Hope you are doing good. I had generated the EC and KO files in standalone version. I would like to import metegenome contribution of both files to qiime2 format (.qza). I had tried to import the file thru biom format but it show an error like this,
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/table.py", line 5025, in _extract_data_from_tsv
values = list(map(dtype, fields[1:-1]))
ValueError: could not convert string to float: 'EC:1.1.1.1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/parse.py", line 672, in load_table
table = parse_biom_table(fp)
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/parse.py", line 416, in parse_biom_table
t = Table.from_tsv(file_obj, None, None, lambda x: x)
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/table.py", line 4875, in from_tsv
t_md_name) = Table._extract_data_from_tsv(lines, **kwargs)
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/table.py", line 5029, in _extract_data_from_tsv
raise TypeError(msg % (lineno, badidx+1, badval))
TypeError: Invalid value on line 1, column 1, value EC:1.1.1.1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/picrust2/miniconda3/bin/biom", line 8, in <module>
sys.exit(cli())
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/cli/table_converter.py", line 114, in convert
table = load_table(input_fp)
File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/parse.py", line 674, in load_table
raise TypeError("%s does not appear to be a BIOM file!" % f)
TypeError: EC_pred/pred_metagenome_contrib.tsv.gz does not appear to be a BIOM file!
Biom version is 2.1.10. Hope to hear from you soon..!