Logging started at 10:03:27 on 06 Aug 2016
QIIME version: 1.9.1

qiime_config values:
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	blastall
seconds_to_sleep	1

parameter file values:
beta_diversity:metrics	unweighted_unifrac,weighted_unifrac,bray_curtis
parallel:jobs_to_start	1

Input file md5 sums:
/home/gerben/qiime/wo_linker/Reference_and_sequenced_data.biom: 178781d0b7151e760dc6d84db767ac72
/home/gerben/qiime/mapping_all.txt: 4ef52b4d855c9558e653fa6b4d20a00f
/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/trees/97_otus.tree: b7e76593bce82913af1cfb06edf15732

Executing commands.

# Sample OTU table at 10000 seqs/sample command 
single_rarefaction.py -i /home/gerben/qiime/wo_linker/Reference_and_sequenced_data.biom -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/Reference_and_sequenced_data_even10000.biom -d 10000

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
beta_diversity.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/Reference_and_sequenced_data_even10000.biom -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data --metrics unweighted_unifrac  -t /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/trees/97_otus.tree 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac) command 
mv /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/unweighted_unifrac_Reference_and_sequenced_data_even10000.txt /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
principal_coordinates.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/unweighted_unifrac_dm.txt -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/unweighted_unifrac_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0277055996081 and the largest is 7.97257587461.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/unweighted_unifrac_pc.txt -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/unweighted_unifrac_emperor_pcoa_plot/ -m /home/gerben/qiime/mapping_all.txt 

Stdout:

Stderr:

# Beta Diversity (weighted_unifrac) command 
beta_diversity.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/Reference_and_sequenced_data_even10000.biom -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data --metrics weighted_unifrac  -t /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/trees/97_otus.tree 

Stdout:

Stderr:

# Rename distance matrix (weighted_unifrac) command 
mv /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/weighted_unifrac_Reference_and_sequenced_data_even10000.txt /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
principal_coordinates.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/weighted_unifrac_dm.txt -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/weighted_unifrac_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0956262722079 and the largest is 3.07869223581.
  RuntimeWarning

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/weighted_unifrac_pc.txt -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/weighted_unifrac_emperor_pcoa_plot/ -m /home/gerben/qiime/mapping_all.txt 

Stdout:

Stderr:

# Beta Diversity (bray_curtis) command 
beta_diversity.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/Reference_and_sequenced_data_even10000.biom -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data --metrics bray_curtis  -t /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/trees/97_otus.tree 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2641: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

# Rename distance matrix (bray_curtis) command 
mv /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/bray_curtis_Reference_and_sequenced_data_even10000.txt /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/bray_curtis_dm.txt

Stdout:

Stderr:

# Principal coordinates (bray_curtis) command 
principal_coordinates.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/bray_curtis_dm.txt -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/bray_curtis_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0661095770733 and the largest is 11.9545036838.
  RuntimeWarning

# Make emperor plots, bray_curtis) command 
make_emperor.py -i /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/bray_curtis_pc.txt -o /home/gerben/qiime/wo_linker/beta_div_even10000_reference_and_sequenced_data/bray_curtis_emperor_pcoa_plot/ -m /home/gerben/qiime/mapping_all.txt 

Stdout:

Stderr:


Logging stopped at 10:04:12 on 06 Aug 2016
