.biom to .tsv or .txt

Hello!

I am new to qiime2 and have a pretty basic question im sure. Im unable to convert the .biom file to .txt or .tsv. i found commands on the forum to do this, but I haven’t been able to.

I have tried variations of this command,

biom convert -i table.biom -o table.tsv --to-tsv

and I get this back,

raceback (most recent call last):
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/bin/biom”, line 6, in
sys.exit(biom.cli.cli())
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 697, in main
rv = self.invoke(ctx)
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 535, in invoke
return callback(*args, **kwargs)
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-macosx-10.7-x86_64.egg/biom/cli/table_converter.py”, line 129, in convert
table_type, process_obs_metadata, tsv_metadata_formatter)
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-macosx-10.7-x86_64.egg/biom/cli/table_converter.py”, line 185, in _convert
metadata_formatter=obs_md_fmt_f)
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-macosx-10.7-x86_64.egg/biom/table.py”, line 4625, in to_tsv
observation_column_name)
File “/Users/Echo_Base/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-macosx-10.7-x86_64.egg/biom/table.py”, line 1470, in delimited_self
raise TableException(“Cannot delimit self if I don’t have data…”)
biom.exception.TableException: Cannot delimit self if I don’t have data…

Im not sure what this means, is there an issue with the .biom file? I made this .biome file from a continency filtered table, is that ok?

Sorry for the rudimentary questions, and thank you so much!!

Hi @swillyb!

This isn’t the support forum for BIOM, so we might not be able to provide a thorough response here, but my guess is that the error is related to your feature table being empty. You can confirm this by running feature-table summarize on your feature table prior to exporting from QIIME 2. Hope that helps! :t_rex: :qiime2:

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