qiime tools import issues (QIIME2 2023.7)

To Whom it May Concern:

Hello. I am trying to run a few practice trials on getting sequences from NCBI via q2-fondue prior to a larger scale analysis. The code was working just fine up until dada2 where I encountered a common error that the forum believes is a storage issue. I have contacted the SCINet Ceres cluster for more information as I am using this resource. However, to see if a smaller set of sequences would work I ran the qiime tools import commands as I did previously. This time, I encountered the following error message:

(fondue) [anthony.frazier@ceres meta_analysis]$ qiime tools import
--type NCBIAccessionIDs
--input-path sample_meta_analysis_new.txt
--output-path sample_meta_analysis_new.qza

Traceback (most recent call last):
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 266, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/qiime2/sdk/result.py", line 300, in import_data
output_dir_fmt = pm.get_directory_format(type_)
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 388, in get_directory_format
raise TypeError(
TypeError: Semantic type NCBIAccessionIDs is invalid, either because it doesn't have a compatible directory format, or because it's not registered.

An unexpected error has occurred:

Semantic type NCBIAccessionIDs is invalid, either because it doesn't have a compatible directory format, or because it's not registered.

See above for debug info.

Again, this worked previously and I have that previous output. So why all of the sudden does this not work? I've changed nothing...very confused! Any and all help is appreciated! Thank you for your time and consideration!

-Nathan

Hi @nathan.frazier35,

Do you mind sharing your sample_meta_analysis_new.txt file (DM is fine if you'd prefer not to share publicly)? I'll try and reproduce this on my end. Thanks!

An off-topic reply has been split into a new topic: error while running dada2 denoise

Please keep replies on-topic in the future.

sample_meta_analysis_new.txt (238 Bytes)

Of Course! Thank you so much for your assistance!

Hi @nathan.frazier35,

Thanks for providing that file! I actually think the issue is coming from the specific environment you're using, rather than the file itself. NCBIAccessionIDs is a type that's registered within q2-fondue, which is installed separately from the core QIIME 2 distribution. You'll need to install q2-fondue in your 2023.7 environment, and then this command should work as expected!

Cheers :lizard:

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