Logging started at 13:16:01 on 14 Mar 2012
QIIME version: 1.4.0-dev, svn revision 2813

qiime_config values:
blastmat_dir	/Applications/blast-2.2.22/data/
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	/Users/caporaso/code/Qiime/scripts/start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/Users/caporaso/data/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.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	6
assign_taxonomy_id_to_taxonomy_fp	/Users/caporaso/data/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt

parameter file values:
parallel:jobs_to_start	2

Input file md5 sums:
otu_table.biom: dda91090fbdc0f69056852247bcd924f
Fasting_Map.txt: e16159d7122035797076d66b1a287962
rep_set.tre: fdd11da9dcf4b2d55187c6021bd0d181

Executing commands.

# Beta Diversity (weighted_unifrac, unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/beta_diversity.py -i otu_table.biom -o bdiv_jk100  -t rep_set.tre

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# Rarefaction command 
python /Users/caporaso/code/Qiime/scripts/multiple_rarefactions_even_depth.py -i otu_table.biom -d 100 -o bdiv_jk100/rarefaction/ 

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# UPGMA on full distance matrix: weighted_unifrac command 
python /Users/caporaso/code/Qiime/scripts/upgma_cluster.py -i bdiv_jk100/weighted_unifrac_otu_table.txt -o bdiv_jk100/weighted_unifrac//otu_table_upgma.tre 

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# Beta diversity on rarefied OTU tables (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/beta_diversity.py -i bdiv_jk100/rarefaction/ -o bdiv_jk100/weighted_unifrac//rare_dm/  -m weighted_unifrac  -t rep_set.tre

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# UPGMA on rarefied distance matrix (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/upgma_cluster.py -i bdiv_jk100/weighted_unifrac//rare_dm/ -o bdiv_jk100/weighted_unifrac//rare_upgma/ 

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# consensus on rarefied distance matrices (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/consensus_tree.py -i bdiv_jk100/weighted_unifrac//rare_upgma/ -o bdiv_jk100/weighted_unifrac//rare_upgma//consensus.tre 

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# Tree compare (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/tree_compare.py -s bdiv_jk100/weighted_unifrac//rare_upgma/ -m bdiv_jk100/weighted_unifrac//rare_upgma//consensus.tre -o bdiv_jk100/weighted_unifrac//upgma_cmp/ 

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# Principal coordinates (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/principal_coordinates.py -i bdiv_jk100/weighted_unifrac//rare_dm/ -o bdiv_jk100/weighted_unifrac//pcoa/ 

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# 2d plots (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_2d_plots.py -i bdiv_jk100/weighted_unifrac//pcoa/ -o bdiv_jk100/weighted_unifrac//2d_plots/ -m Fasting_Map.txt 

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# 3d plots (weighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_3d_plots.py -i bdiv_jk100/weighted_unifrac//pcoa/ -o bdiv_jk100/weighted_unifrac//3d_plots/ -m Fasting_Map.txt 

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# UPGMA on full distance matrix: unweighted_unifrac command 
python /Users/caporaso/code/Qiime/scripts/upgma_cluster.py -i bdiv_jk100/unweighted_unifrac_otu_table.txt -o bdiv_jk100/unweighted_unifrac//otu_table_upgma.tre 

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Stderr:

# Beta diversity on rarefied OTU tables (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/beta_diversity.py -i bdiv_jk100/rarefaction/ -o bdiv_jk100/unweighted_unifrac//rare_dm/  -m unweighted_unifrac  -t rep_set.tre

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Stderr:

# UPGMA on rarefied distance matrix (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/upgma_cluster.py -i bdiv_jk100/unweighted_unifrac//rare_dm/ -o bdiv_jk100/unweighted_unifrac//rare_upgma/ 

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# consensus on rarefied distance matrices (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/consensus_tree.py -i bdiv_jk100/unweighted_unifrac//rare_upgma/ -o bdiv_jk100/unweighted_unifrac//rare_upgma//consensus.tre 

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Stderr:

# Tree compare (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/tree_compare.py -s bdiv_jk100/unweighted_unifrac//rare_upgma/ -m bdiv_jk100/unweighted_unifrac//rare_upgma//consensus.tre -o bdiv_jk100/unweighted_unifrac//upgma_cmp/ 

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Stderr:

# Principal coordinates (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/principal_coordinates.py -i bdiv_jk100/unweighted_unifrac//rare_dm/ -o bdiv_jk100/unweighted_unifrac//pcoa/ 

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Stderr:

# 2d plots (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_2d_plots.py -i bdiv_jk100/unweighted_unifrac//pcoa/ -o bdiv_jk100/unweighted_unifrac//2d_plots/ -m Fasting_Map.txt 

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# 3d plots (unweighted_unifrac) command 
python /Users/caporaso/code/Qiime/scripts/make_3d_plots.py -i bdiv_jk100/unweighted_unifrac//pcoa/ -o bdiv_jk100/unweighted_unifrac//3d_plots/ -m Fasting_Map.txt 

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Logging stopped at 13:16:18 on 14 Mar 2012
