Logging started at 14:49:58 on 12 Oct 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 500 plot_taxa_summary:labels Phylum,Class,Order,Family,Genus,Species plot_taxa_summary:chart_type bar,area,pie core_diversity_analyses:categories Toothpaste Input file md5 sums: qiime_results/data_mc5/final_otu_map_mc5_tax.biom: 62b65ff8eb3b70fd068a850382188a81 meta.txt: d8dc9993bcfe520a325021d8a9c0c21c qiime_results/data_mc5/rep_set_mc5.tre: 4610b9a443b598b091f1ed8ad393e520 Executing commands. # Generate BIOM table summary command biom summarize-table -i qiime_results/data_mc5/final_otu_map_mc5_tax.biom -o qiime_results/cd_mc5/biom_table_summary.txt Stdout: Stderr: # Filter low sequence count samples from table (minimum sequence count: 24507) command filter_samples_from_otu_table.py -i qiime_results/data_mc5/final_otu_map_mc5_tax.biom -o qiime_results/cd_mc5/table_mc24507.biom -n 24507 Stdout: Stderr: # Rarify the OTU table to 24507 sequences/sample command single_rarefaction.py -i qiime_results/cd_mc5/table_mc24507.biom -o qiime_results/cd_mc5/table_even24507.biom -d 24507 Stdout: Stderr: Executing commands. # Beta Diversity (abund_jaccard) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics abund_jaccard -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//abund_jaccard_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//abund_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (abund_jaccard) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//abund_jaccard_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -1.53412573343 and the largest is 4.65347967168. RuntimeWarning # Make emperor plots, abund_jaccard) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//abund_jaccard_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//abund_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chisq) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_chisq -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_chisq_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_chisq_dm.txt Stdout: Stderr: # Principal coordinates (binary_chisq) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_chisq_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_chisq_pc.txt Stdout: Stderr: # Make emperor plots, binary_chisq) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_chisq_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chord) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_chord -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_chord_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_chord_dm.txt Stdout: Stderr: # Principal coordinates (binary_chord) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_chord_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_chord_pc.txt Stdout: Stderr: # Make emperor plots, binary_chord) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_chord_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_euclidean) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_euclidean -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_euclidean_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_euclidean_dm.txt Stdout: Stderr: # Principal coordinates (binary_euclidean) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_euclidean_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_euclidean_pc.txt Stdout: Stderr: # Make emperor plots, binary_euclidean) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_euclidean_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_hamming) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_hamming -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_hamming_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_hamming_dm.txt Stdout: Stderr: # Principal coordinates (binary_hamming) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_hamming_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -19592.5565945 and the largest is 651290.421904. RuntimeWarning # Make emperor plots, binary_hamming) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_hamming_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_hamming_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_jaccard) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_jaccard -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_jaccard_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (binary_jaccard) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_jaccard_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_jaccard_pc.txt Stdout: Stderr: # Make emperor plots, binary_jaccard) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_jaccard_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_lennon) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_lennon -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_lennon_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_lennon_dm.txt Stdout: Stderr: # Principal coordinates (binary_lennon) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_lennon_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -1.06838058874 and the largest is 2.92674871972. RuntimeWarning # Make emperor plots, binary_lennon) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_lennon_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_lennon_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_ochiai) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_ochiai -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_ochiai_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_ochiai_dm.txt Stdout: Stderr: # Principal coordinates (binary_ochiai) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_ochiai_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0310993458585 and the largest is 2.79311476087. RuntimeWarning # Make emperor plots, binary_ochiai) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_ochiai_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_ochiai_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_pearson) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_pearson -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_pearson_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_pearson_dm.txt Stdout: Stderr: # Principal coordinates (binary_pearson) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_pearson_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0367026700949 and the largest is 3.5066412626. RuntimeWarning # Make emperor plots, binary_pearson) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_pearson_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_sorensen_dice) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics binary_sorensen_dice -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//binary_sorensen_dice_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//binary_sorensen_dice_dm.txt Stdout: Stderr: # Principal coordinates (binary_sorensen_dice) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//binary_sorensen_dice_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0282729826695 and the largest is 2.74933873997. RuntimeWarning # Make emperor plots, binary_sorensen_dice) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//binary_sorensen_dice_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//binary_sorensen_dice_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics bray_curtis -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//bray_curtis_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//bray_curtis_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//bray_curtis_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0892318126008 and the largest is 3.40198221667. RuntimeWarning # Make emperor plots, bray_curtis) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//bray_curtis_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//bray_curtis_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis_faith) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics bray_curtis_faith -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//bray_curtis_faith_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//bray_curtis_faith_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_faith) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//bray_curtis_faith_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0892318126008 and the largest is 3.40198221667. RuntimeWarning # Make emperor plots, bray_curtis_faith) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//bray_curtis_faith_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//bray_curtis_faith_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis_magurran) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics bray_curtis_magurran -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//bray_curtis_magurran_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//bray_curtis_magurran_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_magurran) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//bray_curtis_magurran_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0892318126008 and the largest is 3.40198221667. RuntimeWarning # Make emperor plots, bray_curtis_magurran) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//bray_curtis_magurran_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (canberra) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics canberra -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//canberra_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//canberra_dm.txt Stdout: Stderr: # Principal coordinates (canberra) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//canberra_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//canberra_pc.txt Stdout: Stderr: # Make emperor plots, canberra) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//canberra_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//canberra_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chisq) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics chisq -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//chisq_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//chisq_dm.txt Stdout: Stderr: # Principal coordinates (chisq) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//chisq_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//chisq_pc.txt Stdout: Stderr: # Make emperor plots, chisq) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//chisq_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chord) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics chord -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//chord_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//chord_dm.txt Stdout: Stderr: # Principal coordinates (chord) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//chord_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//chord_pc.txt Stdout: Stderr: # Make emperor plots, chord) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//chord_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (euclidean) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics euclidean -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//euclidean_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//euclidean_dm.txt Stdout: Stderr: # Principal coordinates (euclidean) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//euclidean_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//euclidean_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 -7.09828664931e-07 and the largest is 1956246702.15. RuntimeWarning # Make emperor plots, euclidean) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//euclidean_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (gower) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics gower -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//gower_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//gower_dm.txt Stdout: Stderr: # Principal coordinates (gower) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//gower_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -62076.8905343 and the largest is 125614.281423. RuntimeWarning # Make emperor plots, gower) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//gower_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//gower_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (hellinger) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics hellinger -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//hellinger_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//hellinger_dm.txt Stdout: Stderr: # Principal coordinates (hellinger) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//hellinger_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//hellinger_pc.txt Stdout: Stderr: # Make emperor plots, hellinger) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//hellinger_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//hellinger_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (kulczynski) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics kulczynski -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//kulczynski_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//kulczynski_dm.txt Stdout: Stderr: # Principal coordinates (kulczynski) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//kulczynski_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0892318126008 and the largest is 3.40198221667. RuntimeWarning # Make emperor plots, kulczynski) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//kulczynski_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//kulczynski_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (manhattan) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics manhattan -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//manhattan_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//manhattan_dm.txt Stdout: Stderr: # Principal coordinates (manhattan) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//manhattan_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -214368025.59 and the largest is 8172827488.63. RuntimeWarning # Make emperor plots, manhattan) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//manhattan_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//manhattan_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (morisita_horn) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics morisita_horn -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//morisita_horn_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//morisita_horn_dm.txt Stdout: Stderr: # Principal coordinates (morisita_horn) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//morisita_horn_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.326140376395 and the largest is 5.30394955472. RuntimeWarning # Make emperor plots, morisita_horn) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//morisita_horn_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//morisita_horn_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (pearson) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics pearson -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//pearson_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//pearson_dm.txt Stdout: Stderr: # Principal coordinates (pearson) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//pearson_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.368174287596 and the largest is 5.4405213774. RuntimeWarning # Make emperor plots, pearson) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//pearson_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (soergel) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics soergel -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//soergel_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//soergel_dm.txt Stdout: Stderr: # Principal coordinates (soergel) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//soergel_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//soergel_pc.txt Stdout: Stderr: # Make emperor plots, soergel) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//soergel_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//soergel_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (spearman_approx) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics spearman_approx -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//spearman_approx_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//spearman_approx_dm.txt Stdout: Stderr: # Principal coordinates (spearman_approx) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//spearman_approx_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0436182254017 and the largest is 0.360246074297. RuntimeWarning # Make emperor plots, spearman_approx) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//spearman_approx_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//spearman_approx_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (specprof) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics specprof -t qiime_results/data_mc5/rep_set_mc5.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_mc5/bdiv_even24507//specprof_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//specprof_dm.txt Stdout: Stderr: # Principal coordinates (specprof) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//specprof_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//specprof_pc.txt Stdout: Stderr: # Make emperor plots, specprof) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//specprof_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//specprof_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unifrac) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics unifrac -t qiime_results/data_mc5/rep_set_mc5.tre Stdout: Stderr: # Rename distance matrix (unifrac) command mv qiime_results/cd_mc5/bdiv_even24507//unifrac_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unifrac) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//unifrac_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0243676112856 and the largest is 1.52118161117. RuntimeWarning # Make emperor plots, unifrac) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//unifrac_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics unweighted_unifrac -t qiime_results/data_mc5/rep_set_mc5.tre Stdout: Stderr: # Rename distance matrix (unweighted_unifrac) command mv qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0243676112856 and the largest is 1.52118161117. RuntimeWarning # Make emperor plots, unweighted_unifrac) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac_full_tree) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics unweighted_unifrac_full_tree -t qiime_results/data_mc5/rep_set_mc5.tre Stdout: Stderr: # Rename distance matrix (unweighted_unifrac_full_tree) command mv qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_full_tree_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_full_tree_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac_full_tree) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0178134843862 and the largest is 0.498654752922. RuntimeWarning # Make emperor plots, unweighted_unifrac_full_tree) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//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_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics weighted_normalized_unifrac -t qiime_results/data_mc5/rep_set_mc5.tre Stdout: Stderr: # Rename distance matrix (weighted_normalized_unifrac) command mv qiime_results/cd_mc5/bdiv_even24507//weighted_normalized_unifrac_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//weighted_normalized_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_normalized_unifrac) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0637162144728 and the largest is 4.03424004014. RuntimeWarning # Make emperor plots, weighted_normalized_unifrac) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//weighted_normalized_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (weighted_unifrac) command beta_diversity.py -i qiime_results/cd_mc5/table_even24507.biom -o qiime_results/cd_mc5/bdiv_even24507/ --metrics weighted_unifrac -t qiime_results/data_mc5/rep_set_mc5.tre Stdout: Stderr: # Rename distance matrix (weighted_unifrac) command mv qiime_results/cd_mc5/bdiv_even24507//weighted_unifrac_table_even24507.txt qiime_results/cd_mc5/bdiv_even24507//weighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_unifrac) command principal_coordinates.py -i qiime_results/cd_mc5/bdiv_even24507//weighted_unifrac_dm.txt -o qiime_results/cd_mc5/bdiv_even24507//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 -0.0967146487926 and the largest is 2.49800918571. RuntimeWarning # Make emperor plots, weighted_unifrac) command make_emperor.py -i qiime_results/cd_mc5/bdiv_even24507//weighted_unifrac_pc.txt -o qiime_results/cd_mc5/bdiv_even24507//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: Executing commands. # Alpha rarefaction command multiple_rarefactions.py -i qiime_results/cd_mc5/table_mc24507.biom -m 10 -x 24507 -s 2449 -o qiime_results/cd_mc5/arare_max24507//rarefaction/ Stdout: Stderr: # Alpha diversity on rarefied OTU tables command alpha_diversity.py -i qiime_results/cd_mc5/arare_max24507//rarefaction/ -o qiime_results/cd_mc5/arare_max24507//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_mc5/rep_set_mc5.tre Stdout: Stderr: # Collate alpha command collate_alpha.py -i qiime_results/cd_mc5/arare_max24507//alpha_div/ -o qiime_results/cd_mc5/arare_max24507//alpha_div_collated/ Stdout: Stderr: # Removing intermediate files command rm -r qiime_results/cd_mc5/arare_max24507//rarefaction/ qiime_results/cd_mc5/arare_max24507//alpha_div/ Stdout: Stderr: # Rarefaction plot: All metrics command make_rarefaction_plots.py -i qiime_results/cd_mc5/arare_max24507//alpha_div_collated/ -m meta.txt -o qiime_results/cd_mc5/arare_max24507//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_mc5/table_mc24507.biom -o qiime_results/cd_mc5/taxa_plots/table_mc24507_sorted.biom Stdout: Stderr: # Summarize Taxonomy command summarize_taxa.py -i qiime_results/cd_mc5/taxa_plots/table_mc24507_sorted.biom -o qiime_results/cd_mc5/taxa_plots/ --level 2,3,4,5,6,7 Stdout: Stderr: # Plot Taxonomy Summary command plot_taxa_summary.py -i qiime_results/cd_mc5/taxa_plots/table_mc24507_sorted_L2.txt,qiime_results/cd_mc5/taxa_plots/table_mc24507_sorted_L3.txt,qiime_results/cd_mc5/taxa_plots/table_mc24507_sorted_L4.txt,qiime_results/cd_mc5/taxa_plots/table_mc24507_sorted_L5.txt,qiime_results/cd_mc5/taxa_plots/table_mc24507_sorted_L6.txt,qiime_results/cd_mc5/taxa_plots/table_mc24507_sorted_L7.txt -o qiime_results/cd_mc5/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_mc5/table_mc24507.biom Stdout: Stderr: # Compress the rarefied BIOM table command gzip qiime_results/cd_mc5/table_even24507.biom Stdout: Stderr: Logging stopped at 15:33:10 on 12 Oct 2016