Logging started at 10:10:03 on 31 May 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
pick_otus:sortmerna_db	/home/jona1883/software/gg_otus-13_8-release/sortmerna/97_otus.idx

Input file md5 sums:
/home/jona1883/software/American-Gut/ipynb/primary-processing/ag-May-31-2016/02-filtered/sequences-notrim.fna: 409208b8b5e4b249df376f55d4db5362
/home/jona1883/miniconda2/envs/AmericanGut/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta: 50b2269712b3738afb41892bed936c29
/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-May-31-2016/02-filtered/sequences-notrim.fna -o /home/jona1883/software/American-Gut/ipynb/primary-processing/ag-May-31-2016/03-otus/notrim/gg-13_8-97-percent/sortmerna_picked_otus -r /home/jona1883/miniconda2/envs/AmericanGut/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta -m sortmerna --threads 28 --otu_picking_method sortmerna --sortmerna_db /home/jona1883/software/gg_otus-13_8-release/sortmerna/97_otus.idx --suppress_new_clusters

Stdout:

Stderr:

# Make OTU table command 
make_otu_table.py -i /home/jona1883/software/American-Gut/ipynb/primary-processing/ag-May-31-2016/03-otus/notrim/gg-13_8-97-percent/sortmerna_picked_otus/sequences-notrim_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-May-31-2016/03-otus/notrim/gg-13_8-97-percent/otu_table.biom 

Stdout:

Stderr:


Logging stopped at 16:50:02 on 31 May 2016