Logging started at 12:59:00 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"

Input file md5 sums:
metagenome_at_level3.biom: 98e1cd2b262824b87fc3939ea3e95b6d

Executing commands.

# 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 metagenome_at_level3.biom -o plots_at_level3 --absolute_abundance --md_identifier "KEGG_Pathways"

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 plots_at_level3/metagenome_at_level3_L2.txt,plots_at_level3/metagenome_at_level3_L3.txt,plots_at_level3/metagenome_at_level3_L4.txt,plots_at_level3/metagenome_at_level3_L5.txt,plots_at_level3/metagenome_at_level3_L6.txt -o plots_at_level3/taxa_summary_plots/ 

Stdout:

Stderr:


Logging stopped at 13:03:44 on 14 May 2018
