Logging started at 14:08:22 on 12 Apr 2017 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 Group Input file md5 sums: qiime_results/data_mc10/final_otu_map_mc10_tax.biom: d5194461d3beca2ccb6f9dd068bb500a meta.txt: 7c81867d145be1a85d31abaa4dcd1a45 qiime_results/data_mc10/rep_set_mc10.tre: d40f0a37830f0c0289249e872efb9124 Executing commands. # Generate BIOM table summary command biom summarize-table -i qiime_results/data_mc10/final_otu_map_mc10_tax.biom -o qiime_results/cd_mc10/biom_table_summary.txt Stdout: Stderr: # Filter low sequence count samples from table (minimum sequence count: 52489) command filter_samples_from_otu_table.py -i qiime_results/data_mc10/final_otu_map_mc10_tax.biom -o qiime_results/cd_mc10/table_mc52489.biom -n 52489 Stdout: Stderr: # Rarify the OTU table to 52489 sequences/sample command single_rarefaction.py -i qiime_results/cd_mc10/table_mc52489.biom -o qiime_results/cd_mc10/table_even52489.biom -d 52489 Stdout: Stderr: Executing commands. # Beta Diversity (abund_jaccard) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics abund_jaccard -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (abund_jaccard) command mv qiime_results/cd_mc10/bdiv_even52489//abund_jaccard_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//abund_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (abund_jaccard) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//abund_jaccard_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.0157784538684 and the largest is 0.0581579974419. RuntimeWarning # Make emperor plots, abund_jaccard) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//abund_jaccard_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//abund_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chisq) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_chisq -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_chisq) command mv qiime_results/cd_mc10/bdiv_even52489//binary_chisq_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_chisq_dm.txt Stdout: Stderr: # Principal coordinates (binary_chisq) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_chisq_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_chisq_pc.txt Stdout: Stderr: # Make emperor plots, binary_chisq) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_chisq_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_chord) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_chord -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_chord) command mv qiime_results/cd_mc10/bdiv_even52489//binary_chord_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_chord_dm.txt Stdout: Stderr: # Principal coordinates (binary_chord) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_chord_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_chord_pc.txt Stdout: Stderr: # Make emperor plots, binary_chord) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_chord_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_euclidean) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_euclidean -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_euclidean) command mv qiime_results/cd_mc10/bdiv_even52489//binary_euclidean_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_euclidean_dm.txt Stdout: Stderr: # Principal coordinates (binary_euclidean) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_euclidean_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_euclidean_pc.txt Stdout: Stderr: # Make emperor plots, binary_euclidean) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_euclidean_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_hamming) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_hamming -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_hamming) command mv qiime_results/cd_mc10/bdiv_even52489//binary_hamming_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_hamming_dm.txt Stdout: Stderr: # Principal coordinates (binary_hamming) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_hamming_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_hamming_pc.txt Stdout: Stderr: # Make emperor plots, binary_hamming) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_hamming_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_hamming_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_jaccard) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_jaccard -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_jaccard) command mv qiime_results/cd_mc10/bdiv_even52489//binary_jaccard_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_jaccard_dm.txt Stdout: Stderr: # Principal coordinates (binary_jaccard) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_jaccard_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_jaccard_pc.txt Stdout: Stderr: # Make emperor plots, binary_jaccard) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_jaccard_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_jaccard_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_lennon) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_lennon -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_lennon) command mv qiime_results/cd_mc10/bdiv_even52489//binary_lennon_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_lennon_dm.txt Stdout: Stderr: # Principal coordinates (binary_lennon) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_lennon_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.191443677341 and the largest is 0.286961308139. RuntimeWarning # Make emperor plots, binary_lennon) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_lennon_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_lennon_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_ochiai) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_ochiai -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_ochiai) command mv qiime_results/cd_mc10/bdiv_even52489//binary_ochiai_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_ochiai_dm.txt Stdout: Stderr: # Principal coordinates (binary_ochiai) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_ochiai_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_ochiai_pc.txt Stdout: Stderr: # Make emperor plots, binary_ochiai) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_ochiai_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_ochiai_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_pearson) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_pearson -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_pearson) command mv qiime_results/cd_mc10/bdiv_even52489//binary_pearson_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_pearson_dm.txt Stdout: Stderr: # Principal coordinates (binary_pearson) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_pearson_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_pearson_pc.txt Stdout: Stderr: # Make emperor plots, binary_pearson) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_pearson_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (binary_sorensen_dice) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics binary_sorensen_dice -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (binary_sorensen_dice) command mv qiime_results/cd_mc10/bdiv_even52489//binary_sorensen_dice_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//binary_sorensen_dice_dm.txt Stdout: Stderr: # Principal coordinates (binary_sorensen_dice) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//binary_sorensen_dice_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_sorensen_dice_pc.txt Stdout: Stderr: # Make emperor plots, binary_sorensen_dice) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//binary_sorensen_dice_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//binary_sorensen_dice_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics bray_curtis -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (bray_curtis) command mv qiime_results/cd_mc10/bdiv_even52489//bray_curtis_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//bray_curtis_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//bray_curtis_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.0339261850963 and the largest is 1.19767368104. RuntimeWarning # Make emperor plots, bray_curtis) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//bray_curtis_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//bray_curtis_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis_faith) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics bray_curtis_faith -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (bray_curtis_faith) command mv qiime_results/cd_mc10/bdiv_even52489//bray_curtis_faith_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//bray_curtis_faith_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_faith) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//bray_curtis_faith_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.0339261850963 and the largest is 1.19767368104. RuntimeWarning # Make emperor plots, bray_curtis_faith) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//bray_curtis_faith_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//bray_curtis_faith_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (bray_curtis_magurran) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics bray_curtis_magurran -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (bray_curtis_magurran) command mv qiime_results/cd_mc10/bdiv_even52489//bray_curtis_magurran_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//bray_curtis_magurran_dm.txt Stdout: Stderr: # Principal coordinates (bray_curtis_magurran) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//bray_curtis_magurran_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.0339261850963 and the largest is 1.19767368104. RuntimeWarning # Make emperor plots, bray_curtis_magurran) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//bray_curtis_magurran_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//bray_curtis_magurran_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (canberra) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics canberra -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (canberra) command mv qiime_results/cd_mc10/bdiv_even52489//canberra_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//canberra_dm.txt Stdout: Stderr: # Principal coordinates (canberra) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//canberra_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//canberra_pc.txt Stdout: Stderr: # Make emperor plots, canberra) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//canberra_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//canberra_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chisq) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics chisq -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (chisq) command mv qiime_results/cd_mc10/bdiv_even52489//chisq_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//chisq_dm.txt Stdout: Stderr: # Principal coordinates (chisq) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//chisq_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//chisq_pc.txt Stdout: Stderr: # Make emperor plots, chisq) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//chisq_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//chisq_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (chord) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics chord -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (chord) command mv qiime_results/cd_mc10/bdiv_even52489//chord_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//chord_dm.txt Stdout: Stderr: # Principal coordinates (chord) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//chord_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//chord_pc.txt Stdout: Stderr: # Make emperor plots, chord) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//chord_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//chord_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (euclidean) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics euclidean -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (euclidean) command mv qiime_results/cd_mc10/bdiv_even52489//euclidean_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//euclidean_dm.txt Stdout: Stderr: # Principal coordinates (euclidean) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//euclidean_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//euclidean_pc.txt Stdout: Stderr: # Make emperor plots, euclidean) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//euclidean_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//euclidean_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (gower) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics gower -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (gower) command mv qiime_results/cd_mc10/bdiv_even52489//gower_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//gower_dm.txt Stdout: Stderr: # Principal coordinates (gower) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//gower_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -1102.20094506 and the largest is 49542.5291276. RuntimeWarning # Make emperor plots, gower) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//gower_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//gower_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (hellinger) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics hellinger -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (hellinger) command mv qiime_results/cd_mc10/bdiv_even52489//hellinger_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//hellinger_dm.txt Stdout: Stderr: # Principal coordinates (hellinger) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//hellinger_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//hellinger_pc.txt Stdout: Stderr: # Make emperor plots, hellinger) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//hellinger_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//hellinger_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (kulczynski) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics kulczynski -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (kulczynski) command mv qiime_results/cd_mc10/bdiv_even52489//kulczynski_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//kulczynski_dm.txt Stdout: Stderr: # Principal coordinates (kulczynski) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//kulczynski_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.0339261850963 and the largest is 1.19767368104. RuntimeWarning # Make emperor plots, kulczynski) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//kulczynski_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//kulczynski_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (manhattan) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics manhattan -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (manhattan) command mv qiime_results/cd_mc10/bdiv_even52489//manhattan_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//manhattan_dm.txt Stdout: Stderr: # Principal coordinates (manhattan) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//manhattan_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -373879468.133 and the largest is 13198819660.7. RuntimeWarning # Make emperor plots, manhattan) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//manhattan_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//manhattan_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (morisita_horn) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics morisita_horn -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (morisita_horn) command mv qiime_results/cd_mc10/bdiv_even52489//morisita_horn_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//morisita_horn_dm.txt Stdout: Stderr: # Principal coordinates (morisita_horn) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//morisita_horn_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.259512780113 and the largest is 1.43951506042. RuntimeWarning # Make emperor plots, morisita_horn) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//morisita_horn_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//morisita_horn_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (pearson) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics pearson -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (pearson) command mv qiime_results/cd_mc10/bdiv_even52489//pearson_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//pearson_dm.txt Stdout: Stderr: # Principal coordinates (pearson) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//pearson_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.29624047817 and the largest is 1.42238015846. RuntimeWarning # Make emperor plots, pearson) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//pearson_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//pearson_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (soergel) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics soergel -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (soergel) command mv qiime_results/cd_mc10/bdiv_even52489//soergel_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//soergel_dm.txt Stdout: Stderr: # Principal coordinates (soergel) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//soergel_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.000579524159561 and the largest is 1.41853293411. RuntimeWarning # Make emperor plots, soergel) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//soergel_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//soergel_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (spearman_approx) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics spearman_approx -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (spearman_approx) command mv qiime_results/cd_mc10/bdiv_even52489//spearman_approx_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//spearman_approx_dm.txt Stdout: Stderr: # Principal coordinates (spearman_approx) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//spearman_approx_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.00485943482616 and the largest is 0.681813491893. RuntimeWarning # Make emperor plots, spearman_approx) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//spearman_approx_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//spearman_approx_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (specprof) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics specprof -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`. VisibleDeprecationWarning) # Rename distance matrix (specprof) command mv qiime_results/cd_mc10/bdiv_even52489//specprof_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//specprof_dm.txt Stdout: Stderr: # Principal coordinates (specprof) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//specprof_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//specprof_pc.txt Stdout: Stderr: # Make emperor plots, specprof) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//specprof_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//specprof_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unifrac) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics unifrac -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: # Rename distance matrix (unifrac) command mv qiime_results/cd_mc10/bdiv_even52489//unifrac_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unifrac) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//unifrac_pc.txt Stdout: Stderr: # Make emperor plots, unifrac) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics unweighted_unifrac -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: # Rename distance matrix (unweighted_unifrac) command mv qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_pc.txt Stdout: Stderr: # Make emperor plots, unweighted_unifrac) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac_full_tree) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics unweighted_unifrac_full_tree -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: # Rename distance matrix (unweighted_unifrac_full_tree) command mv qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_full_tree_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_full_tree_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac_full_tree) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_full_tree_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.0121274813029 and the largest is 0.365147448122. RuntimeWarning # Make emperor plots, unweighted_unifrac_full_tree) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_full_tree_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//unweighted_unifrac_full_tree_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (weighted_normalized_unifrac) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics weighted_normalized_unifrac -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: # Rename distance matrix (weighted_normalized_unifrac) command mv qiime_results/cd_mc10/bdiv_even52489//weighted_normalized_unifrac_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//weighted_normalized_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_normalized_unifrac) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//weighted_normalized_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.0144943052814 and the largest is 0.706419293876. RuntimeWarning # Make emperor plots, weighted_normalized_unifrac) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//weighted_normalized_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//weighted_normalized_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: # Beta Diversity (weighted_unifrac) command beta_diversity.py -i qiime_results/cd_mc10/table_even52489.biom -o qiime_results/cd_mc10/bdiv_even52489/ --metrics weighted_unifrac -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: # Rename distance matrix (weighted_unifrac) command mv qiime_results/cd_mc10/bdiv_even52489//weighted_unifrac_table_even52489.txt qiime_results/cd_mc10/bdiv_even52489//weighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_unifrac) command principal_coordinates.py -i qiime_results/cd_mc10/bdiv_even52489//weighted_unifrac_dm.txt -o qiime_results/cd_mc10/bdiv_even52489//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 -0.00787867049512 and the largest is 0.396934347201. RuntimeWarning # Make emperor plots, weighted_unifrac) command make_emperor.py -i qiime_results/cd_mc10/bdiv_even52489//weighted_unifrac_pc.txt -o qiime_results/cd_mc10/bdiv_even52489//weighted_unifrac_emperor_pcoa_plot/ -m meta.txt Stdout: Stderr: Executing commands. # Alpha rarefaction command multiple_rarefactions.py -i qiime_results/cd_mc10/table_mc52489.biom -m 10 -x 52489 -s 5247 -o qiime_results/cd_mc10/arare_max52489//rarefaction/ Stdout: Stderr: # Alpha diversity on rarefied OTU tables command alpha_diversity.py -i qiime_results/cd_mc10/arare_max52489//rarefaction/ -o qiime_results/cd_mc10/arare_max52489//alpha_div/ --metrics berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree -t qiime_results/data_mc10/rep_set_mc10.tre Stdout: Stderr: # Collate alpha command collate_alpha.py -i qiime_results/cd_mc10/arare_max52489//alpha_div/ -o qiime_results/cd_mc10/arare_max52489//alpha_div_collated/ Stdout: Stderr: # Removing intermediate files command rm -r qiime_results/cd_mc10/arare_max52489//rarefaction/ qiime_results/cd_mc10/arare_max52489//alpha_div/ Stdout: Stderr: # Rarefaction plot: All metrics command make_rarefaction_plots.py -i qiime_results/cd_mc10/arare_max52489//alpha_div_collated/ -m meta.txt -o qiime_results/cd_mc10/arare_max52489//alpha_rarefaction_plots/ Stdout: Stderr: /usr/local/lib/python2.7/dist-packages/matplotlib/axes/_base.py:2809: UserWarning: Attempting to set identical bottom==top results in singular transformations; automatically expanding. bottom=0, top=0 'bottom=%s, top=%s') % (bottom, top)) Skipping compare_alpha_diversity.py as no categories were provided. Executing commands. # Sort OTU Table command sort_otu_table.py -i qiime_results/cd_mc10/table_mc52489.biom -o qiime_results/cd_mc10/taxa_plots/table_mc52489_sorted.biom Stdout: Stderr: # Summarize Taxonomy command summarize_taxa.py -i qiime_results/cd_mc10/taxa_plots/table_mc52489_sorted.biom -o qiime_results/cd_mc10/taxa_plots/ --level 2,3,4,5,6,7 Stdout: Stderr: # Plot Taxonomy Summary command plot_taxa_summary.py -i qiime_results/cd_mc10/taxa_plots/table_mc52489_sorted_L2.txt,qiime_results/cd_mc10/taxa_plots/table_mc52489_sorted_L3.txt,qiime_results/cd_mc10/taxa_plots/table_mc52489_sorted_L4.txt,qiime_results/cd_mc10/taxa_plots/table_mc52489_sorted_L5.txt,qiime_results/cd_mc10/taxa_plots/table_mc52489_sorted_L6.txt,qiime_results/cd_mc10/taxa_plots/table_mc52489_sorted_L7.txt -o qiime_results/cd_mc10/taxa_plots//taxa_summary_plots/ --labels Phylum,Class,Order,Family,Genus,Species --chart_type bar,area,pie Stdout: Stderr: Executing commands. # Compress the filtered BIOM table command gzip qiime_results/cd_mc10/table_mc52489.biom Stdout: Stderr: # Compress the rarefied BIOM table command gzip qiime_results/cd_mc10/table_even52489.biom Stdout: Stderr: Logging stopped at 14:20:44 on 12 Apr 2017