Logging started at 10:05:38 on 14 May 2018
QIIME version: 1.8.0

qiime_config values:
blastmat_dir	/home/worker/software/qiime-1.8/blast-2.2.22-release/data
sc_queue	all.q
pynast_template_alignment_fp	/home/worker/software/qiime-1.8/core_set_aligned.fasta.imputed
cluster_jobs_fp	/home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/home/worker/software/qiime-1.8/gg_otus-13_8-release/rep_set/97_otus.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/home/worker/software/qiime-1.8/lanemask_in_1s_and_0s
jobs_to_start	1
cloud_environment	False
qiime_scripts_dir	/home/worker/software/qiime-1.8/qiime-1.8.0-release/bin
denoiser_min_per_core	50
working_dir	/tmp/
python_exe_fp	/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python
temp_dir	/tmp/
blastall_fp	/home/worker/software/qiime-1.8/blast-2.2.22-release/bin/blastall
seconds_to_sleep	60
assign_taxonomy_id_to_taxonomy_fp	/home/worker/software/qiime-1.8/gg_otus-13_8-release/taxonomy/97_otu_taxonomy.txt

parameter file values:
beta_diversity:metrics	bray_curtis,spearman_approx,unweighted_unifrac,weighted_unifrac,pearson
alpha_diversity:metrics	chao1,PD_whole_tree,observed_species,shannon,simpson
parallel:jobs_to_start	8

Input file md5 sums:
otus/otu_table.biom: a9e246f919f99b9b4a53cd0f4e3596c7
mapping.txt: 2f7eab2cc48e3903ebc192c122eac5b2
otus/rep_set.tre: c3cf7bff9c9714c39827a9d33fad9fe9

Executing commands.

# Alpha rarefaction command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_multiple_rarefactions.py -T -i otus/otu_table.biom -m 10 -x 26404 -s 2639 -o rarefaction/rarefaction/  --jobs_to_start 8

Stdout:

Stderr:

# Alpha diversity on rarefied OTU tables command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/parallel_alpha_diversity.py -T -i rarefaction/rarefaction/ -o rarefaction/alpha_div/ --metrics chao1,PD_whole_tree,observed_species,shannon,simpson -t otus/rep_set.tre --jobs_to_start 8

Stdout:

Stderr:

# Collate alpha command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/collate_alpha.py -i rarefaction/alpha_div/ -o rarefaction/alpha_div_collated/ 

Stdout:

Stderr:

# Removing intermediate files command 
rm -r rarefaction/rarefaction/ rarefaction/alpha_div/

Stdout:

Stderr:

# Rarefaction plot: All metrics command 
/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python /home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/make_rarefaction_plots.py -i rarefaction/alpha_div_collated/ -m mapping.txt -o rarefaction/alpha_rarefaction_plots/ 

Stdout:

Stderr:


Logging stopped at 10:10:05 on 14 May 2018
