Using Qiime2 (Virtual Box), I am trying to merge feature-table and taxonomy files to create the equivalent of “otu_table_mc2_w_tax.biom” of Qiime 1.9. I want to do this so that I can use the taxonomy barplots function in Qiime 1.9. I found the command to use by searching the forum, however when I run the command, I get the error message below. I assume this has something to do what’s in the first two rows of the taxonomy and feature-table files but I’m not sure what change to make. Below are the code, content of the taxonomy and feature-table files and the error message. Thanks for any suggestions.
Bill
Code:
biom add-metadata -i feature-table.biom -o feature-table-with-taxonomy.biom --observation-metadata-fp taxonomy.tsv
Taxonomy.tsv (first 5 rows):
Feature ID Taxon
#q2:types categorical
e26be733f609ec5e768b922cf69cd54f D_0__Bacteria;D_1__Proteobacteria;D_2__Betaproteobacteria;D_3__Burkholderiales;D_4__Alcaligenaceae
715a13bfab0f175143f3ec02a3303f48 D_0__Bacteria;D_1__Proteobacteria;D_2__Betaproteobacteria;D_3__Burkholderiales;D_4__Comamonadaceae
00311865b066b5d93fdaebbb587dc603 D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Pseudomonadales;D_4__Pseudomonadaceae;D_5__Pseudomonas
Feature-table.qza (first five rows):
'# Constructed from biom file
#OTU ID B17 T1000 T1010 T1034
441604515075282ad1d821bfa586c1f1 0 3524 1907 1867
bec535950291278a371a938c0406b908 0 3690 1845 1914
9c2e207a51aed4e45acd6f2ccab41e6a 0 3350 1778 1938
Error message:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.11/bin/biom”, line 11, in
sys.exit(cli())
File “/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py”, line 555, in invoke
return callback(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/cli/metadata_adder.py”, line 107, in add_metadata
float_fields, sample_header, observation_header)
File “/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/cli/metadata_adder.py”, line 174, in _add_metadata
header=observation_header)
File “/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/parse.py”, line 533, in from_file
raise BiomParseException("No header line was found in mapping "
biom.exception.BiomParseException: No header line was found in mapping file.