(base) niki123@LAPTOP-38ON2FG7:/mnt/d$ biom convert -i otutable.txt -o table.from_txt_json.biom --table-type="OTU table" --to-json Traceback (most recent call last): File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/table.py", line 5018, in _extract_data_from_tsv values = list(map(dtype, fields[1:])) ValueError: could not convert string to float: 'Bacteria' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/parse.py", line 672, in load_table table = parse_biom_table(fp) File "/home/niki123/anaconda3/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/niki123/anaconda3/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/niki123/anaconda3/lib/python3.8/site-packages/biom/table.py", line 5022, in _extract_data_from_tsv raise TypeError(msg % (lineno, badidx+1, badval)) TypeError: Invalid value on line 1, column 2, value Bacteria During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/niki123/anaconda3/bin/biom", line 11, in sys.exit(cli()) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/cli/table_converter.py", line 114, in convert table = load_table(input_fp) File "/home/niki123/anaconda3/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: otutable.txt does not appear to be a BIOM file! (base) niki123@LAPTOP-38ON2FG7:/mnt/d$ biom convert -i otutable.txt -o table.from_txt_hdf5.biom --table-type="OTU table" --to-hdf5 Traceback (most recent call last): File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/table.py", line 5018, in _extract_data_from_tsv values = list(map(dtype, fields[1:])) ValueError: could not convert string to float: 'Bacteria' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/parse.py", line 672, in load_table table = parse_biom_table(fp) File "/home/niki123/anaconda3/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/niki123/anaconda3/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/niki123/anaconda3/lib/python3.8/site-packages/biom/table.py", line 5022, in _extract_data_from_tsv raise TypeError(msg % (lineno, badidx+1, badval)) TypeError: Invalid value on line 1, column 2, value Bacteria During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/niki123/anaconda3/bin/biom", line 11, in sys.exit(cli()) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/cli/table_converter.py", line 114, in convert table = load_table(input_fp) File "/home/niki123/anaconda3/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: otutable.txt does not appear to be a BIOM file! (base) niki123@LAPTOP-38ON2FG7:/mnt/d$ biom convert -i otutable.txt -o new_otu_table.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy Traceback (most recent call last): File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/table.py", line 5018, in _extract_data_from_tsv values = list(map(dtype, fields[1:])) ValueError: could not convert string to float: 'Bacteria' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/parse.py", line 672, in load_table table = parse_biom_table(fp) File "/home/niki123/anaconda3/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/niki123/anaconda3/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/niki123/anaconda3/lib/python3.8/site-packages/biom/table.py", line 5022, in _extract_data_from_tsv raise TypeError(msg % (lineno, badidx+1, badval)) TypeError: Invalid value on line 1, column 2, value Bacteria During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/niki123/anaconda3/bin/biom", line 11, in sys.exit(cli()) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/niki123/anaconda3/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/home/niki123/anaconda3/lib/python3.8/site-packages/biom/cli/table_converter.py", line 114, in convert table = load_table(input_fp) File "/home/niki123/anaconda3/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: otutable.txt does not appear to be a BIOM file!