Hi everyone
I'm trying to convert a .tsv file into a BIOM file, for later convert in a .qza file. But I'm only getting error messages
This file is a decontaminated table exported from R: filtered-table-trim2-decon.tsv (536.9 KB)
Here is my code: biom convert -i filtered-table-trim2-decon.tsv -o filtered-table-trim2-decon.biom --table-type "Table" --to-hdf5
I already have tried "OTU table" or Table without the " ", but give me errors too.
Here is the error:
Traceback (most recent call last):
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/biom/parse.py", line 672, in load_table
table = parse_biom_table(fp)
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/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/joaomiranda/miniconda3/envs/qiime2-2021.4/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/joaomiranda/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/biom/table.py", line 4990, in _extract_data_from_tsv
md_name = header[-1]
IndexError: list index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/bin/biom", line 11, in <module>
sys.exit(cli())
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/biom/cli/table_converter.py", line 114, in convert
table = load_table(input_fp)
File "/home/joaomiranda/miniconda3/envs/qiime2-2021.4/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: filtered-table-trim2-decon.tsv does not appear to be a BIOM file!