Logging started at 00:36:28 on 14 Jan 2018
QIIME version: 1.9.1

qiime_config values:
blastmat_dir	/qiime_software/blast-2.2.22-release/data
pick_otus_reference_seqs_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue	all.q
pynast_template_alignment_fp	/usr/local/lib/python2.7/dist-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	/usr/local/lib/python2.7/dist-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	/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/tmp/
blastall_fp	/qiime_software/blast-2.2.22-release/bin/blastall
seconds_to_sleep	1

parameter file values:
parallel:jobs_to_start	1

Input file md5 sums:
Termite_combined_sequences/combined_seqs.fna: c78eb86460414707847c67d264a4f65e

Executing commands.

# Pick OTUs command 
pick_otus.py -i Termite_combined_sequences/combined_seqs.fna -o Termite_otus/uclust_picked_otus 

Stdout:

Stderr:

# Pick representative set command 
pick_rep_set.py -i Termite_otus/uclust_picked_otus/combined_seqs_otus.txt -f Termite_combined_sequences/combined_seqs.fna -l Termite_otus/rep_set//combined_seqs_rep_set.log -o Termite_otus/rep_set//combined_seqs_rep_set.fasta 

Stdout:

Stderr:

# Assign taxonomy command 
assign_taxonomy.py -o Termite_otus/uclust_assigned_taxonomy -i Termite_otus/rep_set//combined_seqs_rep_set.fasta 

Stdout:

Stderr:

# Make OTU table command 
make_otu_table.py -i Termite_otus/uclust_picked_otus/combined_seqs_otus.txt -t Termite_otus/uclust_assigned_taxonomy/combined_seqs_rep_set_tax_assignments.txt -o Termite_otus/otu_table.biom 

Stdout:

Stderr:

# Align sequences command 
align_seqs.py -i Termite_otus/rep_set//combined_seqs_rep_set.fasta -o Termite_otus/pynast_aligned_seqs 

Stdout:

Stderr:

# Filter alignment command 
filter_alignment.py -o Termite_otus/pynast_aligned_seqs -i Termite_otus/pynast_aligned_seqs/combined_seqs_rep_set_aligned.fasta 

Stdout:

Stderr:

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

Stdout:

Stderr:


Logging stopped at 02:07:55 on 14 Jan 2018