Logging started at 22:37:18 on 29 May 2018 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 Week Input file md5 sums: qiime_results/data_mc100/final_otu_map_mc100_tax.biom: 60258dd092c2592efe13a3d0c2500cad meta.txt: a72086c2ab21804761519933277da0c1 qiime_results/data_mc100/rep_set_mc100.tre: 224c32295983c3295200f980869eae69 Executing commands. # Generate BIOM table summary command biom summarize-table -i qiime_results/data_mc100/final_otu_map_mc100_tax.biom -o qiime_results/cd_mc100/biom_table_summary.txt Stdout: Stderr: # Filter low sequence count samples from table (minimum sequence count: 514) command filter_samples_from_otu_table.py -i qiime_results/data_mc100/final_otu_map_mc100_tax.biom -o qiime_results/cd_mc100/table_mc514.biom -n 514 Stdout: Stderr: # Rarify the OTU table to 514 sequences/sample command single_rarefaction.py -i qiime_results/cd_mc100/table_mc514.biom -o qiime_results/cd_mc100/table_even514.biom -d 514 Stdout: Stderr: Executing commands. # Beta Diversity (abund_jaccard) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics abund_jaccard -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//abund_jaccard_table_even514.txt qiime_results/cd_mc100/bdiv_even514//abund_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (abund_jaccard) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//abund_jaccard_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.594712390837 and the largest is 8.62927456319. RuntimeWarning # Make emperor plots, abund_jaccard) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//abund_jaccard_pc.txt -o qiime_results/cd_mc100/bdiv_even514//abund_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chisq) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_chisq -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_chisq_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_chisq_dm.txt Stdout: Stderr: # Principal coordinates (binary_chisq) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_chisq_dm.txt -o qiime_results/cd_mc100/bdiv_even514//binary_chisq_pc.txt Stdout: Stderr: # Make emperor plots, binary_chisq) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_chisq_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chord) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_chord -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_chord_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_chord_dm.txt Stdout: Stderr: # Principal coordinates (binary_chord) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_chord_dm.txt -o qiime_results/cd_mc100/bdiv_even514//binary_chord_pc.txt Stdout: Stderr: # Make emperor plots, binary_chord) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_chord_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_euclidean) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_euclidean -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_euclidean_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_euclidean_dm.txt Stdout: Stderr: # Principal coordinates (binary_euclidean) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_euclidean_dm.txt -o qiime_results/cd_mc100/bdiv_even514//binary_euclidean_pc.txt Stdout: Stderr: # Make emperor plots, binary_euclidean) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_euclidean_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_hamming) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_hamming -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_hamming_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_hamming_dm.txt Stdout: Stderr: # Principal coordinates (binary_hamming) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_hamming_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -432.533839142 and the largest is 20218.7168316. RuntimeWarning # Make emperor plots, binary_hamming) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_hamming_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_hamming_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_jaccard) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_jaccard -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_jaccard_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (binary_jaccard) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_jaccard_dm.txt -o qiime_results/cd_mc100/bdiv_even514//binary_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 -0.0357020643158 and the largest is 5.33045907866. RuntimeWarning # Make emperor plots, binary_jaccard) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_jaccard_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_lennon) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_lennon -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_lennon_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_lennon_dm.txt Stdout: Stderr: # Principal coordinates (binary_lennon) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_lennon_dm.txt -o qiime_results/cd_mc100/bdiv_even514//binary_lennon_pc.txt Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.59651370558 and the largest is 6.11911514974. RuntimeWarning # Make emperor plots, binary_lennon) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_lennon_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_lennon_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_ochiai) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_ochiai -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_ochiai_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_ochiai_dm.txt Stdout: Stderr: # Principal coordinates (binary_ochiai) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_ochiai_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.170520234944 and the largest is 5.89963005853. RuntimeWarning # Make emperor plots, binary_ochiai) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_ochiai_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_ochiai_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_pearson) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_pearson -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_pearson_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_pearson_dm.txt Stdout: Stderr: # Principal coordinates (binary_pearson) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_pearson_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.195396201882 and the largest is 6.78971744084. RuntimeWarning # Make emperor plots, binary_pearson) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_pearson_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_sorensen_dice) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics binary_sorensen_dice -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//binary_sorensen_dice_table_even514.txt qiime_results/cd_mc100/bdiv_even514//binary_sorensen_dice_dm.txt Stdout: Stderr: # Principal coordinates (binary_sorensen_dice) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//binary_sorensen_dice_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.143202115652 and the largest is 5.88555623367. RuntimeWarning # Make emperor plots, binary_sorensen_dice) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//binary_sorensen_dice_pc.txt -o qiime_results/cd_mc100/bdiv_even514//binary_sorensen_dice_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics bray_curtis -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//bray_curtis_table_even514.txt qiime_results/cd_mc100/bdiv_even514//bray_curtis_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//bray_curtis_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.180978943318 and the largest is 7.6761524933. RuntimeWarning # Make emperor plots, bray_curtis) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//bray_curtis_pc.txt -o qiime_results/cd_mc100/bdiv_even514//bray_curtis_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis_faith) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics bray_curtis_faith -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//bray_curtis_faith_table_even514.txt qiime_results/cd_mc100/bdiv_even514//bray_curtis_faith_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_faith) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//bray_curtis_faith_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.180978943318 and the largest is 7.6761524933. RuntimeWarning # Make emperor plots, bray_curtis_faith) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//bray_curtis_faith_pc.txt -o qiime_results/cd_mc100/bdiv_even514//bray_curtis_faith_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis_magurran) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics bray_curtis_magurran -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//bray_curtis_magurran_table_even514.txt qiime_results/cd_mc100/bdiv_even514//bray_curtis_magurran_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_magurran) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//bray_curtis_magurran_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.180978943318 and the largest is 7.6761524933. RuntimeWarning # Make emperor plots, bray_curtis_magurran) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//bray_curtis_magurran_pc.txt -o qiime_results/cd_mc100/bdiv_even514//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (canberra) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics canberra -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//canberra_table_even514.txt qiime_results/cd_mc100/bdiv_even514//canberra_dm.txt Stdout: Stderr: # Principal coordinates (canberra) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//canberra_dm.txt -o qiime_results/cd_mc100/bdiv_even514//canberra_pc.txt Stdout: Stderr: # Make emperor plots, canberra) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//canberra_pc.txt -o qiime_results/cd_mc100/bdiv_even514//canberra_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chisq) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics chisq -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//chisq_table_even514.txt qiime_results/cd_mc100/bdiv_even514//chisq_dm.txt Stdout: Stderr: # Principal coordinates (chisq) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//chisq_dm.txt -o qiime_results/cd_mc100/bdiv_even514//chisq_pc.txt Stdout: Stderr: # Make emperor plots, chisq) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//chisq_pc.txt -o qiime_results/cd_mc100/bdiv_even514//chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chord) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics chord -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//chord_table_even514.txt qiime_results/cd_mc100/bdiv_even514//chord_dm.txt Stdout: Stderr: # Principal coordinates (chord) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//chord_dm.txt -o qiime_results/cd_mc100/bdiv_even514//chord_pc.txt Stdout: Stderr: # Make emperor plots, chord) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//chord_pc.txt -o qiime_results/cd_mc100/bdiv_even514//chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (euclidean) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics euclidean -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//euclidean_table_even514.txt qiime_results/cd_mc100/bdiv_even514//euclidean_dm.txt Stdout: Stderr: # Principal coordinates (euclidean) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//euclidean_dm.txt -o qiime_results/cd_mc100/bdiv_even514//euclidean_pc.txt Stdout: Stderr: # Make emperor plots, euclidean) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//euclidean_pc.txt -o qiime_results/cd_mc100/bdiv_even514//euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (gower) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics gower -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//gower_table_even514.txt qiime_results/cd_mc100/bdiv_even514//gower_dm.txt Stdout: Stderr: # Principal coordinates (gower) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//gower_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -596.206054988 and the largest is 6890.39180637. RuntimeWarning # Make emperor plots, gower) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//gower_pc.txt -o qiime_results/cd_mc100/bdiv_even514//gower_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (hellinger) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics hellinger -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//hellinger_table_even514.txt qiime_results/cd_mc100/bdiv_even514//hellinger_dm.txt Stdout: Stderr: # Principal coordinates (hellinger) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//hellinger_dm.txt -o qiime_results/cd_mc100/bdiv_even514//hellinger_pc.txt Stdout: Stderr: # Make emperor plots, hellinger) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//hellinger_pc.txt -o qiime_results/cd_mc100/bdiv_even514//hellinger_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (kulczynski) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics kulczynski -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//kulczynski_table_even514.txt qiime_results/cd_mc100/bdiv_even514//kulczynski_dm.txt Stdout: Stderr: # Principal coordinates (kulczynski) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//kulczynski_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.180978943318 and the largest is 7.6761524933. RuntimeWarning # Make emperor plots, kulczynski) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//kulczynski_pc.txt -o qiime_results/cd_mc100/bdiv_even514//kulczynski_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (manhattan) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics manhattan -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//manhattan_table_even514.txt qiime_results/cd_mc100/bdiv_even514//manhattan_dm.txt Stdout: Stderr: # Principal coordinates (manhattan) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//manhattan_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -191255.651635 and the largest is 8112035.13648. RuntimeWarning # Make emperor plots, manhattan) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//manhattan_pc.txt -o qiime_results/cd_mc100/bdiv_even514//manhattan_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (morisita_horn) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics morisita_horn -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//morisita_horn_table_even514.txt qiime_results/cd_mc100/bdiv_even514//morisita_horn_dm.txt Stdout: Stderr: # Principal coordinates (morisita_horn) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//morisita_horn_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.449729177659 and the largest is 8.54191653079. RuntimeWarning # Make emperor plots, morisita_horn) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//morisita_horn_pc.txt -o qiime_results/cd_mc100/bdiv_even514//morisita_horn_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (pearson) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics pearson -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//pearson_table_even514.txt qiime_results/cd_mc100/bdiv_even514//pearson_dm.txt Stdout: Stderr: # Principal coordinates (pearson) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//pearson_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.529986343884 and the largest is 8.83002365686. RuntimeWarning # Make emperor plots, pearson) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//pearson_pc.txt -o qiime_results/cd_mc100/bdiv_even514//pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (soergel) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics soergel -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//soergel_table_even514.txt qiime_results/cd_mc100/bdiv_even514//soergel_dm.txt Stdout: Stderr: # Principal coordinates (soergel) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//soergel_dm.txt -o qiime_results/cd_mc100/bdiv_even514//soergel_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 -0.0321825754868 and the largest is 6.75575221937. RuntimeWarning # Make emperor plots, soergel) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//soergel_pc.txt -o qiime_results/cd_mc100/bdiv_even514//soergel_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (spearman_approx) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics spearman_approx -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//spearman_approx_table_even514.txt qiime_results/cd_mc100/bdiv_even514//spearman_approx_dm.txt Stdout: Stderr: # Principal coordinates (spearman_approx) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//spearman_approx_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.103378508054 and the largest is 0.545454810587. RuntimeWarning # Make emperor plots, spearman_approx) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//spearman_approx_pc.txt -o qiime_results/cd_mc100/bdiv_even514//spearman_approx_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (specprof) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics specprof -t qiime_results/data_mc100/rep_set_mc100.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_mc100/bdiv_even514//specprof_table_even514.txt qiime_results/cd_mc100/bdiv_even514//specprof_dm.txt Stdout: Stderr: # Principal coordinates (specprof) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//specprof_dm.txt -o qiime_results/cd_mc100/bdiv_even514//specprof_pc.txt Stdout: Stderr: # Make emperor plots, specprof) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//specprof_pc.txt -o qiime_results/cd_mc100/bdiv_even514//specprof_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unifrac) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics unifrac -t qiime_results/data_mc100/rep_set_mc100.tre Stdout: Stderr: # Rename distance matrix (unifrac) command mv qiime_results/cd_mc100/bdiv_even514//unifrac_table_even514.txt qiime_results/cd_mc100/bdiv_even514//unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unifrac) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//unifrac_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.0593197230174 and the largest is 3.53561279557. RuntimeWarning # Make emperor plots, unifrac) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//unifrac_pc.txt -o qiime_results/cd_mc100/bdiv_even514//unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics unweighted_unifrac -t qiime_results/data_mc100/rep_set_mc100.tre Stdout: Stderr: # Rename distance matrix (unweighted_unifrac) command mv qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_table_even514.txt qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.0593197230174 and the largest is 3.53561279557. RuntimeWarning # Make emperor plots, unweighted_unifrac) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_pc.txt -o qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac_full_tree) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics unweighted_unifrac_full_tree -t qiime_results/data_mc100/rep_set_mc100.tre Stdout: Stderr: # Rename distance matrix (unweighted_unifrac_full_tree) command mv qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_full_tree_table_even514.txt qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_full_tree_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac_full_tree) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.0297531126758 and the largest is 0.60922481696. RuntimeWarning # Make emperor plots, unweighted_unifrac_full_tree) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_mc100/bdiv_even514//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_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics weighted_normalized_unifrac -t qiime_results/data_mc100/rep_set_mc100.tre Stdout: Stderr: # Rename distance matrix (weighted_normalized_unifrac) command mv qiime_results/cd_mc100/bdiv_even514//weighted_normalized_unifrac_table_even514.txt qiime_results/cd_mc100/bdiv_even514//weighted_normalized_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_normalized_unifrac) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.102781265344 and the largest is 2.65418773307. RuntimeWarning # Make emperor plots, weighted_normalized_unifrac) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_mc100/bdiv_even514//weighted_normalized_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (weighted_unifrac) command beta_diversity.py -i qiime_results/cd_mc100/table_even514.biom -o qiime_results/cd_mc100/bdiv_even514/ --metrics weighted_unifrac -t qiime_results/data_mc100/rep_set_mc100.tre Stdout: Stderr: # Rename distance matrix (weighted_unifrac) command mv qiime_results/cd_mc100/bdiv_even514//weighted_unifrac_table_even514.txt qiime_results/cd_mc100/bdiv_even514//weighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_unifrac) command principal_coordinates.py -i qiime_results/cd_mc100/bdiv_even514//weighted_unifrac_dm.txt -o qiime_results/cd_mc100/bdiv_even514//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 -0.0759412064823 and the largest is 2.19042173753. RuntimeWarning # Make emperor plots, weighted_unifrac) command make_emperor.py -i qiime_results/cd_mc100/bdiv_even514//weighted_unifrac_pc.txt -o qiime_results/cd_mc100/bdiv_even514//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: Executing commands. # Alpha rarefaction command multiple_rarefactions.py -i qiime_results/cd_mc100/table_mc514.biom -m 10 -x 514 -s 50 -o qiime_results/cd_mc100/arare_max514//rarefaction/ Stdout: Stderr: # Alpha diversity on rarefied OTU tables command alpha_diversity.py -i qiime_results/cd_mc100/arare_max514//rarefaction/ -o qiime_results/cd_mc100/arare_max514//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_mc100/rep_set_mc100.tre Stdout: Stderr: # Collate alpha command collate_alpha.py -i qiime_results/cd_mc100/arare_max514//alpha_div/ -o qiime_results/cd_mc100/arare_max514//alpha_div_collated/ Stdout: Stderr: # Removing intermediate files command rm -r qiime_results/cd_mc100/arare_max514//rarefaction/ qiime_results/cd_mc100/arare_max514//alpha_div/ Stdout: Stderr: # Rarefaction plot: All metrics command make_rarefaction_plots.py -i qiime_results/cd_mc100/arare_max514//alpha_div_collated/ -m meta.txt -o qiime_results/cd_mc100/arare_max514//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_mc100/table_mc514.biom -o qiime_results/cd_mc100/taxa_plots/table_mc514_sorted.biom Stdout: Stderr: # Summarize Taxonomy command summarize_taxa.py -i qiime_results/cd_mc100/taxa_plots/table_mc514_sorted.biom -o qiime_results/cd_mc100/taxa_plots/ --level 2,3,4,5,6,7 Stdout: Stderr: # Plot Taxonomy Summary command plot_taxa_summary.py -i qiime_results/cd_mc100/taxa_plots/table_mc514_sorted_L2.txt,qiime_results/cd_mc100/taxa_plots/table_mc514_sorted_L3.txt,qiime_results/cd_mc100/taxa_plots/table_mc514_sorted_L4.txt,qiime_results/cd_mc100/taxa_plots/table_mc514_sorted_L5.txt,qiime_results/cd_mc100/taxa_plots/table_mc514_sorted_L6.txt,qiime_results/cd_mc100/taxa_plots/table_mc514_sorted_L7.txt -o qiime_results/cd_mc100/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_mc100/table_mc514.biom Stdout: Stderr: # Compress the rarefied BIOM table command gzip qiime_results/cd_mc100/table_even514.biom Stdout: Stderr: Logging stopped at 22:49:26 on 29 May 2018