Logging started at 12:47:11 on 14 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:
parallel:jobs_to_start	1

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

Executing commands.

# Beta Diversity (weighted_unifrac, 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/beta_diversity.py -i ../otus/otu_table.biom -o wf_jack  -t ../otus/rep_set.tre

Stdout:

Stderr:

# 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/multiple_rarefactions_even_depth.py -i ../otus/otu_table.biom -d 2000 -o wf_jack/rarefaction/ 

Stdout:

Stderr:

# UPGMA on full distance matrix: 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/upgma_cluster.py -i wf_jack/weighted_unifrac_otu_table.txt -o wf_jack/weighted_unifrac//otu_table_upgma.tre 

Stdout:

Stderr:

# Beta diversity on rarefied OTU tables (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/beta_diversity.py -i wf_jack/rarefaction/ -o wf_jack/weighted_unifrac//rare_dm/  -m weighted_unifrac  -t ../otus/rep_set.tre

Stdout:

Stderr:

# UPGMA on rarefied distance matrix (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/upgma_cluster.py -i wf_jack/weighted_unifrac//rare_dm/ -o wf_jack/weighted_unifrac//rare_upgma/ 

Stdout:

Stderr:

# consensus on rarefied distance matrices (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/consensus_tree.py -i wf_jack/weighted_unifrac//rare_upgma/ -o wf_jack/weighted_unifrac//rare_upgma_consensus.tre 

Stdout:

Stderr:

# Tree compare (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/tree_compare.py -s wf_jack/weighted_unifrac//rare_upgma/ -m wf_jack/weighted_unifrac//rare_upgma_consensus.tre -o wf_jack/weighted_unifrac//upgma_cmp/ 

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 wf_jack/weighted_unifrac//rare_dm/ -o wf_jack/weighted_unifrac//pcoa/ 

Stdout:

Stderr:

# emperor plots (weighted_unifrac) command 
make_emperor.py -i wf_jack/weighted_unifrac//pcoa/ -o wf_jack/weighted_unifrac//emperor_pcoa_plots/ -m ../mapping.txt 

Stdout:

Stderr:

# UPGMA on full distance matrix: 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/upgma_cluster.py -i wf_jack/unweighted_unifrac_otu_table.txt -o wf_jack/unweighted_unifrac//otu_table_upgma.tre 

Stdout:

Stderr:

# Beta diversity on rarefied OTU tables (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/beta_diversity.py -i wf_jack/rarefaction/ -o wf_jack/unweighted_unifrac//rare_dm/  -m unweighted_unifrac  -t ../otus/rep_set.tre

Stdout:

Stderr:

# UPGMA on rarefied distance matrix (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/upgma_cluster.py -i wf_jack/unweighted_unifrac//rare_dm/ -o wf_jack/unweighted_unifrac//rare_upgma/ 

Stdout:

Stderr:

# consensus on rarefied distance matrices (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/consensus_tree.py -i wf_jack/unweighted_unifrac//rare_upgma/ -o wf_jack/unweighted_unifrac//rare_upgma_consensus.tre 

Stdout:

Stderr:

# Tree compare (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/tree_compare.py -s wf_jack/unweighted_unifrac//rare_upgma/ -m wf_jack/unweighted_unifrac//rare_upgma_consensus.tre -o wf_jack/unweighted_unifrac//upgma_cmp/ 

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 wf_jack/unweighted_unifrac//rare_dm/ -o wf_jack/unweighted_unifrac//pcoa/ 

Stdout:

Stderr:

# emperor plots (unweighted_unifrac) command 
make_emperor.py -i wf_jack/unweighted_unifrac//pcoa/ -o wf_jack/unweighted_unifrac//emperor_pcoa_plots/ -m ../mapping.txt 

Stdout:

Stderr:


Logging stopped at 12:48:16 on 14 May 2018
