Importing biom file from R

I am having issues importing a .biom file from R into QIIME2.

Here is the code I tried:

(qiime2-2018.2) [email protected]:~/FrogMicrobiome$ qiime tools import --input-path ‘/media/sf_Shared_Folder/Analysis_with_Carly/test-2.biom’ --type ‘FeatureTable[Frequency]’ --source-format BIOMV100Format --output-path feature-table-fmn-cfa.qza
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/”, line 116, in import_data
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/”, line 214, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/”, line 239, in _from_view
result = transformation(view)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/core/”, line 59, in transformation
new_view = transformer(view)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/core/”, line 207, in wrapped
file_view = transformer(view)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_types/feature_table/”, line 128, in _8
data = _parse_biom_table_v100(ff)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_types/feature_table/”, line 46, in _parse_biom_table_v100
table = biom.Table.from_json(json.load(fh))
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-linux-x86_64.egg/biom/”, line 4190, in from_json
dtype = MATRIX_ELEMENT_TYPE[json_table[‘matrix_element_type’]]
TypeError: unhashable type: 'list’An unexpected error has occurred:
unhashable type: ‘list’
See above for debug info.

I followed this to write a biom file from phyloseq using biomformat.

I believe my issue as the same as this previous post
but I don’t see any resolutions.

Does anyone know how to assist with this??


Hi Sarah,
Have you updated to the latest version of biomformat? It looks like there was an problem outlined in the issue you linked to that you are running into and that this should have been corrected in this pull request Which has been merged.

If, after you update, the biom table created by biomformat is still not able to be loaded into qiime you might want to try validating the table:

biom validate-table -i feature-table.biom

If this passes but QIIME2 fails than it is likely an issue with QIIME2. If this fails, the issue is with biomformat and if you have updated to the lates version, a new issue will need to be posted

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