stdout: Stderr: # Principal coordinates (soergel) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//soergel_dm.txt -o qiime_results/cd_mc10/bdiv_even963//soergel_pc.txt Stdout: Stderr: # Make emperor plots, soergel) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//soergel_pc.txt -o qiime_results/cd_mc10/bdiv_even963//soergel_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (spearman_approx) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//spearman_approx_table_even963.txt qiime_results/cd_mc10/bdiv_even963//spearman_approx_dm.txt Stdout: Stderr: # Principal coordinates (spearman_approx) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//spearman_approx_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.013247001045 and the largest is 0.36279523056. RuntimeWarning # Make emperor plots, spearman_approx) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//spearman_approx_pc.txt -o qiime_results/cd_mc10/bdiv_even963//spearman_approx_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (specprof) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//specprof_table_even963.txt qiime_results/cd_mc10/bdiv_even963//specprof_dm.txt Stdout: Stderr: # Principal coordinates (specprof) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//specprof_dm.txt -o qiime_results/cd_mc10/bdiv_even963//specprof_pc.txt Stdout: Stderr: # Make emperor plots, specprof) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//specprof_pc.txt -o qiime_results/cd_mc10/bdiv_even963//specprof_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unifrac) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --metrics unifrac -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: # Rename distance matrix (unifrac) command mv qiime_results/cd_mc10/bdiv_even963//unifrac_table_even963.txt qiime_results/cd_mc10/bdiv_even963//unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unifrac) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.00394070722166 and the largest is 0.357451499533. RuntimeWarning # Make emperor plots, unifrac) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even963//unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac) command beta_diversity.py -i qiime_results/cd_mc10/table_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//unweighted_unifrac_table_even963.txt qiime_results/cd_mc10/bdiv_even963//unweighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//unweighted_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.00394070722166 and the largest is 0.357451499533. RuntimeWarning # Make emperor plots, unweighted_unifrac) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//unweighted_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even963//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_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//unweighted_unifrac_full_tree_table_even963.txt qiime_results/cd_mc10/bdiv_even963//unweighted_unifrac_full_tree_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac_full_tree) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.00759769372193 and the largest is 0.200137645136. RuntimeWarning # Make emperor plots, unweighted_unifrac_full_tree) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_mc10/bdiv_even963//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_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//weighted_normalized_unifrac_table_even963.txt qiime_results/cd_mc10/bdiv_even963//weighted_normalized_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_normalized_unifrac) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.010232634469 and the largest is 0.575276138731. RuntimeWarning # Make emperor plots, weighted_normalized_unifrac) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even963//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_even963.biom -o qiime_results/cd_mc10/bdiv_even963/ --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_even963//weighted_unifrac_table_even963.txt qiime_results/cd_mc10/bdiv_even963//weighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_unifrac) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even963//weighted_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even963//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 -0.0533063418746 and the largest is 1.87545045668. RuntimeWarning # Make emperor plots, weighted_unifrac) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even963//weighted_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even963//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: Executing commands. # Alpha rarefaction command multiple_rarefactions.py -i qiime_results/cd_mc10/table_mc963.biom -m 10 -x 963 -s 95 -o qiime_results/cd_mc10/arare_max963//rarefaction/ Stdout: Stderr: # Alpha diversity on rarefied OTU tables command alpha_diversity.py -i qiime_results/cd_mc10/arare_max963//rarefaction/ -o qiime_results/cd_mc10/arare_max963//alpha_div/ --metrics berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,michaelis_menten_fit,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: # Collate alpha command collate_alpha.py -i qiime_results/cd_mc10/arare_max963//alpha_div/ -o qiime_results/cd_mc10/arare_max963//alpha_div_collated/ Stdout: Stderr: # Removing intermediate files command rm -r qiime_results/cd_mc10/arare_max963//rarefaction/ qiime_results/cd_mc10/arare_max963//alpha_div/ Stdout: Stderr: # Rarefaction plot: All metrics command make_rarefaction_plots.py -i qiime_results/cd_mc10/arare_max963//alpha_div_collated/ -m meta.txt -o qiime_results/cd_mc10/arare_max963//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_mc963.biom -o qiime_results/cd_mc10/taxa_plots/table_mc963_sorted.biom Stdout: Stderr: # Summarize Taxonomy command summarize_taxa.py -i qiime_results/cd_mc10/taxa_plots/table_mc963_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_mc963_sorted_L2.txt,qiime_results/cd_mc10/taxa_plots/table_mc963_sorted_L3.txt,qiime_results/cd_mc10/taxa_plots/table_mc963_sorted_L4.txt,qiime_results/cd_mc10/taxa_plots/table_mc963_sorted_L5.txt,qiime_results/cd_mc10/taxa_plots/table_mc963_sorted_L6.txt,qiime_results/cd_mc10/taxa_plots/table_mc963_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_mc963.biom Stdout: Stderr: # Compress the rarefied BIOM table command gzip qiime_results/cd_mc10/table_even963.biom Stdout: Stderr: Logging stopped at 12:00:28 on 10 Jun 2016