Biom.convert error

Other Bioinformatics Tools
1

Hi,

I am running Qiime2/2019.4 on an ubuntu system and I have an OTU table produced using vsearch. The file is in tsv format with rows representing OTUs and columnds representing samples with read counts for each OTU.
When I try to use biom.convert to convert the tsv file to biom format for use in qiime I get the following error:

Traceback (most recent call last):
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/biom/parse.py”, line 660, in load_table
table = parse_biom_table(fp)
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/biom/parse.py”, line 412, in parse_biom_table
t = Table.from_tsv(fp, None, None, lambda x: x)
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/biom/table.py”, line 4631, in from_tsv
t_md_name) = Table._extract_data_from_tsv(lines, **kwargs)
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/biom/table.py”, line 4747, in _extract_data_from_tsv
md_name = header[-1]
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/bin/biom”, line 11, in
sys.exit(cli())
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 555, in invoke
return callback(*args, **kwargs)
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/biom/cli/table_converter.py”, line 114, in convert
table = load_table(input_fp)
File “/sw/QFAB/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/biom/parse.py”, line 662, in load_table
raise TypeError("%s does not appear to be a BIOM file!" % f)
TypeError: LP_SitexSpecies.tsv does not appear to be a BIOM file!

2

Hi @Ilha_Byrne,
Welcome in the forum!

Can you share what version of qiime2 are you using and which command you run to convert the tsv to biom.

Luca

3

I am using qiime2/2019.4 and I used this command:
biom convert -i feature-table.tsv -o feature-table.biom --table-type=“OTU table” --to-hdf5

4

Hi @Ilha_Byrne,
Could you try to get the latest qiime2 and see if the command would work in there (it does look correct to me)?
Did you process the feature-table.tsv with any text editor which may have change/added invisible characters to the file (word excel or similar)?
Could you send few lines for the file to see how it looks?
Cheers
Luca

5

Hi, so it worked for my otutable. But not when I try to do my taxonomy I get the same error again. I am using the latest version of qiime2 now.

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image1861×919 74 KB

6

I got it to work now! The headers needed to be changed and the extra columns removed.

7

Hi @Ilha_Byrne ,
glad it worked and thanks for sharing your solution
Happy qiimeing !
Luca