Logging started at 07:01:56 on 15 May 2018
QIIME version: 1.8.0

qiime_config values:
blastmat_dir	/home/worker/software/qiime-1.8/blast-2.2.22-release/data
sc_queue	all.q
pynast_template_alignment_fp	/home/worker/software/qiime-1.8/core_set_aligned.fasta.imputed
cluster_jobs_fp	/home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/home/worker/software/qiime-1.8/gg_otus-13_8-release/rep_set/97_otus.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/home/worker/software/qiime-1.8/lanemask_in_1s_and_0s
jobs_to_start	1
cloud_environment	False
qiime_scripts_dir	/home/worker/software/qiime-1.8/qiime-1.8.0-release/bin
denoiser_min_per_core	50
working_dir	/tmp/
python_exe_fp	/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python
temp_dir	/tmp/
blastall_fp	/home/worker/software/qiime-1.8/blast-2.2.22-release/bin/blastall
seconds_to_sleep	60
assign_taxonomy_id_to_taxonomy_fp	/home/worker/software/qiime-1.8/gg_otus-13_8-release/taxonomy/97_otu_taxonomy.txt

parameter file values:
beta_diversity:metrics	bray_curtis,spearman_approx,unweighted_unifrac,weighted_unifrac,pearson
alpha_diversity:metrics	chao1,PD_whole_tree,observed_species,shannon,simpson
parallel:jobs_to_start	8

Input file md5 sums:
otus/otu_table.biom: a9e246f919f99b9b4a53cd0f4e3596c7
mapping.txt: 2f7eab2cc48e3903ebc192c122eac5b2
otus/rep_set.tre: c3cf7bff9c9714c39827a9d33fad9fe9

Executing commands.

# Generate BIOM table summary command 
biom summarize-table -i otus/otu_table.biom -o core_diversity/biom_table_summary.txt --suppress-md5 

Stdout:

Stderr:
/home/worker/software/qiime-1.8/pyqi-0.3.1-release/bin/pyqi:4: UserWarning: Module pkg_resources was already imported from /home/worker/software/qiime-1.8/setuptools-0.6c11-release/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py, but /home/worker/software/qiime-1.8/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg is being added to sys.path
  import pkg_resources
/home/worker/software/qiime-1.8/pyqi-0.3.1-release/bin/pyqi:4: UserWarning: Module site was already imported from /home/worker/software/qiime-1.8/python-2.7.3-release/lib/python2.7/site.pyc, but /home/worker/software/qiime-1.8/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg is being added to sys.path
  import pkg_resources

# Filter low sequence count samples from table (minimum sequence count: 8000) command 
filter_samples_from_otu_table.py -i otus/otu_table.biom -o core_diversity/table_mc8000.biom -n 8000

Stdout:

Stderr:

# Rarify the OTU table to 8000 sequences/sample command 
single_rarefaction.py -i core_diversity/table_mc8000.biom -o core_diversity/table_even8000.biom -d 8000

Stdout:

Stderr:

Executing commands.

# Beta Diversity (bray_curtis) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_beta_diversity.py -i core_diversity/table_even8000.biom -o core_diversity/bdiv_even8000/ --metrics bray_curtis -T  -t otus/rep_set.tre --jobs_to_start 8

Stdout:

Stderr:

# Rename distance matrix (bray_curtis) command 
mv core_diversity/bdiv_even8000//bray_curtis_table_even8000.txt core_diversity/bdiv_even8000//bray_curtis_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/principal_coordinates.py -i core_diversity/bdiv_even8000//bray_curtis_dm.txt -o core_diversity/bdiv_even8000//bray_curtis_pc.txt 

Stdout:

Stderr:

# Make emperor plots, bray_curtis) command 
make_emperor.py -i core_diversity/bdiv_even8000//bray_curtis_pc.txt -o core_diversity/bdiv_even8000//bray_curtis_emperor_pcoa_plot/ -m mapping.txt 

Stdout:

Stderr:

# Beta Diversity (spearman_approx) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_beta_diversity.py -i core_diversity/table_even8000.biom -o core_diversity/bdiv_even8000/ --metrics spearman_approx -T  -t otus/rep_set.tre --jobs_to_start 8

Stdout:

Stderr:

# Rename distance matrix (spearman_approx) command 
mv core_diversity/bdiv_even8000//spearman_approx_table_even8000.txt core_diversity/bdiv_even8000//spearman_approx_dm.txt

Stdout:

Stderr:

# Principal coordinates (spearman_approx) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/principal_coordinates.py -i core_diversity/bdiv_even8000//spearman_approx_dm.txt -o core_diversity/bdiv_even8000//spearman_approx_pc.txt 

Stdout:

Stderr:

# Make emperor plots, spearman_approx) command 
make_emperor.py -i core_diversity/bdiv_even8000//spearman_approx_pc.txt -o core_diversity/bdiv_even8000//spearman_approx_emperor_pcoa_plot/ -m mapping.txt 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_beta_diversity.py -i core_diversity/table_even8000.biom -o core_diversity/bdiv_even8000/ --metrics unweighted_unifrac -T  -t otus/rep_set.tre --jobs_to_start 8

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac) command 
mv core_diversity/bdiv_even8000//unweighted_unifrac_table_even8000.txt core_diversity/bdiv_even8000//unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/principal_coordinates.py -i core_diversity/bdiv_even8000//unweighted_unifrac_dm.txt -o core_diversity/bdiv_even8000//unweighted_unifrac_pc.txt 

Stdout:

Stderr:

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i core_diversity/bdiv_even8000//unweighted_unifrac_pc.txt -o core_diversity/bdiv_even8000//unweighted_unifrac_emperor_pcoa_plot/ -m mapping.txt 

Stdout:

Stderr:

# Beta Diversity (weighted_unifrac) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_beta_diversity.py -i core_diversity/table_even8000.biom -o core_diversity/bdiv_even8000/ --metrics weighted_unifrac -T  -t otus/rep_set.tre --jobs_to_start 8

Stdout:

Stderr:

# Rename distance matrix (weighted_unifrac) command 
mv core_diversity/bdiv_even8000//weighted_unifrac_table_even8000.txt core_diversity/bdiv_even8000//weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/principal_coordinates.py -i core_diversity/bdiv_even8000//weighted_unifrac_dm.txt -o core_diversity/bdiv_even8000//weighted_unifrac_pc.txt 

Stdout:

Stderr:

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i core_diversity/bdiv_even8000//weighted_unifrac_pc.txt -o core_diversity/bdiv_even8000//weighted_unifrac_emperor_pcoa_plot/ -m mapping.txt 

Stdout:

Stderr:

# Beta Diversity (pearson) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_beta_diversity.py -i core_diversity/table_even8000.biom -o core_diversity/bdiv_even8000/ --metrics pearson -T  -t otus/rep_set.tre --jobs_to_start 8

Stdout:

Stderr:

# Rename distance matrix (pearson) command 
mv core_diversity/bdiv_even8000//pearson_table_even8000.txt core_diversity/bdiv_even8000//pearson_dm.txt

Stdout:

Stderr:

# Principal coordinates (pearson) command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/principal_coordinates.py -i core_diversity/bdiv_even8000//pearson_dm.txt -o core_diversity/bdiv_even8000//pearson_pc.txt 

Stdout:

Stderr:

# Make emperor plots, pearson) command 
make_emperor.py -i core_diversity/bdiv_even8000//pearson_pc.txt -o core_diversity/bdiv_even8000//pearson_emperor_pcoa_plot/ -m mapping.txt 

Stdout:

Stderr:

Executing commands.

# Alpha rarefaction command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_multiple_rarefactions.py -T -i core_diversity/table_mc8000.biom -m 10 -x 8000 -s 799 -o core_diversity/arare_max8000//rarefaction/  --jobs_to_start 8

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_alpha_diversity.py -T -i core_diversity/arare_max8000//rarefaction/ -o core_diversity/arare_max8000//alpha_div/ --metrics chao1,PD_whole_tree,observed_species,shannon,simpson -t otus/rep_set.tre --jobs_to_start 8

Stdout:

Stderr:

# Collate alpha command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/collate_alpha.py -i core_diversity/arare_max8000//alpha_div/ -o core_diversity/arare_max8000//alpha_div_collated/ 

Stdout:

Stderr:

# Removing intermediate files command 
rm -r core_diversity/arare_max8000//rarefaction/ core_diversity/arare_max8000//alpha_div/

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/make_rarefaction_plots.py -i core_diversity/arare_max8000//alpha_div_collated/ -m mapping.txt -o core_diversity/arare_max8000//alpha_rarefaction_plots/ 

Stdout:

Stderr:

Executing commands.

# Sort OTU Table command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/sort_otu_table.py -i core_diversity/table_mc8000.biom -o core_diversity/taxa_plots/table_mc8000_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/summarize_taxa.py -i core_diversity/taxa_plots/table_mc8000_sorted.biom -o core_diversity/taxa_plots/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/plot_taxa_summary.py -i core_diversity/taxa_plots/table_mc8000_sorted_L2.txt,core_diversity/taxa_plots/table_mc8000_sorted_L3.txt,core_diversity/taxa_plots/table_mc8000_sorted_L4.txt,core_diversity/taxa_plots/table_mc8000_sorted_L5.txt,core_diversity/taxa_plots/table_mc8000_sorted_L6.txt -o core_diversity/taxa_plots//taxa_summary_plots/ 

Stdout:

Stderr:

Executing commands.

# Summarize OTU table by Category command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/summarize_otu_by_cat.py -m mapping.txt -i core_diversity/table_mc8000.biom -o core_diversity/taxa_plots_PatNr/PatNr_otu_table.biom -c 'PatNr' 

Stdout:

Stderr:

# Sort OTU Table command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/sort_otu_table.py -i core_diversity/taxa_plots_PatNr/PatNr_otu_table.biom -o core_diversity/taxa_plots_PatNr/PatNr_otu_table_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/summarize_taxa.py -i core_diversity/taxa_plots_PatNr/PatNr_otu_table_sorted.biom -o core_diversity/taxa_plots_PatNr/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/plot_taxa_summary.py -i core_diversity/taxa_plots_PatNr/PatNr_otu_table_sorted_L2.txt,core_diversity/taxa_plots_PatNr/PatNr_otu_table_sorted_L3.txt,core_diversity/taxa_plots_PatNr/PatNr_otu_table_sorted_L4.txt,core_diversity/taxa_plots_PatNr/PatNr_otu_table_sorted_L5.txt,core_diversity/taxa_plots_PatNr/PatNr_otu_table_sorted_L6.txt -o core_diversity/taxa_plots_PatNr//taxa_summary_plots/ 

Stdout:

Stderr:

Executing commands.

# Summarize OTU table by Category command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/summarize_otu_by_cat.py -m mapping.txt -i core_diversity/table_mc8000.biom -o core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table.biom -c 'Meta_Grp' 

Stdout:

Stderr:

# Sort OTU Table command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/sort_otu_table.py -i core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table.biom -o core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/summarize_taxa.py -i core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table_sorted.biom -o core_diversity/taxa_plots_Meta_Grp/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/plot_taxa_summary.py -i core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table_sorted_L2.txt,core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table_sorted_L3.txt,core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table_sorted_L4.txt,core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table_sorted_L5.txt,core_diversity/taxa_plots_Meta_Grp/Meta_Grp_otu_table_sorted_L6.txt -o core_diversity/taxa_plots_Meta_Grp//taxa_summary_plots/ 

Stdout:

Stderr:

Executing commands.

# Summarize OTU table by Category command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/summarize_otu_by_cat.py -m mapping.txt -i core_diversity/table_mc8000.biom -o core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table.biom -c 'Zeitpunkt' 

Stdout:

Stderr:

# Sort OTU Table command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/sort_otu_table.py -i core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table.biom -o core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table_sorted.biom

Stdout:

Stderr:

# Summarize Taxonomy command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/summarize_taxa.py -i core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table_sorted.biom -o core_diversity/taxa_plots_Zeitpunkt/ 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/plot_taxa_summary.py -i core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table_sorted_L2.txt,core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table_sorted_L3.txt,core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table_sorted_L4.txt,core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table_sorted_L5.txt,core_diversity/taxa_plots_Zeitpunkt/Zeitpunkt_otu_table_sorted_L6.txt -o core_diversity/taxa_plots_Zeitpunkt//taxa_summary_plots/ 

Stdout:

Stderr:

Executing commands.

# Boxplots (PatNr) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//bray_curtis_dm.txt -f PatNr -o core_diversity/bdiv_even8000//bray_curtis_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Meta_Grp) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//bray_curtis_dm.txt -f Meta_Grp -o core_diversity/bdiv_even8000//bray_curtis_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Zeitpunkt) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//bray_curtis_dm.txt -f Zeitpunkt -o core_diversity/bdiv_even8000//bray_curtis_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (PatNr) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//spearman_approx_dm.txt -f PatNr -o core_diversity/bdiv_even8000//spearman_approx_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Meta_Grp) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//spearman_approx_dm.txt -f Meta_Grp -o core_diversity/bdiv_even8000//spearman_approx_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Zeitpunkt) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//spearman_approx_dm.txt -f Zeitpunkt -o core_diversity/bdiv_even8000//spearman_approx_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (PatNr) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//unweighted_unifrac_dm.txt -f PatNr -o core_diversity/bdiv_even8000//unweighted_unifrac_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Meta_Grp) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//unweighted_unifrac_dm.txt -f Meta_Grp -o core_diversity/bdiv_even8000//unweighted_unifrac_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Zeitpunkt) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//unweighted_unifrac_dm.txt -f Zeitpunkt -o core_diversity/bdiv_even8000//unweighted_unifrac_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (PatNr) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//weighted_unifrac_dm.txt -f PatNr -o core_diversity/bdiv_even8000//weighted_unifrac_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Meta_Grp) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//weighted_unifrac_dm.txt -f Meta_Grp -o core_diversity/bdiv_even8000//weighted_unifrac_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Zeitpunkt) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//weighted_unifrac_dm.txt -f Zeitpunkt -o core_diversity/bdiv_even8000//weighted_unifrac_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (PatNr) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//pearson_dm.txt -f PatNr -o core_diversity/bdiv_even8000//pearson_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Meta_Grp) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//pearson_dm.txt -f Meta_Grp -o core_diversity/bdiv_even8000//pearson_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Boxplots (Zeitpunkt) command 
make_distance_boxplots.py -d core_diversity/bdiv_even8000//pearson_dm.txt -f Zeitpunkt -o core_diversity/bdiv_even8000//pearson_boxplots/ -m mapping.txt -n 999 

Stdout:

Stderr:

# Compare alpha diversity (chao1) command 
compare_alpha_diversity.py -i core_diversity/arare_max8000//alpha_div_collated/chao1.txt -m mapping.txt -c PatNr,Meta_Grp,Zeitpunkt -o core_diversity/arare_max8000//compare_chao1 -n 999 

Stdout:

Stderr:

# Compare alpha diversity (PD_whole_tree) command 
compare_alpha_diversity.py -i core_diversity/arare_max8000//alpha_div_collated/PD_whole_tree.txt -m mapping.txt -c PatNr,Meta_Grp,Zeitpunkt -o core_diversity/arare_max8000//compare_PD_whole_tree -n 999 

Stdout:

Stderr:

# Compare alpha diversity (observed_species) command 
compare_alpha_diversity.py -i core_diversity/arare_max8000//alpha_div_collated/observed_species.txt -m mapping.txt -c PatNr,Meta_Grp,Zeitpunkt -o core_diversity/arare_max8000//compare_observed_species -n 999 

Stdout:

Stderr:

# Compare alpha diversity (shannon) command 
compare_alpha_diversity.py -i core_diversity/arare_max8000//alpha_div_collated/shannon.txt -m mapping.txt -c PatNr,Meta_Grp,Zeitpunkt -o core_diversity/arare_max8000//compare_shannon -n 999 

Stdout:

Stderr:

# Compare alpha diversity (simpson) command 
compare_alpha_diversity.py -i core_diversity/arare_max8000//alpha_div_collated/simpson.txt -m mapping.txt -c PatNr,Meta_Grp,Zeitpunkt -o core_diversity/arare_max8000//compare_simpson -n 999 

Stdout:

Stderr:

# Group significance (PatNr) command 
group_significance.py -i core_diversity/table_even8000.biom -m mapping.txt -c PatNr -o core_diversity/group_significance_PatNr.txt 

Stdout:

Stderr:

# Group significance (Meta_Grp) command 
group_significance.py -i core_diversity/table_even8000.biom -m mapping.txt -c Meta_Grp -o core_diversity/group_significance_Meta_Grp.txt 

Stdout:

Stderr:

# Group significance (Zeitpunkt) command 
group_significance.py -i core_diversity/table_even8000.biom -m mapping.txt -c Zeitpunkt -o core_diversity/group_significance_Zeitpunkt.txt 

Stdout:

Stderr:

# Compress the filtered BIOM table command 
gzip core_diversity/table_mc8000.biom

Stdout:

Stderr:

# Compress the rarified BIOM table command 
gzip core_diversity/table_even8000.biom

Stdout:

Stderr:


Logging stopped at 09:35:46 on 15 May 2018
