Logging started at 01:39:18 on 20 Apr 2016
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp	/macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue	all.q
topiaryexplorer_project_dir	~/Downloads/te_1.0/
pynast_template_alignment_fp	/macqiime/anaconda/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	/macqiime/anaconda/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	/macqiime/anaconda/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	60

parameter file values:
parallel:jobs_to_start	1
pick_otus:otu_picking_method	swarm

Input file md5 sums:
uninhabited_habitats/split_libraries_fastq_uninhab/seqs.fna: 270782d29b44fbf4b3b297e2d4d4db84

Executing commands.

# Pick OTUs command 
pick_otus.py -i uninhabited_habitats/split_libraries_fastq_uninhab/seqs.fna -o uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/swarm_picked_otus --otu_picking_method swarm

Stdout:

Stderr:

# Pick representative set command 
pick_rep_set.py -i uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/swarm_picked_otus/seqs_otus.txt -f uninhabited_habitats/split_libraries_fastq_uninhab/seqs.fna -l uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/rep_set//seqs_rep_set.log -o uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/rep_set//seqs_rep_set.fasta 

Stdout:

Stderr:

# Assign taxonomy command 
assign_taxonomy.py -o uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/uclust_assigned_taxonomy -i uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/rep_set//seqs_rep_set.fasta 

Stdout:

Stderr:

# Make OTU table command 
make_otu_table.py -i uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/swarm_picked_otus/seqs_otus.txt -t uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/uclust_assigned_taxonomy/seqs_rep_set_tax_assignments.txt -o uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/otu_table.biom 

Stdout:

Stderr:

# Align sequences command 
align_seqs.py -i uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/rep_set//seqs_rep_set.fasta -o uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/pynast_aligned_seqs 

Stdout:

Stderr:

# Filter alignment command 
filter_alignment.py -o uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/pynast_aligned_seqs -i uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/pynast_aligned_seqs/seqs_rep_set_aligned.fasta 

Stdout:

Stderr:

# Build phylogenetic tree command 
make_phylogeny.py -i uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta -o uninhabited_habitats/Silva119_denovo_splitfastq_uninhab_swarm3/rep_set.tre 

Stdout:

Stderr:


Logging stopped at 01:57:00 on 20 Apr 2016