Logging started at 20:36:55 on 12 Apr 2018 QIIME version: 1.9.1 qiime_config values: pick_otus_reference_seqs_fp /lustre/home/d411/alorax1/silva128/SILVA_128_QIIME_release/rep_set/rep_set_16S_only/97/97_otus_16S.fasta sc_queue all.q pynast_template_alignment_fp /lustre/home/d411/alorax1/silva128/SILVA_128_QIIME_release/rep_set_aligned/97/97_otus_aligned.fasta cluster_jobs_fp start_parallel_jobs.py assign_taxonomy_reference_seqs_fp /lustre/home/d411/alorax1/silva128/SILVA_128_QIIME_release/rep_set/rep_set_16S_only/97/97_otus_16S.fasta torque_queue friendlyq jobs_to_start 1 denoiser_min_per_core 50 assign_taxonomy_id_to_taxonomy_fp /lustre/home/d411/alorax1/silva128/SILVA_128_QIIME_release/taxonomy/16S_only/97/consensus_taxonomy_7_levels.txt temp_dir /lustre/home/d411/alorax1/qiime_tmp/ blastall_fp blastall seconds_to_sleep 1 parameter file values: parallel:jobs_to_start 18 Input file md5 sums: /lustre/home/d411/alorax1/all/all_closed_otus/otu_table.biom: 755f07f2b522d4874b1957f89058d25d /lustre/home/d411/alorax1/all/allyears_map.txt: 8467aceadc88ab3e41cd962626e5d474 /lustre/home/d411/alorax1/silva128/SILVA_128_QIIME_release/trees/97/97_otus.tre: 9ed6c235cdff636963de40045ab2a4df Executing commands. # Generate BIOM table summary command biom summarize-table -i /lustre/home/d411/alorax1/all/all_closed_otus/otu_table.biom -o /lustre/home/d411/alorax1/all/all_cda_closed/biom_table_summary.txt Stdout: Stderr: # Filter low sequence count samples from table (minimum sequence count: 630) command filter_samples_from_otu_table.py -i /lustre/home/d411/alorax1/all/all_closed_otus/otu_table.biom -o /lustre/home/d411/alorax1/all/all_cda_closed/table_mc630.biom -n 630 Stdout: Stderr: # Rarify the OTU table to 630 sequences/sample command single_rarefaction.py -i /lustre/home/d411/alorax1/all/all_cda_closed/table_mc630.biom -o /lustre/home/d411/alorax1/all/all_cda_closed/table_even630.biom -d 630 Stdout: Stderr: Executing commands. # Beta Diversity (weighted_unifrac) command parallel_beta_diversity.py -i /lustre/home/d411/alorax1/all/all_cda_closed/table_even630.biom -o /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630/ --metrics weighted_unifrac -T -t /lustre/home/d411/alorax1/silva128/SILVA_128_QIIME_release/trees/97/97_otus.tre --jobs_to_start 18 Stdout: Stderr: # Rename distance matrix (weighted_unifrac) command mv /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//weighted_unifrac_table_even630.txt /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//weighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (weighted_unifrac) command principal_coordinates.py -i /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//weighted_unifrac_dm.txt -o /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//weighted_unifrac_pc.txt Stdout: Stderr: /lustre/home/d411/alorax1/.conda/envs/qiime1/lib/python2.7/site-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 -0.00421980589932 and the largest is 0.543903646014. RuntimeWarning # Make emperor plots, weighted_unifrac) command make_emperor.py -i /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//weighted_unifrac_pc.txt -o /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//weighted_unifrac_emperor_pcoa_plot/ -m /lustre/home/d411/alorax1/all/allyears_map.txt Stdout: Stderr: # Beta Diversity (unweighted_unifrac) command parallel_beta_diversity.py -i /lustre/home/d411/alorax1/all/all_cda_closed/table_even630.biom -o /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630/ --metrics unweighted_unifrac -T -t /lustre/home/d411/alorax1/silva128/SILVA_128_QIIME_release/trees/97/97_otus.tre --jobs_to_start 18 Stdout: Stderr: # Rename distance matrix (unweighted_unifrac) command mv /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//unweighted_unifrac_table_even630.txt /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//unweighted_unifrac_dm.txt Stdout: Stderr: # Principal coordinates (unweighted_unifrac) command principal_coordinates.py -i /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//unweighted_unifrac_dm.txt -o /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//unweighted_unifrac_pc.txt Stdout: Stderr: # Make emperor plots, unweighted_unifrac) command make_emperor.py -i /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//unweighted_unifrac_pc.txt -o /lustre/home/d411/alorax1/all/all_cda_closed/bdiv_even630//unweighted_unifrac_emperor_pcoa_plot/ -m /lustre/home/d411/alorax1/all/allyears_map.txt Stdout: Stderr: Executing commands. # Alpha rarefaction command parallel_multiple_rarefactions.py -T -i /lustre/home/d411/alorax1/all/all_cda_closed/table_mc630.biom -m 10 -x 630 -s 62 -o /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//rarefaction/ --jobs_to_start 18 Stdout: Stderr: # Alpha diversity on rarefied OTU tables command parallel_alpha_diversity.py -T -i /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//rarefaction/ -o /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//alpha_div/ -t /lustre/home/d411/alorax1/silva128/SILVA_128_QIIME_release/trees/97/97_otus.tre --jobs_to_start 18 Stdout: Stderr: # Collate alpha command collate_alpha.py -i /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//alpha_div/ -o /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//alpha_div_collated/ Stdout: Stderr: # Removing intermediate files command rm -r /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//rarefaction/ /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//alpha_div/ Stdout: Stderr: # Rarefaction plot: All metrics command make_rarefaction_plots.py -i /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//alpha_div_collated/ -m /lustre/home/d411/alorax1/all/allyears_map.txt -o /lustre/home/d411/alorax1/all/all_cda_closed/arare_max630//alpha_rarefaction_plots/ Stdout: Stderr: /lustre/home/d411/alorax1/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison if self._edgecolors == str('face'): Skipping compare_alpha_diversity.py as no categories were provided. Executing commands. # Sort OTU Table command sort_otu_table.py -i /lustre/home/d411/alorax1/all/all_cda_closed/table_mc630.biom -o /lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots/table_mc630_sorted.biom Stdout: Stderr: # Summarize Taxonomy command summarize_taxa.py -i /lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots/table_mc630_sorted.biom -o /lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots/ Stdout: Stderr: # Plot Taxonomy Summary command plot_taxa_summary.py -i /lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots/table_mc630_sorted_L2.txt,/lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots/table_mc630_sorted_L3.txt,/lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots/table_mc630_sorted_L4.txt,/lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots/table_mc630_sorted_L5.txt,/lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots/table_mc630_sorted_L6.txt -o /lustre/home/d411/alorax1/all/all_cda_closed/taxa_plots//taxa_summary_plots/ Stdout: Stderr: /lustre/home/d411/alorax1/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison if self._edgecolors == str('face'): Executing commands. # Compress the filtered BIOM table command gzip /lustre/home/d411/alorax1/all/all_cda_closed/table_mc630.biom Stdout: Stderr: # Compress the rarefied BIOM table command gzip /lustre/home/d411/alorax1/all/all_cda_closed/table_even630.biom Stdout: Stderr: Logging stopped at 21:03:24 on 12 Apr 2018