Hi,
When running, ‘qiime diversity alpha-rarefaction’ I get the following error when I pass this command along with my metadata file:
'Plugin error from diversity:
‘labels [‘std’ ‘mean’] not contained in axis’
I’ve checked my metadata with Keemei and all is well, any thoughts?
Thanks
–L
Hi @Lorinda! In order for us to help you, can you please provide the following:
--verbose output, or attach the log file)?Thanks! 
Yes, here you go @thermokarst :
1. System versions
Python version: 3.5.4
QIIME 2 release: 2017.8
QIIME 2 version: 2017.8.0
q2cli version: 2017.8.0
2. Command:
qiime diversity alpha-rarefaction
--i-table table-NoContams.qza
--p-max-depth 1000
--m-metadata-file metadata-ASSP-Gradient-Foliar.txt
--o-visualization Rarefaction-Curve
3. Log File
Traceback (most recent call last):
File "/Users/lbullington/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/commands.py", line 222, in call
results = action(**arguments)
File "", line 2, in alpha_rarefaction
File "/Users/lbullington/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 201, in callable_wrapper
output_types, provenance)
File "/Users/lbullington/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 392, in callable_executor
ret_val = callable(output_dir=temp_dir, **view_args)
File "/Users/lbullington/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_diversity/_alpha/_visualizer.py", line 326, in alpha_rarefaction
c_df = _compute_summary(reindexed_df, category, counts=counts)
File "/Users/lbullington/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_diversity/_alpha/_visualizer.py", line 219, in _compute_summary
summary_df.drop(['std', 'mean'], axis=1, inplace=True)
File "/Users/lbullington/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/pandas/core/generic.py", line 2161, in drop
new_axis = axis.drop(labels, errors=errors)
File "/Users/lbullington/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/pandas/core/indexes/base.py", line 3624, in drop
labels[mask])
ValueError: labels ['std' 'mean'] not contained in axis
4. Metadata Sample
Wow! Thanks for the great followup @Lorinda! Something certainly seems a bit 
y here on the QIIME 2 side of things.
Can I ask for a few more pieces on information?
conda list, when run in an activate QIIME 2 conda environmentpip freeze, when run in an activate QIIME 2 conda environmentI am wondering if you have a different version of pandas somehow installed in this environment (or really any other third-party dependency). Thanks!
@thermokarst, thanks for your time! I hope this helps, its a bit over my head at this point…
Output from conda list:
# packages in environment at /Users/lbullington/miniconda3/envs/qiime2-2017.8:
#
appnope 0.1.0 py35_0
bioconductor-biobase 2.34.0 r3.3.1_0 bioconda
bioconductor-biocgenerics 0.20.0 r3.3.1_0 bioconda
bioconductor-biocparallel 1.6.6 r3.3.1_0 bioconda
bioconductor-biostrings 2.42.1 r3.3.1_0 bioconda
bioconductor-dada2 1.4.0 r3.3.1_0 bioconda
bioconductor-genomeinfodb 1.10.3 r3.3.1_0 bioconda
bioconductor-genomicalignments 1.8.4 r3.3.1_0 bioconda
bioconductor-genomicranges 1.26.4 r3.3.1_0 bioconda
bioconductor-iranges 2.8.2 r3.3.1_0 bioconda
bioconductor-rsamtools 1.24.0 r3.3.1_0 bioconda
bioconductor-s4vectors 0.12.2 r3.3.1_0 bioconda
bioconductor-shortread 1.32.0 r3.3.1_0 bioconda
bioconductor-summarizedexperiment 1.2.3 r3.3.1_0 bioconda
bioconductor-xvector 0.14.1 r3.3.1_0 bioconda
bioconductor-zlibbioc 1.20.0 r3.3.1_0 bioconda
biom-format 2.1.5 py35_3 qiime2
bkcharts 0.2 py35_0
blast 2.6.0 boost1.61_1 bioconda
bleach 1.5.0 py35_0
bokeh 0.12.7 py35_0
cachecontrol 0.12.3 py35_0
click 6.7 py35_0
curl 7.54.1 0
cycler 0.10.0 py35_0
deblur 1.0.2 py35_0 biocore
decorator 4.1.2 py35_0
emperor 1.0.0beta8 py35_2 conda-forge
entrypoints 0.2.3 py35_0
fastcluster 1.1.23 np113py35_0 conda-forge
fasttree 2.1.9 2 bioconda
freetype 2.5.5 2
future 0.16.0 py35_1
gneiss 0.4.1 py35ha7bfd4e_6 biocore
gsl 2.2.1 0
h5py 2.7.0 np113py35_0
hdf5 1.8.17 2
html5lib 0.9999999 py35_0
icu 54.1 0
ijson 2.3 py35_0 qiime2
ipykernel 4.6.1 py35_0
ipython 6.1.0 py35_0
ipython_genutils 0.2.0 py35_0
ipywidgets 6.0.0 py35_0
jbig 2.1 0
jedi 0.10.2 py35_2
jinja2 2.9.6 py35_0
jpeg 9b 0
jsonschema 2.6.0 py35_0
jupyter_client 5.1.0 py35_0
jupyter_core 4.3.0 py35_0
krb5 1.13.2 0
libgcc 4.8.5 1
libiconv 1.14 0
libpng 1.6.30 1
libssh2 1.8.0 0
libtiff 4.0.6 3
libxml2 2.9.4 0
lockfile 0.12.2 py35_0
mafft 7.221 0 bioconda
markupsafe 1.0 py35_0
matplotlib 2.0.2 np113py35_0
mistune 0.7.4 py35_0
mkl 2017.0.3 0
msgpack-python 0.4.8 py35_0
natsort 5.1.0 py35_0
nbconvert 5.2.1 py35_0
nbformat 4.4.0 py35_0
ncurses 5.9 10
nose 1.3.7 py35_1
notebook 5.0.0 py35_0
numpy 1.13.1 py35_0
openssl 1.0.2l 0
pandas 0.20.3 py35_0
pandocfilters 1.4.2 py35_0
path.py 10.3.1 py35_0
patsy 0.4.1 py35_0
pcre 8.39 1
pexpect 4.2.1 py35_0
pickleshare 0.7.4 py35_0
pip 9.0.1 py35_1
prompt_toolkit 1.0.15 py35_0
psutil 5.2.2 py35_0
ptyprocess 0.5.2 py35_0
pygments 2.2.0 py35_0
pyparsing 2.2.0 py35_0
pyqt 5.6.0 py35_2
python 3.5.4 0
python-dateutil 2.6.1 py35_0
pytz 2017.2 py35_0
pyyaml 3.12 py35_0
pyzmq 16.0.2 py35_0
q2-alignment 2017.8.0 py35_0 qiime2/label/r2017.8
q2-composition 2017.8.0 py35_0 qiime2/label/r2017.8
q2-dada2 2017.8.0 py35_0 qiime2/label/r2017.8
q2-deblur 2017.8.0 py35_0 qiime2/label/r2017.8
q2-demux 2017.8.0 py35_0 qiime2/label/r2017.8
q2-diversity 2017.8.0 py35_0 qiime2/label/r2017.8
q2-emperor 2017.8.0 py35_0 qiime2/label/r2017.8
q2-feature-classifier 2017.8.0 py35_0 qiime2/label/r2017.8
q2-feature-table 2017.8.0 py35_0 qiime2/label/r2017.8
q2-gneiss 2017.8.0 py35_0 qiime2/label/r2017.8
q2-longitudinal 2017.8.0 py35_0 qiime2/label/r2017.8
q2-metadata 2017.8.0 py35_0 qiime2/label/r2017.8
q2-phylogeny 2017.8.0 py35_0 qiime2/label/r2017.8
q2-quality-filter 2017.8.0 py35_0 qiime2/label/r2017.8
q2-sample-classifier 2017.8.0 py35_0 qiime2/label/r2017.8
q2-taxa 2017.8.0 py35_0 qiime2/label/r2017.8
q2-types 2017.8.0 py35_0 qiime2/label/r2017.8
q2cli 2017.8.0 py35_0 qiime2/label/r2017.8
q2templates 2017.8.0 py35_0 qiime2/label/r2017.8
qiime2 2017.8.0 py35_0 qiime2/label/r2017.8
qt 5.6.2 2
r 3.3.1 r3.3.1_0
r-base 3.3.1 0
r-bh 1.60.0_2 r3.3.1_0
r-bitops 1.0_6 r3.3.1_2
r-boot 1.3_18 r3.3.1_0
r-chron 2.3_47 r3.3.1_0
r-class 7.3_14 r3.3.1_0
r-cluster 2.0.4 r3.3.1_0
r-codetools 0.2_14 r3.3.1_0
r-colorspace 1.2_6 r3.3.1_0
r-data.table 1.9.6 r3.3.1_0
r-dichromat 2.0_0 r3.3.1_2
r-digest 0.6.9 r3.3.1_0
r-foreign 0.8_66 r3.3.1_0
r-futile.logger 1.4.1 r3.3.1_0 bioconda
r-futile.options 1.0.0 r3.3.1_0 bioconda
r-ggplot2 2.1.0 r3.3.1_0
r-gtable 0.2.0 r3.3.1_0
r-hwriter 1.3.2 r3.3.1_0 bioconda
r-kernsmooth 2.23_15 r3.3.1_0
r-labeling 0.3 r3.3.1_2
r-lambda.r 1.1.7 r3.3.1_0 bioconda
r-lattice 0.20_33 r3.3.1_0
r-latticeextra 0.6_28 r3.3.1_0
r-magrittr 1.5 r3.3.1_2
r-mass 7.3_45 r3.3.1_0
r-matrix 1.2_6 r3.3.1_0
r-mgcv 1.8_12 r3.3.1_0
r-munsell 0.4.3 r3.3.1_0
r-nlme 3.1_128 r3.3.1_0
r-nnet 7.3_12 r3.3.1_0
r-plyr 1.8.4 r3.3.1_0
r-rcolorbrewer 1.1_2 r3.3.1_3
r-rcpp 0.12.5 r3.3.1_0
r-rcppparallel 4.3.20 r3.3.1_1 bioconda
r-rcurl 1.95_4.8 r3.3.1_0
r-recommended 3.3.1 r3.3.1_0
r-reshape2 1.4.1 1a
r-rpart 4.1_10 r3.3.1_0
r-scales 0.4.0 r3.3.1_0
r-snow 0.4_1 r3.3.1_0 bioconda
r-spatial 7.3_11 r3.3.1_0
r-stringi 1.1.1 r3.3.1_0
r-stringr 1.0.0 r3.3.1_0
r-survival 2.39_4 r3.3.1_0
readline 6.2 2
requests 2.14.2 py35_0
scikit-bio 0.5.1 np113py35_0
scikit-learn 0.19.0 np113py35_0
scipy 0.19.1 np113py35_0
seaborn 0.8 py35_0
setuptools 27.2.0 py35_0
simplegeneric 0.8.1 py35_1
sip 4.18 py35_0
six 1.10.0 py35_0
sortmerna 2.0 1 bioconda
sqlite 3.13.0 0
statsmodels 0.8.0 np113py35_0
terminado 0.6 py35_0
testpath 0.3.1 py35_0
tk 8.5.18 0
tornado 4.5.2 py35_0
traitlets 4.3.2 py35_0
tzlocal 1.3 py35_0 qiime2
vsearch 2.0.3 1 bioconda
wcwidth 0.1.7 py35_0
wheel 0.29.0 py35_0
widgetsnbextension 3.0.2 py35_0
xz 5.2.3 0
yaml 0.1.6 0
zlib 1.2.11 0
Output from pip freeze:
appnope==0.1.0
biom-format==2.1.5
bkcharts==0.2
bleach==1.5.0
bokeh==0.12.7
CacheControl==0.12.3
click==6.7
cycler==0.10.0
deblur==1.0.2
decorator==4.1.2
emperor==1.0.0b8
entrypoints==0.2.3
fastcluster==1.1.23
future==0.16.0
gneiss==0.4.1
h5py==2.7.0
html5lib==0.9999999
ijson==2.3
ipykernel==4.6.1
ipython==6.1.0
ipython-genutils==0.2.0
ipywidgets==6.0.0
jedi==0.10.2
Jinja2==2.9.6
jsonschema==2.6.0
jupyter-client==5.1.0
jupyter-core==4.3.0
lockfile==0.12.2
MarkupSafe==1.0
matplotlib==2.0.2
mistune==0.7.4
msgpack-python==0.4.8
natsort==5.1.0
nbconvert==5.2.1
nbformat==4.4.0
nose==1.3.7
notebook==5.0.0
numpy==1.13.1
pandas==0.20.3
pandocfilters==1.4.2
patsy==0.4.1
pexpect==4.2.1
pickleshare==0.7.4
prompt-toolkit==1.0.15
psutil==5.2.2
ptyprocess==0.5.2
Pygments==2.2.0
pyparsing==2.2.0
python-dateutil==2.6.1
pytz==2017.2
PyYAML==3.12
pyzmq==16.0.2
q2-alignment==2017.8.0
q2-composition==2017.8.0
q2-dada2==2017.8.0
q2-deblur==2017.8.0
q2-demux==2017.8.0
q2-diversity==2017.8.0
q2-emperor==2017.8.0
q2-feature-classifier==2017.8.0
q2-feature-table==2017.8.0
q2-gneiss==2017.8.0
q2-longitudinal==2017.8.0
q2-metadata==2017.8.0
q2-phylogeny==2017.8.0
q2-quality-filter==2017.8.0
q2-sample-classifier==2017.8.0
q2-taxa==2017.8.0
q2-types==2017.8.0
q2cli==2017.8.0
q2templates==2017.8.0
qiime2==2017.8.0
requests==2.14.2
scikit-bio==0.5.1
scikit-learn==0.19.0
scipy==0.19.1
seaborn==0.8
simplegeneric==0.8.1
six==1.10.0
statsmodels==0.8.0
terminado==0.6
testpath==0.3
tornado==4.5.2
traitlets==4.3.2
tzlocal==1.3
wcwidth==0.1.7
widgetsnbextension==3.0.2
Bummer, I was hoping something would jump out at me here, but this all looks just as expected 
.
Would it be possible for you to share your files (table-NoContams.qza and metadata-ASSP-Gradient-Foliar.txt) with me in a direct message? Without those files I am unsure as to how I can attempt to recreate this error! Thanks!
@thermokarst Sure, I should also mention that alpha rarefaction does work when I omit the metadata file.
Thanks for sharing your data via DM @Lorinda! I think I found the problem - the column Treatment is entirely empty, and the alpha-rarefaction viz doesn’t handle itself well in this case (note: bug report here!). In the meantime, if you just delete the Treatment column, you should be good to go (this worked fine for me when testing locally). Let me know how it goes, and thanks for your patience!!!
Hey @thermokarst I’m not sure I follow you. The description column is populated with ‘gradient’, at least as I see it when I open it up in excel and google sheets, and validating using Keemei. I did try deleting this column though, and still am getting the same error. Maybe you can send me a copy of the metadata that you got to work?
Sorry, I meant the column labeled Treatment - I have edited the above comment to reflect the correct column name!
@thermokarst, It worked! 
So for future reference, alpha rarefaction will not work if your metadata file contains a column filled entirely with ‘NA’. Thanks so much for your time on this.
The jury is still out on that - perhaps we just don't try and plot the rarefaction curves for that category/column (and show some kind of warning in the viz); or else maybe this is enforced at a higher level - maybe QIIME 2 won't accept any metadata with an empty column? But in the near term, yeah, you should probably just drop any empty columns (I guess there is a higher level question in play here, too --- what does it even mean to have an empty category?)
Thanks so much for sticking with us through this!
There’s a bug fix in the 2017.9 release that ignores empty metadata columns and lists the ignored columns in the output visualization! 
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