BIOM conversion to tsv

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1

Hi,
I faced a problem while my trial for getting the OTU table.
I think there is no problem in BIOM exporting, I successfully did using the following tutorial
https://docs.qiime2.org/2020.8/tutorials/exporting/

However, when I tried running the following command
biom convert -i feature-table.biom -o feature-table.from_biom.txt --to-tsv
, I got this error
Error: Invalid value for "-i" / "--input-fp": File "feature-table.biom" does not exist.

I wish you can help me.

Thanks for consideration

BR

Sayed

2

Hi!
If you followed the tutorial, your biom table should be in the exported-feature-table subdirectory (unless you changed it).
So, cd to exported-feature-table subdirectory before running the command or provide the variable with a path exported-feature-table/feature-table.biom as an input

1 Like
3

Ok. I understood.
Thanks a lot