Hi,
My colleague wants me to run analyses on QIIME2. He gave me files OTU, taxonomy and metadata files.
I made a BIOM file from OTU file using a biomformat package in R (with a make_biom command).
Now I'm trying to import into QIIME2 and save it as a table.qza and I got an error. I tried to edit the OTU table but still I get error that I don't fully understand what the meaning of it is.
I'll appreciate your help. Thank you very much,
(qiime2-2022.8) qiime2@DESKTOP-N1TS9JQ:~/Jordan/nifh/Final$ qiime tools import --input-path jodan_biom.biom --type 'FeatureTable[Frequency]' --input-format BIOMV100Format --output-path jodan_table.qza
Traceback (most recent call last):
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 299, in import_data
return cls._from_view(type_, view, view_type, provenance_capture,
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 327, in _from_view
result = transformation(view, validate_level)
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/transform.py", line 221, in wrapped
file_view = transformer(view)
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_types/feature_table/_transformer.py", line 124, in _8
data = _parse_biom_table_v100(ff)
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_types/feature_table/_transformer.py", line 46, in _parse_biom_table_v100
table = biom.Table.from_json(json.load(fh))
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/biom/table.py", line 4696, in from_json
table_obj = Table(data, obs_ids, sample_ids,
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/biom/table.py", line 468, in __init__
self._data = Table._to_sparse(data, input_is_dense=input_is_dense,
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/biom/table.py", line 628, in _to_sparse
mat = coo_arrays_to_sparse((d.data, (d.row, d.col)),
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/biom/table.py", line 5264, in coo_arrays_to_sparse
matrix = coo_matrix(data, shape=(n_rows, n_cols), dtype=dtype)
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/scipy/sparse/_coo.py", line 160, in __init__
self.data = getdata(obj, copy=copy, dtype=dtype)
File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/scipy/sparse/_sputils.py", line 124, in getdata
data = np.array(obj, dtype=dtype, copy=copy)
ValueError: could not convert string to float: 'nifH_ASV_1480'
An unexpected error has occurred:
could not convert string to float: 'nifH_ASV_1480'