Logging started at 12:58:52 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:
beta_diversity:metrics	bray_curtis
summarize_taxa:absolute_abundance	True
summarize_taxa:md_identifier	"KEGG_Pathways"
parallel:jobs_to_start	1

Input file md5 sums:
metagenome_predictions.biom: 1ab38c706c38338dbc97f5afd138b3be
../../mapping.txt: 2f7eab2cc48e3903ebc192c122eac5b2

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/beta_diversity.py -i metagenome_predictions.biom -o beta_diversity --metrics bray_curtis 

Stdout:

Stderr:

# Rename distance matrix (bray_curtis) command 
mv beta_diversity/bray_curtis_metagenome_predictions.txt beta_diversity/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 beta_diversity/bray_curtis_dm.txt -o beta_diversity/bray_curtis_pc.txt 

Stdout:

Stderr:

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

Stdout:

Stderr:


Logging stopped at 12:58:57 on 14 May 2018
