Logging started at 01:08:27 on 30 Apr 2016
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp	/home/jona1883/miniconda2/envs/AmericanGut/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue	all.q
pynast_template_alignment_fp	/home/jona1883/miniconda2/envs/AmericanGut/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
cluster_jobs_fp	start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/home/jona1883/miniconda2/envs/AmericanGut/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue	friendlyq
jobs_to_start	1
denoiser_min_per_core	50
assign_taxonomy_id_to_taxonomy_fp	/home/jona1883/miniconda2/envs/AmericanGut/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/tmp/
blastall_fp	blastall
seconds_to_sleep	1

parameter file values:
parallel:jobs_to_start	1
pick_otus:threads	28
pick_otus:otu_picking_method	sortmerna

Input file md5 sums:
/home/jona1883/software/American-Gut/ipynb/primary-processing/ag-April-29-2016/02-filtered/fecal-sequences.fna: 0ce3defc1df124ad0337f84d24525fc2
/home/jona1883/software/American-Gut/data/AG/BLOOM.fasta: e14373617a6f1f06674ab29e06d15e1b
/home/jona1883/miniconda2/envs/AmericanGut/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt: 56ef15dccf2e931ec173f4f977ed649b

Forcing --suppress_new_clusters as this is closed-reference OTU picking.

Executing commands.

# Pick OTUs command 
pick_otus.py -i /home/jona1883/software/American-Gut/ipynb/primary-processing/ag-April-29-2016/02-filtered/fecal-sequences.fna -o /home/jona1883/software/American-Gut/ipynb/primary-processing/ag-April-29-2016/02-filtered/observed-blooms/sortmerna_picked_otus -r /home/jona1883/software/American-Gut/data/AG/BLOOM.fasta -m sortmerna --threads 28 --otu_picking_method sortmerna --suppress_new_clusters

Stdout:

Stderr:

# Make OTU table command 
make_otu_table.py -i /home/jona1883/software/American-Gut/ipynb/primary-processing/ag-April-29-2016/02-filtered/observed-blooms/sortmerna_picked_otus/fecal-sequences_otus.txt -t /home/jona1883/miniconda2/envs/AmericanGut/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt -o /home/jona1883/software/American-Gut/ipynb/primary-processing/ag-April-29-2016/02-filtered/observed-blooms/otu_table.biom 

Stdout:

Stderr:


Logging stopped at 02:14:38 on 30 Apr 2016