Logging started at 14:51:27 on 05 May 2013
QIIME version: 1.6.0-dev, issue-163@35f75cd

qiime_config values:
sc_queue	all.q
pynast_template_alignment_fp	/home/jrideout/dev/qiime-deps/qiime-deps/core_set_aligned.fasta.imputed
cluster_jobs_fp	/home/jrideout/.virtualenvs/qiime/qiime/scripts/start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/home/jrideout/dev/qiime-deps/qiime-deps/gg_otus-12_10-release/rep_set/61_otus.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/home/jrideout/dev/qiime-deps/qiime-deps/lanemask_in_1s_and_0s
jobs_to_start	1
cloud_environment	False
qiime_scripts_dir	/home/jrideout/.virtualenvs/qiime/qiime/scripts/
denoiser_min_per_core	50
python_exe_fp	python
temp_dir	/tmp/
blastall_fp	blastall
seconds_to_sleep	60
assign_taxonomy_id_to_taxonomy_fp	/home/jrideout/dev/qiime-deps/qiime-deps/gg_otus-12_10-release/taxonomy/61_otu_taxonomy.txt

parameter file values:

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

Executing commands.

# Summarize OTU table by Category command 
python /home/jrideout/.virtualenvs/qiime/qiime/scripts//summarize_otu_by_cat.py -i Fasting_Map.txt -c otu_table.biom -o taxa_summary_by_treatment/Treatment_otu_table.biom -m 'Treatment' 

Stdout:

Stderr:

# Summarize Taxonomy command 
python /home/jrideout/.virtualenvs/qiime/qiime/scripts//summarize_taxa.py -i taxa_summary_by_treatment/Treatment_otu_table.biom -o taxa_summary_by_treatment 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
python /home/jrideout/.virtualenvs/qiime/qiime/scripts//plot_taxa_summary.py -i taxa_summary_by_treatment/Treatment_otu_table_L2.txt,taxa_summary_by_treatment/Treatment_otu_table_L3.txt,taxa_summary_by_treatment/Treatment_otu_table_L4.txt,taxa_summary_by_treatment/Treatment_otu_table_L5.txt,taxa_summary_by_treatment/Treatment_otu_table_L6.txt -o taxa_summary_by_treatment/taxa_summary_plots/ 

Stdout:

Stderr:


Logging stopped at 14:51:30 on 05 May 2013
