Logging started at 08:05:51 on 04 Apr 2013
QIIME version: 1.6.0-dev

qiime_config values:
blastmat_dir	/Applications/blast-2.2.22/data/
sc_queue	all.q
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	start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/Users/caporaso/data/gg_12_10_otus/rep_set/97_otus.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/Users/caporaso/data/greengenes_core_sets/lanemask_in_1s_and_0s.txt
jobs_to_start	4
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	1
assign_taxonomy_id_to_taxonomy_fp	/Users/caporaso/data/gg_12_10_otus/taxonomy/97_otu_taxonomy.txt

parameter file values:
parallel:jobs_to_start	4
pick_otus:otu_picking_method	usearch_ref
pick_otus:suppress_reference_chimera_detection	True

Input file md5 sums:
/Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/seqs.fna: e5e7fe1c3112f7655114702343c5fe54
/Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/refseqs.fna: 54d38db8a909a129a2729e2111b9adb0
/Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/taxa.txt: 5736d521cff9cbe17e00617e2b15122a

Forcing --suppress_new_clusters as this is reference-based OTU picking.

Executing commands.

# Pick OTUs command 
python /Users/caporaso/code/Qiime/scripts/pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/seqs.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/otus_usearch//usearch_ref_picked_otus -r /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/refseqs.fna -m usearch_ref --otu_picking_method usearch_ref --suppress_reference_chimera_detection --suppress_new_clusters

Stdout:

Stderr:

# Make OTU table command 
python /Users/caporaso/code/Qiime/scripts/make_otu_table.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/otus_usearch//usearch_ref_picked_otus/seqs_otus.txt -t /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/taxa.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/otus_usearch//otu_table.biom 

Stdout:

Stderr:


Logging stopped at 08:05:54 on 04 Apr 2013
