-

[yvbaeza@class07 qiime-tutorial]$ sh -xe  commands.sh 
+ module load qiime
++ /bioware/modulecmd//Modules/3.2.6/bin/modulecmd bash load qiime
+ eval
+ validate_mapping_file.py -m map.tsv -o validated
Errors and/or warnings detected in mapping file.  Please check the log and html file for details.

real	0m2.034s
user	0m1.179s
sys	0m0.212s
+ filter_otus_from_otu_table.py -i otu_table.biom -o filtered-table.biom -n 25

real	0m2.055s
user	0m1.453s
sys	0m0.239s
+ single_rarefaction.py -i filtered-table.biom -o filtered-table.even1000.biom -d 1000

real	0m1.962s
user	0m1.357s
sys	0m0.234s
+ summarize_taxa_through_plots.py -i filtered-table.even1000.biom -o taxa_summaries/

real	1m3.291s
user	0m59.079s
sys	0m2.515s
+ alpha_diversity.py -i filtered-table.even1000.biom -o alpha.txt -t 97_otus.tree

real	0m18.253s
user	0m17.226s
sys	0m0.379s
+ add_alpha_to_mapping_file.py -i alpha.txt -m map.tsv -o map.alpha.tsv

real	0m1.628s
user	0m1.087s
sys	0m0.195s
+ beta_diversity_through_plots.py -i filtered-table.even1000.biom -m map.alpha.tsv -o beta -t 97_otus.tree
/class/stamps-software/miniconda/lib/python2.7/site-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 -0.0343282674844 and the largest is 5.68842937733.
  RuntimeWarning
/class/stamps-software/miniconda/lib/python2.7/site-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 -0.00220993891902 and the largest is 2.91800120783.
  RuntimeWarning

real	0m45.436s
user	0m39.500s
sys	0m1.835s
+ group_significance.py -i filtered-table.even1000.biom -m map.tsv -c sample_type -o gs_sampletype.txt

real	0m2.227s
user	0m1.677s
sys	0m0.177s
+ differential_abundance.py -i otu_table.biom -o diff_otus.txt -m map.tsv -a DESeq2_nbinom -c sample_type -x gut -y tongue -d

real	0m47.770s
user	0m46.579s
sys	0m0.652s