Logging started at 07:40:38 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

Executing commands.

# Generate BIOM table summary command 
biom summarize-table -i pick_close_ref/otu_table.biom -o core_diversity/biom_table_summary.txt 

Stdout:

Stderr:

# 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:

Executing commands.

# Beta Diversity (weighted_unifrac) command 
beta_diversity.py -i core_diversity/table_even250.biom -o core_diversity/bdiv_even250/ --metrics weighted_unifrac  -t /Users/antoniog/svn_programs/gg_13_8_otus/trees/97_otus.tree 

Stdout:

Stderr:

# Rename distance matrix (weighted_unifrac) command 
mv core_diversity/bdiv_even250//weighted_unifrac_table_even250.txt core_diversity/bdiv_even250//weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
principal_coordinates.py -i core_diversity/bdiv_even250//weighted_unifrac_dm.txt -o core_diversity/bdiv_even250//weighted_unifrac_pc.txt 

Stdout:

Stderr:
/Users/antoniog/svn_programs/scikit-bio/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 -0.311683122628 and the largest is 8.76221201061.
  RuntimeWarning

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i core_diversity/bdiv_even250//weighted_unifrac_pc.txt -o core_diversity/bdiv_even250//weighted_unifrac_emperor_pcoa_plot/ -m mapping_file.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
beta_diversity.py -i core_diversity/table_even250.biom -o core_diversity/bdiv_even250/ --metrics unweighted_unifrac  -t /Users/antoniog/svn_programs/gg_13_8_otus/trees/97_otus.tree 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac) command 
mv core_diversity/bdiv_even250//unweighted_unifrac_table_even250.txt core_diversity/bdiv_even250//unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
principal_coordinates.py -i core_diversity/bdiv_even250//unweighted_unifrac_dm.txt -o core_diversity/bdiv_even250//unweighted_unifrac_pc.txt 

Stdout:

Stderr:
/Users/antoniog/svn_programs/scikit-bio/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 -0.046201322561 and the largest is 7.15620494246.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i core_diversity/bdiv_even250//unweighted_unifrac_pc.txt -o core_diversity/bdiv_even250//unweighted_unifrac_emperor_pcoa_plot/ -m mapping_file.txt 

Stdout:

Stderr:

Executing commands.

# Alpha rarefaction command 
multiple_rarefactions.py -i core_diversity/table_mc250.biom -m 10 -x 250 -s 24 -o core_diversity/arare_max250//rarefaction/ 

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
alpha_diversity.py -i core_diversity/arare_max250//rarefaction/ -o core_diversity/arare_max250//alpha_div/  -t /Users/antoniog/svn_programs/gg_13_8_otus/trees/97_otus.tree

Stdout:

Stderr:

# Collate alpha command 
collate_alpha.py -i core_diversity/arare_max250//alpha_div/ -o core_diversity/arare_max250//alpha_div_collated/ 

Stdout:

Stderr:

# Removing intermediate files command 
rm -r core_diversity/arare_max250//rarefaction/ core_diversity/arare_max250//alpha_div/

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
make_rarefaction_plots.py -i core_diversity/arare_max250//alpha_div_collated/ -m mapping_file.txt -o core_diversity/arare_max250//alpha_rarefaction_plots/ 

Stdout:

Stderr:

Skipping compare_alpha_diversity.py as no categories were provided.

Executing commands.

# Sort OTU Table command 
sort_otu_table.py -i core_diversity/table_mc250.biom -o core_diversity/taxa_plots/table_mc250_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i core_diversity/taxa_plots/table_mc250_sorted.biom -o core_diversity/taxa_plots/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
plot_taxa_summary.py -i core_diversity/taxa_plots/table_mc250_sorted_L2.txt,core_diversity/taxa_plots/table_mc250_sorted_L3.txt,core_diversity/taxa_plots/table_mc250_sorted_L4.txt,core_diversity/taxa_plots/table_mc250_sorted_L5.txt,core_diversity/taxa_plots/table_mc250_sorted_L6.txt -o core_diversity/taxa_plots//taxa_summary_plots/ 

Stdout:

Stderr:

Executing commands.

# Compress the filtered BIOM table command 
gzip core_diversity/table_mc250.biom

Stdout:

Stderr:

# Compress the rarefied BIOM table command 
gzip core_diversity/table_even250.biom

Stdout:

Stderr:


Logging stopped at 08:11:12 on 12 Aug 2015
