Name 'EMPPairedEndSequences' is not a defined QIIME type?

Hi there!

A totally newbie to qiime2, and here is probably a very rudimentary question. I kept running into this error message when importing tutorial data. Any one knows how to fix this problem? Thanks!

(qiime2-2017.12) Hes-iMac:~ he$ qiime tools import \

–type EMPPairedEndSequences
–input-path emp-paired-end-sequences
–output-path emp-paired-end-sequences.qza
Traceback (most recent call last):
File “/Users/he/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/util.py”, line 62, in parse_type
type_expr = eval(string, {‘builtins’: {}}, locals_)
File “”, line 1, in
NameError: name ‘EMPPairedEndSequences’ is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Users/he/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/tools.py”, line 116, in import_data
view_type=source_format)
File “/Users/he/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 177, in import_data
type_ = qiime2.sdk.parse_type(type_)
File “/Users/he/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/util.py”, line 82, in parse_type
" may be needed to define it." % name)
qiime2.sdk.util.UnknownTypeError: Name ‘EMPPairedEndSequences’ is not a defined QIIME type, a plugin may be needed to define it.

An unexpected error has occurred:

Name ‘EMPPairedEndSequences’ is not a defined QIIME type, a plugin may be needed to define it.

See above for debug info.

Hi @Andrew! That is strange! It looks like your installation might be incomplete. Can you run the following commands, and provide their full output (after activating your QIIME 2 environment)?

$ qiime info
$ conda list

Thanks! :t_rex:

Hi! Sure thing.

Here are the output:

1. (qiime2-2017.12) Hes-iMac:~ he$ qiime info
System versions
Python version: 3.5.4
QIIME 2 release: 2017.12
QIIME 2 version: 2017.12.1
q2cli version: 2017.12.0

Installed plugins
No plugins are currently installed.
You can browse the official QIIME 2 plugins at https://qiime2.org

Application config directory
/Users/he/Library/Application Support/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME 2 and all installed plugins, run:

  qiime info --citations

2.(qiime2-2017.12) Hes-iMac:~ he$ conda list
# packages in environment at /Users/he/miniconda3/envs/qiime2-2017.12:
#
appnope                   0.1.0                    py35_0    conda-forge
asn1crypto                0.22.0                   py35_0    conda-forge
backports                 1.0                      py35_1    conda-forge
backports.functools_lru_cache 1.4                      py35_1    conda-forge
bioconductor-biocgenerics 0.24.0                 r3.4.1_0    bioconda
bioconductor-genomeinfodbdata 1.0.0                  r3.4.1_1    bioconda
bioconductor-zlibbioc     1.24.0                 r3.4.1_0    bioconda
biom-format               2.1.6                    py35_8    qiime2
blast                     2.6.0               boost1.64_2    bioconda
bleach                    2.0.0                    py35_0    conda-forge
bokeh                     0.12.13                  py35_0    conda-forge
ca-certificates           2017.11.5                     0    conda-forge
cairo                     1.14.6                        4    conda-forge
certifi                   2017.11.5                py35_0    conda-forge
cffi                      1.11.2                   py35_0    conda-forge
chardet                   3.0.4                    py35_0    conda-forge
clangdev                  5.0.0                 default_0    conda-forge
click                     6.7                        py_1    conda-forge
cryptography              2.1.4                    py35_0    conda-forge
curl                      7.54.1                        0    conda-forge
cutadapt                  1.15                     py35_0    bioconda
cycler                    0.10.0                   py35_0    conda-forge
cython                    0.27.3                   py35_0    conda-forge
decorator                 4.1.2                    py35_0    conda-forge
entrypoints               0.2.3                    py35_1    conda-forge
fastcluster               1.1.24                   py35_0    conda-forge
fasttree                  2.1.10                        0    bioconda
fontconfig                2.12.1                        6    conda-forge
freetype                  2.7                           1    conda-forge
future                    0.16.0                   py35_0    conda-forge
gettext                   0.19.8.1                      0    conda-forge
glib                      2.51.4                        0    conda-forge
graphite2                 1.3.10                        0    conda-forge
gsl                       2.1                           2    conda-forge
h5py                      2.7.0               np112py35_0    conda-forge
harfbuzz                  1.4.3                         0    conda-forge
hdf5                      1.8.17                       11    conda-forge
html5lib                  1.0.1                      py_0    conda-forge
icu                       58.2                          0    conda-forge
idna                      2.6                      py35_1    conda-forge
ijson                     2.3                      py35_0    qiime2
intel-openmp              2018.0.0             h8158457_8  
ipykernel                 4.7.0                    py35_0    conda-forge
ipython                   6.2.1                    py35_1    conda-forge
ipython_genutils          0.2.0                    py35_0    conda-forge
jedi                      0.10.2                   py35_0    conda-forge
jinja2                    2.10                     py35_0    conda-forge
jpeg                      9b                            2    conda-forge
jsonschema                2.6.0                    py35_0    conda-forge
jupyter_client            5.2.1                    py35_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
krb5                      1.14.2                        0    conda-forge
libcxx                    5.0.0                         0    conda-forge
libffi                    3.2.1                         3    conda-forge
libgcc                    4.8.5               hdbeacc1_10  
libgfortran               3.0.1                h93005f0_2  
libiconv                  1.15                          0    conda-forge
libpng                    1.6.28                        1    conda-forge
libsodium                 1.0.15                        1    conda-forge
libssh2                   1.8.0                         1    conda-forge
libtiff                   4.0.7                         0    conda-forge
libxml2                   2.9.5                         0    conda-forge
llvmdev                   5.0.0                 default_0    conda-forge
lockfile                  0.12.2                   py35_0    conda-forge
mafft                     7.310                         0    bioconda
markupsafe                1.0                      py35_0    conda-forge
matplotlib                2.1.1                    py35_0    conda-forge
mistune                   0.8.3                      py_0    conda-forge
mkl                       2018.0.1             hfbd8650_4  
msgpack-python            0.4.8                    py35_0    conda-forge
natsort                   5.0.2                    py35_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                    py35_0    conda-forge
ncurses                   5.9                          10    conda-forge
nose                      1.3.7                    py35_2    conda-forge
numpy                     1.12.1           py35h655160a_1  
openjdk                   8.0.121                       1  
openssl                   1.0.2n                        0    conda-forge
pandas                    0.22.0                   py35_0    conda-forge
pandoc                    2.1                           0    conda-forge
pandocfilters             1.4.1                    py35_0    conda-forge
pango                     1.40.4                        0    conda-forge
patsy                     0.5.0                    py35_0    conda-forge
pcre                      8.39                          0    conda-forge
pexpect                   4.3.1                    py35_0    conda-forge
pickleshare               0.7.4                    py35_0    conda-forge
pigz                      2.3.4                         0    conda-forge
pip                       9.0.1                    py35_1    conda-forge
pixman                    0.34.0                        1    conda-forge
prompt_toolkit            1.0.15                   py35_0    conda-forge
psutil                    5.4.0                    py35_0    conda-forge
ptyprocess                0.5.2                    py35_0    conda-forge
pycparser                 2.18                     py35_0    conda-forge
pygments                  2.2.0                    py35_0    conda-forge
pyopenssl                 17.4.0                   py35_0    conda-forge
pyparsing                 2.2.0                    py35_0    conda-forge
pysocks                   1.6.7                    py35_0    conda-forge
python                    3.5.4                         0    conda-forge
python-dateutil           2.6.1                    py35_0    conda-forge
pytz                      2017.3                     py_2    conda-forge
pyyaml                    3.12                     py35_1    conda-forge
pyzmq                     16.0.2                   py35_2    conda-forge
q2cli                     2017.12.0                py35_0    qiime2/label/r2017.12
q2templates               2017.12.0                py35_0    qiime2/label/r2017.12
qiime2                    2017.12.1                py35_0    qiime2/label/r2017.12
r-base                    3.4.1                         0    conda-forge
r-bh                      1.65.0_1               r3.4.1_0    conda-forge
readline                  6.2                           0    conda-forge
scikit-learn              0.19.1           py35h2b554eb_0  
scipy                     0.19.1           py35hf362045_3  
seaborn                   0.8.1                    py35_0    conda-forge
setuptools                38.4.0                   py35_0    conda-forge
simplegeneric             0.8.1                    py35_0    conda-forge
six                       1.11.0                   py35_1    conda-forge
sortmerna                 2.0                           1    bioconda
sqlite                    3.13.0                        1    conda-forge
statsmodels               0.8.0                    py35_0    conda-forge
terminado                 0.8.1                    py35_0    conda-forge
testpath                  0.3.1                    py35_0    conda-forge
tk                        8.5.19                        2    conda-forge
tornado                   4.5.2                    py35_0    conda-forge
traitlets                 4.3.2                    py35_0    conda-forge
tzlocal                   1.3                      py35_0    qiime2
urllib3                   1.22                     py35_0    conda-forge
vsearch                   2.6.0                         0    bioconda
wcwidth                   0.1.7                    py35_0    conda-forge
webencodings              0.5                      py35_0    conda-forge
wget                      1.18                          0  
wheel                     0.30.0                   py35_2    conda-forge
xopen                     0.3.2                    py35_0    bioconda
xz                        5.2.3                         0    conda-forge
yaml                      0.1.7                         0    conda-forge
zeromq                    4.2.3                         0    conda-forge
zlib                      1.2.8                         3    conda-forge

I think my suspicion was right — you have no QIIME 2 plugins installed! Did you follow the directions in the official Install Guide? You can remove this environment so that you can try again by running the following:

$ conda env remove -n qiime2-2017.12

After that, follow the install guide, and when you run qiime info again, you should see something like this:

Installed plugins
alignment 2017.12.0
composition 2017.12.0
cutadapt 2017.12.0
dada2 2017.12.1
deblur 2017.12.0
demux 2017.12.0
diversity 2017.12.0
emperor 2017.12.0
feature-classifier 2017.12.0
feature-table 2017.12.0
gneiss 2017.12.0
longitudinal 2017.12.0
metadata 2017.12.0
phylogeny 2017.12.0
quality-control 2017.12.0
quality-filter 2017.12.0
sample-classifier 2017.12.0
taxa 2017.12.0
types 2017.12.0
vsearch 2017.12.0

Let us know if you get stuck! Good luck! :t_rex:

hmmm, got the error 500:

"Hes-iMac:~ he$ wget https://data.qiime2.org/distro/core/qiime2-2017.12-py35-osx-conda.yml
–2018-01-11 10:31:49-- https://data.qiime2.org/distro/core/qiime2-2017.12-py35-osx-conda.yml
Resolving data.qiime2.org… 104.27.170.158, 104.27.171.158
Connecting to data.qiime2.org|104.27.170.158|:443… connected.
HTTP request sent, awaiting response… 302 FOUND
Location: https://raw.githubusercontent.com/qiime2/environment-files/master/2017.12/release/qiime2-2017.12-py35-osx-conda.yml [following]
–2018-01-11 10:31:49-- https://raw.githubusercontent.com/qiime2/environment-files/master/2017.12/release/qiime2-2017.12-py35-osx-conda.yml
Resolving raw.githubusercontent.com… 151.101.56.133
Connecting to raw.githubusercontent.com|151.101.56.133|:443… connected.
HTTP request sent, awaiting response… 500 Internal Server Error
2018-01-11 10:32:03 ERROR 500: Internal Server Error.

Hes-iMac:~ he$ conda env create -n qiime2-2017.12 --file qiime2-2017.12-py35-osx-conda.yml

SpecNotFound: Invalid name, try the format: user/package

Hes-iMac:~ he$ # OPTIONAL CLEANUP
Hes-iMac:~ he$ rm qiime2-2017.12-py35-osx-conda.yml"

Hi @Andrew, looks like github is down :frowning:. They are normally good at fixing things up quickly when an issue like this happens. Sorry, check back again in 15 minutes or so!

The Github status page indicates that they have resumed normal operations! :tada:

Yup. Problem solved.

(qiime2-2017.12) Hes-iMac:~ he$ qiime info
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
System versions
Python version: 3.5.4
QIIME 2 release: 2017.12
QIIME 2 version: 2017.12.1
q2cli version: 2017.12.0

Installed plugins
alignment 2017.12.0
composition 2017.12.0
cutadapt 2017.12.0
dada2 2017.12.1
deblur 2017.12.0
demux 2017.12.0
diversity 2017.12.0
emperor 2017.12.0
feature-classifier 2017.12.0
feature-table 2017.12.0
gneiss 2017.12.0
longitudinal 2017.12.0
metadata 2017.12.0
phylogeny 2017.12.0
quality-control 2017.12.0
quality-filter 2017.12.0
sample-classifier 2017.12.0
taxa 2017.12.0
types 2017.12.0
vsearch 2017.12.0

Application config directory
/Users/he/Library/Application Support/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME 2 and all installed plugins, run:

qiime info --citations

Thank you!!

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