error in importing BIOM file


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) [email protected]:~/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/", 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/", 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/", 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/", line 70, in transformation
    new_view = transformer(view)
  File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/", 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/", 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/", 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/", 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/", 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/", line 628, in _to_sparse
    mat = coo_arrays_to_sparse((, (d.row, d.col)),
  File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/biom/", 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/", line 160, in __init__ = getdata(obj, copy=copy, dtype=dtype)
  File "/home/qiime2/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/scipy/sparse/", 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'

Hello @EGvibrio,

It's a problem with format validation, you have a string, that is mentioned in error, somewhere in values cells. Inspect your biom table carefully, and make sure that strings are only found in indexes and columns, not in value cells.


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Thank you for your quick reply, I inspected the table before.
There are no strings outside of indexes.


Yes, I cannot locate them as well in raw data. Maybe something went wrong during BIOM creation? Please, send created BIOM.


Thanks, please see the attached BIOM:


there are strings in your cell values. Please, check make_biom documentation and make sure ASV are recorded as indexes and not as part of values.

Example line:
["nifH_ASV_4892"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 10"," 0"," 0"," 8"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"," 0"]


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That's weird. I'll try to record ASV as indexes.

Edit: Worked. Thank you very much!

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