Error importing data - semantic type does not have a compatible directory format

Hi I have been trying to import some files into qiime2 which I downloaded from the SILVA database.
I used the following code from the RESCRIPt tutorial.

qiime tools import
–type ‘FeatureData[SILVATaxonomy]’
–input-path tax_slv_lsu_138.1.txt
–output-path taxranks-silva-138.1-lsu-nr99.qza \

I got the following error message:

[[email protected] SILVAref]$ cat 16287.err
Traceback (most recent call last):
** File “/trinity/shared/apps/site-local/qiime2/2020.11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/builtin/tools.py”, line 158, in import_data**
** view_type=input_format)**
** File “/trinity/shared/apps/site-local/qiime2/2020.11/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 213, in import_data**
** output_dir_fmt = pm.get_directory_format(type_)**
** File “/trinity/shared/apps/site-local/qiime2/2020.11/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 313, in get_directory_format**
** % semantic_type)**
TypeError: Semantic type FeatureData[SILVATaxonomy] does not have a compatible directory format.

An unexpected error has occurred:

** Semantic type FeatureData[SILVATaxonomy] does not have a compatible directory format.**

See above for debug info

Any help on this would be great.

Thanks

Hi @avtober!

Do you have rescript installed in your conda environment? That poorly-written warning is a sign that the types and formats defined by rescript aren’t present in your current environment. You can check by running:

conda activate qiime2-2020.11  # or whatever your env name is
conda list rescript

Let us know what it says and we can come with a plan from there.

:qiime2:

2 Likes

Hi @thermokarst, yes I realised today that I had not actually activated the rescript conda environment. Everything has seemed to have worked since then. Thanks!

Anya

2 Likes

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