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