# Alpha rarefaction plugin error

**URL:** <https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282>\
**Category:** User Support\
**Tags:** alpha-rarefaction\
**Created:** [September 19, 2017, 4:32pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282 "2017-09-19T16:32:30Z")\
**Posts on this page:** 14\
**Page:** 1

<div class="post-metadata">

**Author:** ![Lorinda](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lorinda/32/5966_2.png) [@Lorinda](https://forum.qiime2.org/u/Lorinda)\
**Post date:** [September 19, 2017, 4:32pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/1 "2017-09-19T16:32:30Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\
**Post date:** [September 19, 2017, 5:01pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/3 "2017-09-19T17:01:35Z")

</div>

Hi @Lorinda! In order for us to help you, can you please provide the following:

1. What version of QIIME 2 are you using?
2. What was the exact command you ran (copy-and-paste)?
3. What was the complete error you saw (copy and paste the `--verbose` output, or attach the `log` file)?
4. Can you provide a sample of your metadata file?

Thanks! 🦖

---

<div class="post-metadata">

**Author:** ![Lorinda](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lorinda/32/5966_2.png) [@Lorinda](https://forum.qiime2.org/u/Lorinda)\
**Post date:** [September 19, 2017, 5:10pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/4 "2017-09-19T17:10:45Z")

</div>

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

- I tried multiple sampling depths

**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**

 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/1X/71c12b0aec8c5a11045fd079702a6e2377f37779.png)

---

<div class="post-metadata">

**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\
**Post date:** [September 19, 2017, 8:36pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/5 "2017-09-19T20:36:03Z")

</div>

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?

- The output from the command `conda list`, when run in an activate QIIME 2 conda environment
- The output from the command `pip freeze`, when run in an activate QIIME 2 conda environment

I am wondering if you have a different version of `pandas` somehow installed in this environment (or really any other third-party dependency). Thanks!

---

<div class="post-metadata">

**Author:** ![Lorinda](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lorinda/32/5966_2.png) [@Lorinda](https://forum.qiime2.org/u/Lorinda)\
**Post date:** [September 19, 2017, 8:43pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/7 "2017-09-19T20:43:35Z")

</div>

@thermokarst, thanks for your time! I hope this helps, its a bit over my head at this point...

**Output from conda list:**

```bash
# 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:**

```bash
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

```

---

<div class="post-metadata">

**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\
**Post date:** [September 19, 2017, 8:52pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/9 "2017-09-19T20:52:56Z")

</div>

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! 🦖

---

<div class="post-metadata">

**Author:** ![Lorinda](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lorinda/32/5966_2.png) [@Lorinda](https://forum.qiime2.org/u/Lorinda)\
**Post date:** [September 19, 2017, 8:55pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/10 "2017-09-19T20:55:38Z")

</div>

@thermokarst Sure, I should also mention that alpha rarefaction does work when I omit the metadata file.

---

<div class="post-metadata">

**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\
**Post date:** [September 19, 2017, 9:42pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/11 "2017-09-19T21:42:51Z")

</div>

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!](https://github.com/qiime2/q2-diversity/issues/141)). 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!!!!

---

<div class="post-metadata">

**Author:** ![Lorinda](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lorinda/32/5966_2.png) [@Lorinda](https://forum.qiime2.org/u/Lorinda)\
**Post date:** [September 19, 2017, 9:56pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/13 "2017-09-19T21:56:12Z")

</div>

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?

---

<div class="post-metadata">

**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\
**Post date:** [September 19, 2017, 9:59pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/14 "2017-09-19T21:59:59Z")

</div>

Sorry, I meant the column labeled `Treatment` - I have edited the above comment to reflect the correct column name!

---

<div class="post-metadata">

**Author:** ![Lorinda](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lorinda/32/5966_2.png) [@Lorinda](https://forum.qiime2.org/u/Lorinda)\
**Post date:** [September 19, 2017, 10:03pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/15 "2017-09-19T22:03:45Z")

</div>

@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.

---

<div class="post-metadata">

**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\
**Post date:** [September 19, 2017, 10:08pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/16 "2017-09-19T22:08:30Z")

</div>

> [@Lorinda](#):
>
> So for future reference, alpha rarefaction will not work if your metadata file contains a column filled entirely with ‘NA’.

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!

---

<div class="post-metadata">

**Author:** ![jairideout](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jairideout/32/9_2.png) [@jairideout](https://forum.qiime2.org/u/jairideout)\
**Post date:** [September 29, 2017, 7:29pm UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/20 "2017-09-29T19:29:31Z")

</div>

There's a bug fix in the 2017.9 release that ignores empty metadata columns and lists the ignored columns in the output visualization! 🎉

---

<div class="post-metadata">

**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\
**Post date:** [October 31, 2017, 1:29am UTC](https://forum.qiime2.org/t/alpha-rarefaction-plugin-error/1282/22 "2017-10-31T01:29:37Z")

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