Logging started at 08:20:38 on 12 Aug 2015
QIIME version: 1.9.1-dev, master@24ef510

qiime_config values:
profile	default
pick_otus_reference_seqs_fp	/Users/antoniog/.virtualenvs/qiita/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	/Users/antoniog/.virtualenvs/qiita/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.fasta
cluster_jobs_fp	start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/Users/antoniog/.virtualenvs/qiita/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue	friendlyq
n_engines	2
jobs_to_start	1
denoiser_min_per_core	50
assign_taxonomy_id_to_taxonomy_fp	/Users/antoniog/.virtualenvs/qiita/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/var/folders/17/c40mmrx56w918s7lp6ds2jvw0000gq/T/
blastall_fp	blastall
seconds_to_sleep	1

parameter file values:
make_distance_boxplots:num_permutations	10
compare_alpha_diversity:num_permutations	10
parallel:jobs_to_start	1

Input file md5 sums:
pick_close_ref/otu_table.biom: 1fe946a73a2eca651936e318128114f0
mapping_file.txt: bb159d30acec6d4cf2ba02d971b52cb5
/Users/antoniog/svn_programs/gg_13_8_otus/trees/97_otus.tree: b7e76593bce82913af1cfb06edf15732

Skipping 'biom summarize-table' as core_diversity/biom_table_summary.txt exists.

Executing commands.

# Filter low sequence count samples from table (minimum sequence count: 250) command 
filter_samples_from_otu_table.py -i pick_close_ref/otu_table.biom -o core_diversity/table_mc250.biom -n 250

Stdout:

Stderr:

# Rarify the OTU table to 250 sequences/sample command 
single_rarefaction.py -i core_diversity/table_mc250.biom -o core_diversity/table_even250.biom -d 250

Stdout:

Stderr:

Skipping beta_diversity_through_plots.py as core_diversity/bdiv_even250/unweighted_unifrac_dm.txt, core_diversity/bdiv_even250/weighted_unifrac_dm.txt exist(s).

Skipping alpha_rarefaction.py as core_diversity/arare_max250//alpha_rarefaction_plots/rarefaction_plots.html exists.

Skipping summarize_taxa_through_plots.py for as core_diversity/taxa_plots/taxa_summary_plots/area_charts.html, core_diversity/taxa_plots/taxa_summary_plots/bar_charts.html exist(s).

Executing commands.

# Collapse samples in OTU table by categories command 
collapse_samples.py -m mapping_file.txt -b core_diversity/table_mc250.biom --output_biom_fp core_diversity/taxa_plots_body_site/body_site_otu_table.biom --output_mapping_fp core_diversity/taxa_plots_body_site/body_site_map.txt --collapse_fields 'body_site' 

Stdout:

Stderr:

# Sort OTU Table command 
sort_otu_table.py -i core_diversity/taxa_plots_body_site/body_site_otu_table.biom -o core_diversity/taxa_plots_body_site/body_site_otu_table_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i core_diversity/taxa_plots_body_site/body_site_otu_table_sorted.biom -o core_diversity/taxa_plots_body_site/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
plot_taxa_summary.py -i core_diversity/taxa_plots_body_site/body_site_otu_table_sorted_L2.txt,core_diversity/taxa_plots_body_site/body_site_otu_table_sorted_L3.txt,core_diversity/taxa_plots_body_site/body_site_otu_table_sorted_L4.txt,core_diversity/taxa_plots_body_site/body_site_otu_table_sorted_L5.txt,core_diversity/taxa_plots_body_site/body_site_otu_table_sorted_L6.txt -o core_diversity/taxa_plots_body_site//taxa_summary_plots/ 

Stdout:

Stderr:

Skipping compressing of filtered BIOM table as core_diversity/table_mc250.biom.gz exists.

Skipping compressing of rarefied BIOM table as core_diversity/table_even250.biom.gz exists.

Executing commands.

# Boxplots (body_site) command 
make_distance_boxplots.py -d core_diversity/bdiv_even250/unweighted_unifrac_dm.txt -f body_site -o core_diversity/bdiv_even250//unweighted_unifrac_boxplots/ -m mapping_file.txt -n 999 --num_permutations 10

Stdout:

Stderr:
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/tight_layout.py:225: UserWarning: tight_layout : falling back to Agg renderer
  warnings.warn("tight_layout : falling back to Agg renderer")

# Boxplots (body_site) command 
make_distance_boxplots.py -d core_diversity/bdiv_even250/weighted_unifrac_dm.txt -f body_site -o core_diversity/bdiv_even250//weighted_unifrac_boxplots/ -m mapping_file.txt -n 999 --num_permutations 10

Stdout:

Stderr:
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/tight_layout.py:225: UserWarning: tight_layout : falling back to Agg renderer
  warnings.warn("tight_layout : falling back to Agg renderer")

# Compare alpha diversity (chao1) command 
compare_alpha_diversity.py -i core_diversity/arare_max250//alpha_div_collated/chao1.txt -m mapping_file.txt -c body_site -o core_diversity/arare_max250//compare_chao1 -n 999 --num_permutations 10

Stdout:

Stderr:
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/tight_layout.py:225: UserWarning: tight_layout : falling back to Agg renderer
  warnings.warn("tight_layout : falling back to Agg renderer")

# Compare alpha diversity (observed_otus) command 
compare_alpha_diversity.py -i core_diversity/arare_max250//alpha_div_collated/observed_otus.txt -m mapping_file.txt -c body_site -o core_diversity/arare_max250//compare_observed_otus -n 999 --num_permutations 10

Stdout:

Stderr:
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/tight_layout.py:225: UserWarning: tight_layout : falling back to Agg renderer
  warnings.warn("tight_layout : falling back to Agg renderer")

# Compare alpha diversity (PD_whole_tree) command 
compare_alpha_diversity.py -i core_diversity/arare_max250//alpha_div_collated/PD_whole_tree.txt -m mapping_file.txt -c body_site -o core_diversity/arare_max250//compare_PD_whole_tree -n 999 --num_permutations 10

Stdout:

Stderr:
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/tight_layout.py:225: UserWarning: tight_layout : falling back to Agg renderer
  warnings.warn("tight_layout : falling back to Agg renderer")

# Group significance (body_site) command 
group_significance.py -i core_diversity/table_even250.biom -m mapping_file.txt -c body_site -o core_diversity/group_significance_body_site.txt 

Stdout:

Stderr:


Logging stopped at 08:22:52 on 12 Aug 2015
