Logging started at 12:19:41 on 13 May 2013
QIIME version: 1.6.0-dev

qiime_config values:
blastmat_dir	/Applications/blast-2.2.22/data/
sc_queue	all.q
topiaryexplorer_project_dir	/Users/caporaso/code/TopiaryExplorer-0.9.1/
pynast_template_alignment_fp	/Users/caporaso/data/greengenes_core_sets/core_set_aligned_imputed.fasta_11_8_07.no_dots
cluster_jobs_fp	start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/Users/caporaso/data/gg_12_10_otus/rep_set/97_otus.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/Users/caporaso/data/greengenes_core_sets/lanemask_in_1s_and_0s.txt
jobs_to_start	2
cloud_environment	False
qiime_scripts_dir	/Users/caporaso/code/Qiime/scripts
denoiser_min_per_core	50
python_exe_fp	python
temp_dir	/Users/caporaso/temp
blastall_fp	blastall
seconds_to_sleep	1
assign_taxonomy_id_to_taxonomy_fp	/Users/caporaso/data/gg_12_10_otus/taxonomy/97_otu_taxonomy.txt

parameter file values:
parallel:jobs_to_start	2

Input file md5 sums:
/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/otu_table.biom: 27c6ffe253527068c82cc1835adeda8f
/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt: 6e1bde9b7cf3815113518a497102884f
/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/rep_set.tre: e4294036510aa68b15f59b0e05f06b18

Executing commands.

# Generate BIOM table summary command 
print_biom_table_summary.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/otu_table.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/biom_table_summary.txt --suppress_md5 

Stdout:

Stderr:

# Filter low sequence count samples from table (minimum sequence count: 20) command 
filter_samples_from_otu_table.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/otu_table.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom -n 20

Stdout:

Stderr:

Executing commands.

# Sample OTU table at 20 seqs/sample command 
python /Users/caporaso/code/Qiime/scripts/single_rarefaction.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//table_mc20_even20.biom -d 20

Stdout:

Stderr:

# Build prefs file command 
python /Users/caporaso/code/Qiime/scripts/make_prefs_file.py -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//prefs.txt  --mapping_headers_to_use BarcodeSequence,SampleType,day,days_since_epoch

Stdout:

Stderr:

# Beta Diversity (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/beta_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//table_mc20_even20.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20/ --metrics weighted_unifrac  -t /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/rep_set.tre 

Stdout:

Stderr:
/Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime/beta_metrics.py:132: UserWarning: unifrac had no information for sample not16S.1. Distances involving that sample aren't meaningful
  sam_i + ". Distances involving that sample aren't meaningful")

# Rename distance matrix (weighted_unifrac) command 
mv /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_table_mc20_even20.txt /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/principal_coordinates.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_dm.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_pc.txt 

Stdout:

Stderr:

# Make 3D plots (continuous coloring, weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_3d_plots.py -p /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//prefs.txt -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_pc.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_3d_continuous/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt 

Stdout:

Stderr:

# Make 3D plots (discrete coloring, weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_3d_plots.py -b "BarcodeSequence,SampleType,day,days_since_epoch" -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_pc.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_3d_discrete/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt 

Stdout:

Stderr:

# Make 2D plots (continuous coloring, weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_2d_plots.py -p /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//prefs.txt -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_pc.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_2d_continuous/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt 

Stdout:

Stderr:

# Make 2D plots (discrete coloring, weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_2d_plots.py -b "BarcodeSequence,SampleType,day,days_since_epoch" -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_pc.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_2d_discrete/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/beta_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//table_mc20_even20.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20/ --metrics unweighted_unifrac  -t /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/rep_set.tre 

Stdout:

Stderr:
/Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime/beta_metrics.py:132: UserWarning: unifrac had no information for sample not16S.1. Distances involving that sample aren't meaningful
  sam_i + ". Distances involving that sample aren't meaningful")

# Rename distance matrix (unweighted_unifrac) command 
mv /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_table_mc20_even20.txt /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/principal_coordinates.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_dm.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_pc.txt 

Stdout:

Stderr:

# Make 3D plots (continuous coloring, unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_3d_plots.py -p /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//prefs.txt -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_pc.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_3d_continuous/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt 

Stdout:

Stderr:

# Make 3D plots (discrete coloring, unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_3d_plots.py -b "BarcodeSequence,SampleType,day,days_since_epoch" -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_pc.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_3d_discrete/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt 

Stdout:

Stderr:

# Make 2D plots (continuous coloring, unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_2d_plots.py -p /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//prefs.txt -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_pc.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_2d_continuous/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt 

Stdout:

Stderr:

# Make 2D plots (discrete coloring, unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_2d_plots.py -b "BarcodeSequence,SampleType,day,days_since_epoch" -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_pc.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_2d_discrete/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt 

Stdout:

Stderr:

Executing commands.

# Alpha rarefaction command 
python /Users/caporaso/code/Qiime/scripts/multiple_rarefactions.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom -m 10 -x 20 -s 1 -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//rarefaction/ 

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//rarefaction/ -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div/  -t /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/rep_set.tre

Stdout:

Stderr:

# Collate alpha command 
python /Users/caporaso/code/Qiime/scripts/collate_alpha.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div/ -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/ 

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
python /Users/caporaso/code/Qiime/scripts/make_rarefaction_plots.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_rarefaction_plots/ 

Stdout:

Stderr:

Executing commands.

# Sort OTU Table command 
python /Users/caporaso/code/Qiime/scripts/sort_otu_table.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots/table_mc20_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
python /Users/caporaso/code/Qiime/scripts/summarize_taxa.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots/table_mc20_sorted.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
python /Users/caporaso/code/Qiime/scripts/plot_taxa_summary.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots/table_mc20_sorted_L2.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots/table_mc20_sorted_L3.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots/table_mc20_sorted_L4.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots/table_mc20_sorted_L5.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots/table_mc20_sorted_L6.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots//taxa_summary_plots/ 

Stdout:

Stderr:

Executing commands.

# Summarize OTU table by Category command 
python /Users/caporaso/code/Qiime/scripts/summarize_otu_by_cat.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table.biom -m 'SampleType' 

Stdout:

Stderr:

# Sort OTU Table command 
python /Users/caporaso/code/Qiime/scripts/sort_otu_table.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
python /Users/caporaso/code/Qiime/scripts/summarize_taxa.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table_sorted.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
python /Users/caporaso/code/Qiime/scripts/plot_taxa_summary.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table_sorted_L2.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table_sorted_L3.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table_sorted_L4.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table_sorted_L5.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/SampleType_otu_table_sorted_L6.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType//taxa_summary_plots/ 

Stdout:

Stderr:

Executing commands.

# Summarize OTU table by Category command 
python /Users/caporaso/code/Qiime/scripts/summarize_otu_by_cat.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table.biom -m 'day' 

Stdout:

Stderr:

# Sort OTU Table command 
python /Users/caporaso/code/Qiime/scripts/sort_otu_table.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
python /Users/caporaso/code/Qiime/scripts/summarize_taxa.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table_sorted.biom -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
python /Users/caporaso/code/Qiime/scripts/plot_taxa_summary.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table_sorted_L2.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table_sorted_L3.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table_sorted_L4.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table_sorted_L5.txt,/Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/day_otu_table_sorted_L6.txt -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day//taxa_summary_plots/ 

Stdout:

Stderr:

Executing commands.

# Boxplots (SampleType) command 
make_distance_boxplots.py -d /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_dm.txt -f SampleType -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_boxplots/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -n 999 

Stdout:

Stderr:

# Boxplots (day) command 
make_distance_boxplots.py -d /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_dm.txt -f day -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//weighted_unifrac_boxplots/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -n 999 

Stdout:

Stderr:

# Boxplots (SampleType) command 
make_distance_boxplots.py -d /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_dm.txt -f SampleType -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_boxplots/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -n 999 

Stdout:

Stderr:

# Boxplots (day) command 
make_distance_boxplots.py -d /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_dm.txt -f day -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/bdiv_even20//unweighted_unifrac_boxplots/ -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -n 999 

Stdout:

Stderr:

# Compare alpha diversity (SampleType, chao1) command 
compare_alpha_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/chao1.txt -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c SampleType -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//SampleType_chao1.txt -n 999 

Stdout:

Stderr:

# Compare alpha diversity (SampleType, observed_species) command 
compare_alpha_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/observed_species.txt -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c SampleType -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//SampleType_observed_species.txt -n 999 

Stdout:

Stderr:

# Compare alpha diversity (SampleType, PD_whole_tree) command 
compare_alpha_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/PD_whole_tree.txt -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c SampleType -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//SampleType_PD_whole_tree.txt -n 999 

Stdout:

Stderr:

# Compare alpha diversity (day, chao1) command 
compare_alpha_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/chao1.txt -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c day -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//day_chao1.txt -n 999 

Stdout:

Stderr:

# Compare alpha diversity (day, observed_species) command 
compare_alpha_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/observed_species.txt -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c day -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//day_observed_species.txt -n 999 

Stdout:

Stderr:

# Compare alpha diversity (day, PD_whole_tree) command 
compare_alpha_diversity.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/PD_whole_tree.txt -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c day -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/arare_max20//day_PD_whole_tree.txt -n 999 

Stdout:

Stderr:

# OTU category significance (SampleType) command 
otu_category_significance.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c SampleType -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/category_significance_SampleType.txt 

Stdout:

Stderr:

# OTU category significance (day) command 
otu_category_significance.py -i /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom -m /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/map.txt -c day -o /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/category_significance_day.txt 

Stdout:

Stderr:

# Compress the filtered BIOM table command 
gzip /Users/caporaso/code/qiime/qiime_test_data/core_diversity_analyses/core_output/table_mc20.biom

Stdout:

Stderr:


Logging stopped at 12:21:00 on 13 May 2013
