I am trying to import a BIOM table from RiboTagger into Qiime2 as a .qza frequency table for OTU clustering. I am running qiime2-2019.4 in a conda environment on a HPC cluster.
I am following the instructions at,
https://docs.qiime2.org/2019.4/tutorials/importing/#feature-table-data
but I get an error which is not very clear to me when I run the command.
(qiime2-2019.4) [prhr3@login-s2 ribotagger]$ qiime tools import --input-path Amplicon_and_Metagenome_V4.biom --type 'FeatureTable[Frequency]' --input-format BIOMV100Format --output-path feature-table-2.qza
Traceback (most recent call last):
File "/nv/hmicro1/prhr3/data/software/pkg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data
view_type=input_format)
File "/nv/hmicro1/prhr3/data/software/pkg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data
return cls._from_view(type_, view, view_type, provenance_capture)
File "/nv/hmicro1/prhr3/data/software/pkg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 265, in _from_view
result = transformation(view)
File "/nv/hmicro1/prhr3/data/software/pkg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/nv/hmicro1/prhr3/data/software/pkg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 220, in wrapped
file_view = transformer(view)
File "/nv/hmicro1/prhr3/data/software/pkg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/feature_table/_transformer.py", line 141, in _8
data = _parse_biom_table_v100(ff)
File "/nv/hmicro1/prhr3/data/software/pkg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/feature_table/_transformer.py", line 46, in _parse_biom_table_v100
table = biom.Table.from_json(json.load(fh))
File "/nv/hmicro1/prhr3/data/software/pkg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/biom/table.py", line 4423, in from_json
generated_by=json_table['generated_by'],
KeyError: 'generated_by'
An unexpected error has occurred:
'generated_by'
See above for debug info.