Logging started at 10:54:04 on 13 Dec 2016 QIIME version: 1.9.1 qiime_config values: blastmat_dir /qiime_software/blast-2.2.22-release/data pick_otus_reference_seqs_fp /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta sc_queue all.q pynast_template_alignment_fp /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta cluster_jobs_fp start_parallel_jobs.py assign_taxonomy_reference_seqs_fp /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta torque_queue friendlyq jobs_to_start 1 denoiser_min_per_core 50 assign_taxonomy_id_to_taxonomy_fp /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt temp_dir /tmp/ blastall_fp /qiime_software/blast-2.2.22-release/bin/blastall seconds_to_sleep 1 parameter file values: alpha_diversity:metrics berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree beta_diversity:metrics abund_jaccard,binary_chisq,binary_chord,binary_euclidean,binary_hamming,binary_jaccard,binary_lennon,binary_ochiai,binary_pearson,binary_sorensen_dice,bray_curtis,bray_curtis_faith,bray_curtis_magurran,canberra,chisq,chord,euclidean,gower,hellinger,kulczynski,manhattan,morisita_horn,pearson,soergel,spearman_approx,specprof,unifrac,unweighted_unifrac,unweighted_unifrac_full_tree,weighted_normalized_unifrac,weighted_unifrac summarize_taxa:level 2,3,4,5,6,7 parallel:jobs_to_start 1 filter_samples_from_otu_table:min_count 3000 plot_taxa_summary:labels Phylum,Class,Order,Family,Genus,Species plot_taxa_summary:chart_type bar,area,pie core_diversity_analyses:categories Status Input file md5 sums: qiime_results/data_all/final_otu_map_all_tax.biom: 674bad527ef4c133077a3cfff5b8a4a2 meta.txt: 13073d4a61ad0a90ce6a6e480a1cbaad qiime_results/data_all/rep_set_all.tre: 134fc1aabb14266341051c996daaca49 Executing commands. # Generate BIOM table summary command biom summarize-table -i qiime_results/data_all/final_otu_map_all_tax.biom -o qiime_results/cd_all/biom_table_summary.txt Stdout: Stderr: # Filter low sequence count samples from table (minimum sequence count: 4254) command filter_samples_from_otu_table.py -i qiime_results/data_all/final_otu_map_all_tax.biom -o qiime_results/cd_all/table_mc4254.biom -n 4254 Stdout: Stderr: # Rarify the OTU table to 4254 sequences/sample command single_rarefaction.py -i qiime_results/cd_all/table_mc4254.biom -o qiime_results/cd_all/table_even4254.biom -d 4254 Stdout: Stderr: Executing commands. # Beta Diversity (abund_jaccard) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics abund_jaccard -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (abund_jaccard) command mv qiime_results/cd_all/bdiv_even4254//abund_jaccard_table_even4254.txt qiime_results/cd_all/bdiv_even4254//abund_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (abund_jaccard) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//abund_jaccard_dm.txt -o qiime_results/cd_all/bdiv_even4254//abund_jaccard_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.747591095584 and the largest is 2.2159374855. RuntimeWarning # Make emperor plots, abund_jaccard) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//abund_jaccard_pc.txt -o qiime_results/cd_all/bdiv_even4254//abund_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chisq) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_chisq -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_chisq) command mv qiime_results/cd_all/bdiv_even4254//binary_chisq_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_chisq_dm.txt Stdout: Stderr: # Principal coordinates (binary_chisq) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_chisq_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_chisq_pc.txt Stdout: Stderr: # Make emperor plots, binary_chisq) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_chisq_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chord) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_chord -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_chord) command mv qiime_results/cd_all/bdiv_even4254//binary_chord_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_chord_dm.txt Stdout: Stderr: # Principal coordinates (binary_chord) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_chord_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_chord_pc.txt Stdout: Stderr: # Make emperor plots, binary_chord) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_chord_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_euclidean) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_euclidean -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_euclidean) command mv qiime_results/cd_all/bdiv_even4254//binary_euclidean_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_euclidean_dm.txt Stdout: Stderr: # Principal coordinates (binary_euclidean) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_euclidean_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_euclidean_pc.txt Stdout: Stderr: # Make emperor plots, binary_euclidean) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_euclidean_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_hamming) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_hamming -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_hamming) command mv qiime_results/cd_all/bdiv_even4254//binary_hamming_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_hamming_dm.txt Stdout: Stderr: # Principal coordinates (binary_hamming) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_hamming_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_hamming_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -4233.42847164 and the largest is 74214.770203. RuntimeWarning # Make emperor plots, binary_hamming) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_hamming_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_hamming_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_jaccard) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_jaccard -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_jaccard) command mv qiime_results/cd_all/bdiv_even4254//binary_jaccard_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (binary_jaccard) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_jaccard_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_jaccard_pc.txt Stdout: Stderr: # Make emperor plots, binary_jaccard) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_jaccard_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_lennon) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_lennon -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_lennon) command mv qiime_results/cd_all/bdiv_even4254//binary_lennon_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_lennon_dm.txt Stdout: Stderr: # Principal coordinates (binary_lennon) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_lennon_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_lennon_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -1.04505774424 and the largest is 1.37596741922. RuntimeWarning # Make emperor plots, binary_lennon) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_lennon_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_lennon_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_ochiai) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_ochiai -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_ochiai) command mv qiime_results/cd_all/bdiv_even4254//binary_ochiai_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_ochiai_dm.txt Stdout: Stderr: # Principal coordinates (binary_ochiai) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_ochiai_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_ochiai_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.00632596342932 and the largest is 1.34965972779. RuntimeWarning # Make emperor plots, binary_ochiai) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_ochiai_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_ochiai_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_pearson) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_pearson -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_pearson) command mv qiime_results/cd_all/bdiv_even4254//binary_pearson_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_pearson_dm.txt Stdout: Stderr: # Principal coordinates (binary_pearson) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_pearson_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_pearson_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0063297096301 and the largest is 1.61310915882. RuntimeWarning # Make emperor plots, binary_pearson) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_pearson_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_sorensen_dice) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics binary_sorensen_dice -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_sorensen_dice) command mv qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_table_even4254.txt qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_dm.txt Stdout: Stderr: # Principal coordinates (binary_sorensen_dice) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_dm.txt -o qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.000645544950963 and the largest is 1.63724948402. RuntimeWarning # Make emperor plots, binary_sorensen_dice) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_pc.txt -o qiime_results/cd_all/bdiv_even4254//binary_sorensen_dice_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics bray_curtis -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (bray_curtis) command mv qiime_results/cd_all/bdiv_even4254//bray_curtis_table_even4254.txt qiime_results/cd_all/bdiv_even4254//bray_curtis_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_dm.txt -o qiime_results/cd_all/bdiv_even4254//bray_curtis_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.066790750884 and the largest is 2.02524057377. RuntimeWarning # Make emperor plots, bray_curtis) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_pc.txt -o qiime_results/cd_all/bdiv_even4254//bray_curtis_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis_faith) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics bray_curtis_faith -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (bray_curtis_faith) command mv qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_table_even4254.txt qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_faith) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_dm.txt -o qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.066790750884 and the largest is 2.02524057377. RuntimeWarning # Make emperor plots, bray_curtis_faith) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_pc.txt -o qiime_results/cd_all/bdiv_even4254//bray_curtis_faith_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis_magurran) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics bray_curtis_magurran -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (bray_curtis_magurran) command mv qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_table_even4254.txt qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_magurran) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_dm.txt -o qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.066790750884 and the largest is 2.02524057377. RuntimeWarning # Make emperor plots, bray_curtis_magurran) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_pc.txt -o qiime_results/cd_all/bdiv_even4254//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (canberra) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics canberra -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (canberra) command mv qiime_results/cd_all/bdiv_even4254//canberra_table_even4254.txt qiime_results/cd_all/bdiv_even4254//canberra_dm.txt Stdout: Stderr: # Principal coordinates (canberra) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//canberra_dm.txt -o qiime_results/cd_all/bdiv_even4254//canberra_pc.txt Stdout: Stderr: # Make emperor plots, canberra) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//canberra_pc.txt -o qiime_results/cd_all/bdiv_even4254//canberra_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chisq) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics chisq -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (chisq) command mv qiime_results/cd_all/bdiv_even4254//chisq_table_even4254.txt qiime_results/cd_all/bdiv_even4254//chisq_dm.txt Stdout: Stderr: # Principal coordinates (chisq) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//chisq_dm.txt -o qiime_results/cd_all/bdiv_even4254//chisq_pc.txt Stdout: Stderr: # Make emperor plots, chisq) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//chisq_pc.txt -o qiime_results/cd_all/bdiv_even4254//chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chord) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics chord -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (chord) command mv qiime_results/cd_all/bdiv_even4254//chord_table_even4254.txt qiime_results/cd_all/bdiv_even4254//chord_dm.txt Stdout: Stderr: # Principal coordinates (chord) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//chord_dm.txt -o qiime_results/cd_all/bdiv_even4254//chord_pc.txt Stdout: Stderr: # Make emperor plots, chord) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//chord_pc.txt -o qiime_results/cd_all/bdiv_even4254//chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (euclidean) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics euclidean -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (euclidean) command mv qiime_results/cd_all/bdiv_even4254//euclidean_table_even4254.txt qiime_results/cd_all/bdiv_even4254//euclidean_dm.txt Stdout: Stderr: # Principal coordinates (euclidean) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//euclidean_dm.txt -o qiime_results/cd_all/bdiv_even4254//euclidean_pc.txt Stdout: Stderr: # Make emperor plots, euclidean) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//euclidean_pc.txt -o qiime_results/cd_all/bdiv_even4254//euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (gower) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics gower -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (gower) command mv qiime_results/cd_all/bdiv_even4254//gower_table_even4254.txt qiime_results/cd_all/bdiv_even4254//gower_dm.txt Stdout: Stderr: # Principal coordinates (gower) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//gower_dm.txt -o qiime_results/cd_all/bdiv_even4254//gower_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -8083.67511708 and the largest is 14903.8009369. RuntimeWarning # Make emperor plots, gower) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//gower_pc.txt -o qiime_results/cd_all/bdiv_even4254//gower_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (hellinger) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics hellinger -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (hellinger) command mv qiime_results/cd_all/bdiv_even4254//hellinger_table_even4254.txt qiime_results/cd_all/bdiv_even4254//hellinger_dm.txt Stdout: Stderr: # Principal coordinates (hellinger) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//hellinger_dm.txt -o qiime_results/cd_all/bdiv_even4254//hellinger_pc.txt Stdout: Stderr: # Make emperor plots, hellinger) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//hellinger_pc.txt -o qiime_results/cd_all/bdiv_even4254//hellinger_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (kulczynski) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics kulczynski -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (kulczynski) command mv qiime_results/cd_all/bdiv_even4254//kulczynski_table_even4254.txt qiime_results/cd_all/bdiv_even4254//kulczynski_dm.txt Stdout: Stderr: # Principal coordinates (kulczynski) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//kulczynski_dm.txt -o qiime_results/cd_all/bdiv_even4254//kulczynski_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.066790750884 and the largest is 2.02524057377. RuntimeWarning # Make emperor plots, kulczynski) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//kulczynski_pc.txt -o qiime_results/cd_all/bdiv_even4254//kulczynski_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (manhattan) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics manhattan -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (manhattan) command mv qiime_results/cd_all/bdiv_even4254//manhattan_table_even4254.txt qiime_results/cd_all/bdiv_even4254//manhattan_dm.txt Stdout: Stderr: # Principal coordinates (manhattan) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//manhattan_dm.txt -o qiime_results/cd_all/bdiv_even4254//manhattan_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -4834719.56809 and the largest is 146599193.788. RuntimeWarning # Make emperor plots, manhattan) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//manhattan_pc.txt -o qiime_results/cd_all/bdiv_even4254//manhattan_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (morisita_horn) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics morisita_horn -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (morisita_horn) command mv qiime_results/cd_all/bdiv_even4254//morisita_horn_table_even4254.txt qiime_results/cd_all/bdiv_even4254//morisita_horn_dm.txt Stdout: Stderr: # Principal coordinates (morisita_horn) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//morisita_horn_dm.txt -o qiime_results/cd_all/bdiv_even4254//morisita_horn_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.284603321963 and the largest is 2.93891375593. RuntimeWarning # Make emperor plots, morisita_horn) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//morisita_horn_pc.txt -o qiime_results/cd_all/bdiv_even4254//morisita_horn_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (pearson) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics pearson -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (pearson) command mv qiime_results/cd_all/bdiv_even4254//pearson_table_even4254.txt qiime_results/cd_all/bdiv_even4254//pearson_dm.txt Stdout: Stderr: # Principal coordinates (pearson) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//pearson_dm.txt -o qiime_results/cd_all/bdiv_even4254//pearson_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.346676769024 and the largest is 3.14750373244. RuntimeWarning # Make emperor plots, pearson) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//pearson_pc.txt -o qiime_results/cd_all/bdiv_even4254//pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (soergel) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics soergel -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (soergel) command mv qiime_results/cd_all/bdiv_even4254//soergel_table_even4254.txt qiime_results/cd_all/bdiv_even4254//soergel_dm.txt Stdout: Stderr: # Principal coordinates (soergel) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//soergel_dm.txt -o qiime_results/cd_all/bdiv_even4254//soergel_pc.txt Stdout: Stderr: # Make emperor plots, soergel) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//soergel_pc.txt -o qiime_results/cd_all/bdiv_even4254//soergel_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (spearman_approx) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics spearman_approx -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (spearman_approx) command mv qiime_results/cd_all/bdiv_even4254//spearman_approx_table_even4254.txt qiime_results/cd_all/bdiv_even4254//spearman_approx_dm.txt Stdout: Stderr: # Principal coordinates (spearman_approx) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//spearman_approx_dm.txt -o qiime_results/cd_all/bdiv_even4254//spearman_approx_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0227359222732 and the largest is 0.15189171353. RuntimeWarning # Make emperor plots, spearman_approx) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//spearman_approx_pc.txt -o qiime_results/cd_all/bdiv_even4254//spearman_approx_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (specprof) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics specprof -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (specprof) command mv qiime_results/cd_all/bdiv_even4254//specprof_table_even4254.txt qiime_results/cd_all/bdiv_even4254//specprof_dm.txt Stdout: Stderr: # Principal coordinates (specprof) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//specprof_dm.txt -o qiime_results/cd_all/bdiv_even4254//specprof_pc.txt Stdout: Stderr: # Make emperor plots, specprof) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//specprof_pc.txt -o qiime_results/cd_all/bdiv_even4254//specprof_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unifrac) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics unifrac -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: # Rename distance matrix (unifrac) command mv qiime_results/cd_all/bdiv_even4254//unifrac_table_even4254.txt qiime_results/cd_all/bdiv_even4254//unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unifrac) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//unifrac_dm.txt -o qiime_results/cd_all/bdiv_even4254//unifrac_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.00064077718732 and the largest is 1.77095884051. RuntimeWarning # Make emperor plots, unifrac) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//unifrac_pc.txt -o qiime_results/cd_all/bdiv_even4254//unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics unweighted_unifrac -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: # Rename distance matrix (unweighted_unifrac) command mv qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_table_even4254.txt qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.00064077718732 and the largest is 1.77095884051. RuntimeWarning # Make emperor plots, unweighted_unifrac) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac_full_tree) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics unweighted_unifrac_full_tree -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: # Rename distance matrix (unweighted_unifrac_full_tree) command mv qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_table_even4254.txt qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac_full_tree) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0131511095181 and the largest is 0.356185881689. RuntimeWarning # Make emperor plots, unweighted_unifrac_full_tree) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_all/bdiv_even4254//unweighted_unifrac_full_tree_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (weighted_normalized_unifrac) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics weighted_normalized_unifrac -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: # Rename distance matrix (weighted_normalized_unifrac) command mv qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_table_even4254.txt qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_normalized_unifrac) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0461890329583 and the largest is 1.28976320534. RuntimeWarning # Make emperor plots, weighted_normalized_unifrac) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even4254//weighted_normalized_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (weighted_unifrac) command beta_diversity.py -i qiime_results/cd_all/table_even4254.biom -o qiime_results/cd_all/bdiv_even4254/ --metrics weighted_unifrac -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: # Rename distance matrix (weighted_unifrac) command mv qiime_results/cd_all/bdiv_even4254//weighted_unifrac_table_even4254.txt qiime_results/cd_all/bdiv_even4254//weighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_unifrac) command principal_coordinates.py -i qiime_results/cd_all/bdiv_even4254//weighted_unifrac_dm.txt -o qiime_results/cd_all/bdiv_even4254//weighted_unifrac_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0601973759946 and the largest is 2.12089734225. RuntimeWarning # Make emperor plots, weighted_unifrac) command make_emperor.py -i qiime_results/cd_all/bdiv_even4254//weighted_unifrac_pc.txt -o qiime_results/cd_all/bdiv_even4254//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: Executing commands. # Alpha rarefaction command multiple_rarefactions.py -i qiime_results/cd_all/table_mc4254.biom -m 10 -x 4254 -s 424 -o qiime_results/cd_all/arare_max4254//rarefaction/ Stdout: Stderr: # Alpha diversity on rarefied OTU tables command alpha_diversity.py -i qiime_results/cd_all/arare_max4254//rarefaction/ -o qiime_results/cd_all/arare_max4254//alpha_div/ --metrics berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree -t qiime_results/data_all/rep_set_all.tre Stdout: Stderr: # Collate alpha command collate_alpha.py -i qiime_results/cd_all/arare_max4254//alpha_div/ -o qiime_results/cd_all/arare_max4254//alpha_div_collated/ Stdout: Stderr: # Removing intermediate files command rm -r qiime_results/cd_all/arare_max4254//rarefaction/ qiime_results/cd_all/arare_max4254//alpha_div/ Stdout: Stderr: # Rarefaction plot: All metrics command make_rarefaction_plots.py -i qiime_results/cd_all/arare_max4254//alpha_div_collated/ -m meta.txt -o qiime_results/cd_all/arare_max4254//alpha_rarefaction_plots/ Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/matplotlib/axes/_base.py:2809: UserWarning: Attempting to set identical bottom==top results in singular transformations; automatically expanding. bottom=0, top=0 'bottom=%s, top=%s') % (bottom, top)) Skipping compare_alpha_diversity.py as no categories were provided. Executing commands. # Sort OTU Table command sort_otu_table.py -i qiime_results/cd_all/table_mc4254.biom -o qiime_results/cd_all/taxa_plots/table_mc4254_sorted.biom Stdout: Stderr: # Summarize Taxonomy command summarize_taxa.py -i qiime_results/cd_all/taxa_plots/table_mc4254_sorted.biom -o qiime_results/cd_all/taxa_plots/ --level 2,3,4,5,6,7 Stdout: Stderr: # Plot Taxonomy Summary command plot_taxa_summary.py -i qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L2.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L3.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L4.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L5.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L6.txt,qiime_results/cd_all/taxa_plots/table_mc4254_sorted_L7.txt -o qiime_results/cd_all/taxa_plots//taxa_summary_plots/ --labels Phylum,Class,Order,Family,Genus,Species --chart_type bar,area,pie Stdout: Stderr: Executing commands. # Compress the filtered BIOM table command gzip qiime_results/cd_all/table_mc4254.biom Stdout: Stderr: # Compress the rarefied BIOM table command gzip qiime_results/cd_all/table_even4254.biom Stdout: Stderr: Logging stopped at 11:11:28 on 13 Dec 2016