Andrew
January 11, 2018, 3:05pm
#1
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 builtins ’: {}}, locals_)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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.
thermokarst
January 11, 2018, 3:07pm
#3
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!
Andrew
January 11, 2018, 3:14pm
#5
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
thermokarst
January 11, 2018, 3:18pm
#7
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!
Andrew
January 11, 2018, 3:41pm
#9
hmmm, got the error 500:
"Hes-iMac:~ he$ wget https://data.qiime2.org/distro/core/qiime2-2017.12-py35-osx-conda.yml https://data.qiime2.org/distro/core/qiime2-2017.12-py35-osx-conda.yml data.qiime2.org … 104.27.170.158, 104.27.171.158https://raw.githubusercontent.com/qiime2/environment-files/master/2017.12/release/qiime2-2017.12-py35-osx-conda.yml [following]https://raw.githubusercontent.com/qiime2/environment-files/master/2017.12/release/qiime2-2017.12-py35-osx-conda.yml raw.githubusercontent.com … 151.101.56.133
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
thermokarst
January 11, 2018, 3:43pm
#10
Hi @Andrew , looks like github is down
thermokarst
January 11, 2018, 3:49pm
#11
The Github status page indicates that they have resumed normal operations!
Andrew
January 11, 2018, 3:57pm
#12
Yup. Problem solved.
(qiime2-2017.12) Hes-iMac:~ he$ qiime info
Installed plugins
Application config directory
Getting helphttps://qiime2.org
Citing QIIME 2
qiime info --citations
Thank you!!
2 Likes
system
February 11, 2018, 9:58pm
#13
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.
. They are normally good at fixing things up quickly when an issue like this happens. Sorry, check back again in 15 minutes or so!