biom.exception.BiomParseException: No header line was found in mapping file


(Fangzhou Chen) #1

Hi Matthew,

I have tried to do the same as @jairideout. Below are the command lines.

$ qiime tools export
–input-path table.qza
–output-path exported

$ qiime tools export
–input-path taxonomy.qza
–output-path exported

$ biom add-metadata -i exported/feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp biom-taxonomy.tsv --sc-separated taxonomy

But the “biom add-metadata” showed some error as below.

(qiime2-2018.8) [[email protected] Run6]$ biom add-metadata -i exported/feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp biom-taxonomy.tsv --sc-separated taxonomy
Traceback (most recent call last):
File “/home/biostack/anaconda3/envs/qiime2-2018.8/bin/biom”, line 6, in
sys.exit(biom.cli.cli())
File “/home/biostack/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/home/biostack/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 697, in main
rv = self.invoke(ctx)
File “/home/biostack/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/biostack/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/biostack/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 535, in invoke
return callback(*args, **kwargs)
File “/home/biostack/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-linux-x86_64.egg/biom/cli/metadata_adder.py”, line 107, in add_metadata
float_fields, sample_header, observation_header)
File “/home/biostack/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-linux-x86_64.egg/biom/cli/metadata_adder.py”, line 174, in _add_metadata
header=observation_header)
File “/home/biostack/anaconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-linux-x86_64.egg/biom/parse.py”, line 527, in from_file
raise BiomParseException("No header line was found in mapping "
biom.exception.BiomParseException: No header line was found in mapping file.

I have checked to use “tab” between #OTUID taxonomy confidence.
But still could not fix the issue.
here are mine "biom-taxonomy"biom-taxonomy.tsv (3.3 MB)

I would also like to upload the “feature-table.biom” feature-table.biom

Any suggestion for what could go wrong?

I am trying to export my data to run PICRUSt.

Thanks a lot!
Fangzhou


Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)
(Nicholas Bokulich) #2

Hi @dimitely,
I have moved your question to a new topic and categorized as “other bioinformatics tools” because this is a question about biom-format, not QIIME 2. Thus, we might not be able to answer (we are not biom-format developers!) but others in the community may help.

What happens if you put a space between “OTU” and “ID”? Looking at the biom-format documentation, it looks like “OTU ID” might be the expected header?

Let me know if that works!


(Fangzhou Chen) #3

Thank you so much @Nicholas_Bokulich !
I have tried to put a space between OUT and ID, but it still the output is same as before.