alpha_diversity.py -i some.biom -m observed_species,shannon,chao1,simpson,ace,goods_coverage
在运行时报错
File "/share/work/biosoft/python/Python-v2.7.11/lib/python2.7/site-p...
alpha_diversity.py -i some.biom -m observed_species,shannon,chao1,simpson,ace,goods_coverage
在运行时报错
File "/share/work/biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/scikit_bio-0.2.3-py2.7-linux-x86_64.egg/skbio/diversity/alpha/_ace.py", line 70, in ace
raise ValueError("The only rare OTUs are singletons, so the ACE "
ValueError: The only rare OTUs are singletons, so the ACE metric is undefined. EstimateS suggests using bias-corrected Chao1 instead.
这是因为ace指数通过那些稀有otu来估计整个群落的物种数,但是如果所有的稀有otu都是单例 的(即只测到了一个)那就无法使用ace 的计算方法,只使用chao1就好
