Logging started at 21:34:42 on 14 Mar 2012
QIIME version: 1.4.0-dev, svn revision 2835

qiime_config values:
blastmat_dir	/Applications/blast-2.2.22/data/
topiaryexplorer_project_dir	/Users/caporaso/code/TopiaryExplorer-0.9.1/
pynast_template_alignment_fp	/Users/caporaso/data/greengenes_core_sets/core_set_aligned_imputed.fasta_11_8_07.no_dots
cluster_jobs_fp	/Users/caporaso/code/Qiime/scripts/start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/Users/caporaso/data/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/Users/caporaso/data/greengenes_core_sets/lanemask_in_1s_and_0s.txt
jobs_to_start	2
cloud_environment	False
qiime_scripts_dir	/Users/caporaso/code/Qiime/scripts
denoiser_min_per_core	50
python_exe_fp	python
temp_dir	/Users/caporaso/temp
blastall_fp	blastall
seconds_to_sleep	6
assign_taxonomy_id_to_taxonomy_fp	/Users/caporaso/data/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt

parameter file values:
parallel:jobs_to_start	2

Input file md5 sums:
/Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/seqs.fna: e5e7fe1c3112f7655114702343c5fe54

Executing commands.

# Pick OTUs command 
python /Users/caporaso/code/Qiime/scripts/pick_otus.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/seqs.fna -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//uclust_picked_otus 

Stdout:

Stderr:

# Pick representative set command 
python /Users/caporaso/code/Qiime/scripts/pick_rep_set.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//uclust_picked_otus/seqs_otus.txt -f /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/seqs.fna -l /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set//seqs_rep_set.log -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set//seqs_rep_set.fasta 

Stdout:

Stderr:

# Assign taxonomy command 
python /Users/caporaso/code/Qiime/scripts/assign_taxonomy.py -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rdp_assigned_taxonomy -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set//seqs_rep_set.fasta 

Stdout:

Stderr:

# Make OTU table command 
python /Users/caporaso/code/Qiime/scripts/make_otu_table.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//uclust_picked_otus/seqs_otus.txt -t /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//otu_table.biom 

Stdout:

Stderr:

# Align sequences command 
python /Users/caporaso/code/Qiime/scripts/align_seqs.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set//seqs_rep_set.fasta -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//pynast_aligned_seqs 

Stdout:

Stderr:

# Filter alignment command 
python /Users/caporaso/code/Qiime/scripts/filter_alignment.py -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//pynast_aligned_seqs -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//pynast_aligned_seqs/seqs_rep_set_aligned.fasta 

Stdout:

Stderr:

# Build phylogenetic tree command 
python /Users/caporaso/code/Qiime/scripts/make_phylogeny.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set.tre 

Stdout:

Stderr:


Logging stopped at 21:36:13 on 14 Mar 2012
