biom convert is not working

Question

[tokeemdtareq]

I was trying to convert the qiime1 output from biom format to tsv format. The command I used is this:

biom convert -i otu_table.biom -o otu_table.txt --to-tsv --table-type "OTU table"

but it's showing error that I do not understand, any suggestion would be greatly appreciated

File "/usr/local/bin/biom", line 11, in <module> load_entry_point('biom-format==2.1.6', 'console_scripts', 'biom')() File "/usr/local/lib/python2.7/dist-packages/click-6.7-py2.7.egg/click/core.py", line 722, in __call__ return self.main(args, *kwargs) File "/usr/local/lib/python2.7/dist-packages/click-6.7-py2.7.egg/click/core.py", line 697, in main rv = self.invoke(ctx) File "/usr/local/lib/python2.7/dist-packages/click-6.7-py2.7.egg/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python2.7/dist-packages/click-6.7-py2.7.egg/click/core.py", line 895, in invoke return ctx.invoke(self.callback, *ctx.params) File "/usr/local/lib/python2.7/dist-packages/click-6.7-py2.7.egg/click/core.py", line 535, in invoke return callback(args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/biom/cli/table_converter.py", line 129, in convert table_type, process_obs_metadata, tsv_metadata_formatter) File "/usr/local/lib/python2.7/dist-packages/biom/cli/table_converter.py", line 185, in _convert metadata_formatter=obs_md_fmt_f) File "/usr/local/lib/python2.7/dist-packages/biom/table.py", line 4625, in to_tsv observation_column_name) File "/usr/local/lib/python2.7/dist-packages/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...

Answer 1

[Tm]

Command, which you are using is correct, so you should check whether the biom file generated is proper or not.

Try to get the summary of biom file using:

biom summarize-table -i otu_table.biom

second, try converting biom into json format using:

biom convert -i otu_table.biom -o otu_table.json.biom --table-type="OTU table" --to-json

If both of these commands don't run properly, then there is a problem with your biom file.

[tokeemdtareq]

Sorry, it looks like the biom file did not have any data in it. I used a wrong option in previous step, so the qiime1 output (biom file) did not find any OTUs. Thanks for the reply.