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) [biostack@LFE0616 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