Logging started at 15:18:42 on 03 Aug 2017
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp	/usr/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue	all.q
pynast_template_alignment_fp	/usr/lib/python2.7/site-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/lib/python2.7/site-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/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/tmp/
blastall_fp	blastall
seconds_to_sleep	1

parameter file values:
parallel:jobs_to_start	1

Input file md5 sums:
otus_less100.biom: 3da1d19a7813ea48f04f1e12b2a94308
mapping.csv: 2b254187ea686e24dd4b273c1408c338
phylogeny.tre: b1382e3296ff12a2dd73df5e07f228f8

Executing commands.

# Generate BIOM table summary command 
biom summarize-table -i otus_less100.biom -o cdout_diet100/biom_table_summary.txt 

Stdout:

Stderr:

# Filter low sequence count samples from table (minimum sequence count: 5000) command 
filter_samples_from_otu_table.py -i otus_less100.biom -o cdout_diet100/table_mc5000.biom -n 5000

Stdout:

Stderr:

# Rarify the OTU table to 5000 sequences/sample command 
single_rarefaction.py -i cdout_diet100/table_mc5000.biom -o cdout_diet100/table_even5000.biom -d 5000

Stdout:

Stderr:

Executing commands.

# Beta Diversity (weighted_unifrac) command 
beta_diversity.py -i cdout_diet100/table_even5000.biom -o cdout_diet100/bdiv_even5000/ --metrics weighted_unifrac  -t phylogeny.tre 

Stdout:

Stderr:

# Rename distance matrix (weighted_unifrac) command 
mv cdout_diet100/bdiv_even5000//weighted_unifrac_table_even5000.txt cdout_diet100/bdiv_even5000//weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
principal_coordinates.py -i cdout_diet100/bdiv_even5000//weighted_unifrac_dm.txt -o cdout_diet100/bdiv_even5000//weighted_unifrac_pc.txt 

Stdout:

Stderr:
/usr/lib64/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 -0.00122844653316 and the largest is 0.0892472139006.
  RuntimeWarning

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i cdout_diet100/bdiv_even5000//weighted_unifrac_pc.txt -o cdout_diet100/bdiv_even5000//weighted_unifrac_emperor_pcoa_plot/ -m mapping.csv 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
beta_diversity.py -i cdout_diet100/table_even5000.biom -o cdout_diet100/bdiv_even5000/ --metrics unweighted_unifrac  -t phylogeny.tre 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac) command 
mv cdout_diet100/bdiv_even5000//unweighted_unifrac_table_even5000.txt cdout_diet100/bdiv_even5000//unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
principal_coordinates.py -i cdout_diet100/bdiv_even5000//unweighted_unifrac_dm.txt -o cdout_diet100/bdiv_even5000//unweighted_unifrac_pc.txt 

Stdout:

Stderr:

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i cdout_diet100/bdiv_even5000//unweighted_unifrac_pc.txt -o cdout_diet100/bdiv_even5000//unweighted_unifrac_emperor_pcoa_plot/ -m mapping.csv 

Stdout:

Stderr:

Executing commands.

# Alpha rarefaction command 
multiple_rarefactions.py -i cdout_diet100/table_mc5000.biom -m 10 -x 5000 -s 499 -o cdout_diet100/arare_max5000//rarefaction/ 

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
alpha_diversity.py -i cdout_diet100/arare_max5000//rarefaction/ -o cdout_diet100/arare_max5000//alpha_div/  -t phylogeny.tre

Stdout:

Stderr:

# Collate alpha command 
collate_alpha.py -i cdout_diet100/arare_max5000//alpha_div/ -o cdout_diet100/arare_max5000//alpha_div_collated/ 

Stdout:

Stderr:

# Removing intermediate files command 
rm -r cdout_diet100/arare_max5000//rarefaction/ cdout_diet100/arare_max5000//alpha_div/

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
make_rarefaction_plots.py -i cdout_diet100/arare_max5000//alpha_div_collated/ -m mapping.csv -o cdout_diet100/arare_max5000//alpha_rarefaction_plots/ 

Stdout:

Stderr:
/usr/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py:50: MatplotlibDeprecationWarning: The set_axis_bgcolor function was deprecated in version 2.0. Use set_facecolor instead.
  ax.set_axis_bgcolor(background_color)

Executing commands.

# Sort OTU Table command 
sort_otu_table.py -i cdout_diet100/table_mc5000.biom -o cdout_diet100/taxa_plots/table_mc5000_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i cdout_diet100/taxa_plots/table_mc5000_sorted.biom -o cdout_diet100/taxa_plots/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
plot_taxa_summary.py -i cdout_diet100/taxa_plots/table_mc5000_sorted_L2.txt,cdout_diet100/taxa_plots/table_mc5000_sorted_L3.txt,cdout_diet100/taxa_plots/table_mc5000_sorted_L4.txt,cdout_diet100/taxa_plots/table_mc5000_sorted_L5.txt,cdout_diet100/taxa_plots/table_mc5000_sorted_L6.txt -o cdout_diet100/taxa_plots//taxa_summary_plots/ 

Stdout:

Stderr:
/usr/lib64/python2.7/site-packages/matplotlib/cbook.py:136: MatplotlibDeprecationWarning: The axisbg attribute was deprecated in version 2.0. Use facecolor instead.
  warnings.warn(message, mplDeprecation, stacklevel=1)

Executing commands.

# Collapse samples in OTU table by categories command 
collapse_samples.py -m mapping.csv -b cdout_diet100/table_mc5000.biom --output_biom_fp cdout_diet100/taxa_plots_Diet/Diet_otu_table.biom --output_mapping_fp cdout_diet100/taxa_plots_Diet/Diet_map.txt --collapse_fields 'Diet' 

Stdout:

Stderr:

# Sort OTU Table command 
sort_otu_table.py -i cdout_diet100/taxa_plots_Diet/Diet_otu_table.biom -o cdout_diet100/taxa_plots_Diet/Diet_otu_table_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i cdout_diet100/taxa_plots_Diet/Diet_otu_table_sorted.biom -o cdout_diet100/taxa_plots_Diet/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
plot_taxa_summary.py -i cdout_diet100/taxa_plots_Diet/Diet_otu_table_sorted_L2.txt,cdout_diet100/taxa_plots_Diet/Diet_otu_table_sorted_L3.txt,cdout_diet100/taxa_plots_Diet/Diet_otu_table_sorted_L4.txt,cdout_diet100/taxa_plots_Diet/Diet_otu_table_sorted_L5.txt,cdout_diet100/taxa_plots_Diet/Diet_otu_table_sorted_L6.txt -o cdout_diet100/taxa_plots_Diet//taxa_summary_plots/ 

Stdout:

Stderr:
/usr/lib64/python2.7/site-packages/matplotlib/cbook.py:136: MatplotlibDeprecationWarning: The axisbg attribute was deprecated in version 2.0. Use facecolor instead.
  warnings.warn(message, mplDeprecation, stacklevel=1)

Executing commands.

# Boxplots (Diet) command 
make_distance_boxplots.py -d cdout_diet100/bdiv_even5000//weighted_unifrac_dm.txt -f Diet -o cdout_diet100/bdiv_even5000//weighted_unifrac_boxplots/ -m mapping.csv -n 999 

Stdout:

Stderr:

# Boxplots (Diet) command 
make_distance_boxplots.py -d cdout_diet100/bdiv_even5000//unweighted_unifrac_dm.txt -f Diet -o cdout_diet100/bdiv_even5000//unweighted_unifrac_boxplots/ -m mapping.csv -n 999 

Stdout:

Stderr:

# Compare alpha diversity (PD_whole_tree) command 
compare_alpha_diversity.py -i cdout_diet100/arare_max5000//alpha_div_collated/PD_whole_tree.txt -m mapping.csv -c Diet -o cdout_diet100/arare_max5000//compare_PD_whole_tree -n 999 

Stdout:

Stderr:

# Compare alpha diversity (chao1) command 
compare_alpha_diversity.py -i cdout_diet100/arare_max5000//alpha_div_collated/chao1.txt -m mapping.csv -c Diet -o cdout_diet100/arare_max5000//compare_chao1 -n 999 

Stdout:

Stderr:

# Compare alpha diversity (observed_otus) command 
compare_alpha_diversity.py -i cdout_diet100/arare_max5000//alpha_div_collated/observed_otus.txt -m mapping.csv -c Diet -o cdout_diet100/arare_max5000//compare_observed_otus -n 999 

Stdout:

Stderr:

# Group significance (Diet) command 
group_significance.py -i cdout_diet100/table_even5000.biom -m mapping.csv -c Diet -o cdout_diet100/group_significance_Diet.txt 

Stdout:

Stderr:

# Compress the filtered BIOM table command 
gzip cdout_diet100/table_mc5000.biom

Stdout:

Stderr:

# Compress the rarefied BIOM table command 
gzip cdout_diet100/table_even5000.biom

Stdout:

Stderr:


Logging stopped at 15:27:02 on 03 Aug 2017