Logging started at 08:04:11 on 07 Dec 2017
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp	/anaconda2/envs/qiime1/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	/anaconda2/envs/qiime1/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	/anaconda2/envs/qiime1/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	/anaconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/var/folders/8f/y12y4srx5z3gww29gc5kqdwm0000gn/T/
blastall_fp	blastall
seconds_to_sleep	1

parameter file values:
parallel:jobs_to_start	1

Input file md5 sums:
GSCID_Seqs_4Nauder.fna: 013db75ecc217dec49d203dc2fef477e

Executing commands.

# Pick OTUs command 
pick_otus.py -i GSCID_Seqs_4Nauder.fna -o ./qiime_output/uclust_picked_otus 

Stdout:

Stderr:

# Pick representative set command 
pick_rep_set.py -i ./qiime_output/uclust_picked_otus/GSCID_Seqs_4Nauder_otus.txt -f GSCID_Seqs_4Nauder.fna -l ./qiime_output/rep_set//GSCID_Seqs_4Nauder_rep_set.log -o ./qiime_output/rep_set//GSCID_Seqs_4Nauder_rep_set.fasta 

Stdout:

Stderr:

# Assign taxonomy command 
assign_taxonomy.py -o ./qiime_output/uclust_assigned_taxonomy -i ./qiime_output/rep_set//GSCID_Seqs_4Nauder_rep_set.fasta 

Stdout:

Stderr:

# Make OTU table command 
make_otu_table.py -i ./qiime_output/uclust_picked_otus/GSCID_Seqs_4Nauder_otus.txt -t ./qiime_output/uclust_assigned_taxonomy/GSCID_Seqs_4Nauder_rep_set_tax_assignments.txt -o ./qiime_output/otu_table.biom 

Stdout:

Stderr:

# Align sequences command 
align_seqs.py -i ./qiime_output/rep_set//GSCID_Seqs_4Nauder_rep_set.fasta -o ./qiime_output/pynast_aligned_seqs 

Stdout:

Stderr:

# Filter alignment command 
filter_alignment.py -o ./qiime_output/pynast_aligned_seqs -i ./qiime_output/pynast_aligned_seqs/GSCID_Seqs_4Nauder_rep_set_aligned.fasta 

Stdout:

Stderr:

# Build phylogenetic tree command 
make_phylogeny.py -i ./qiime_output/pynast_aligned_seqs/GSCID_Seqs_4Nauder_rep_set_aligned_pfiltered.fasta -o ./qiime_output/rep_set.tre 

Stdout:

Stderr:


Logging stopped at 10:12:52 on 07 Dec 2017