MemoryError when i convert .biom to .txt

feature-classifier

(wangjianing) #1

Hi.
When I used the following command to convert .biom to .txt,

biom convert -i table.biom -o table.tsv --to-tsv

and I got this back.

My .biom file is about 110 MB and my linux server is 4 core and 16 G. I’m not sure what this means, is it the .biom file is too large for my linux?

I am fresh man for QIIME, sorry for the rudimentary questions, and thank you so much!!


(Luca) #2

Hi,
It may be an issue with the version of biom package you using.
Within a qiime2 env, I use the following command and usually works:
biom convert -i feature-table.biom -o otu_table.classic.txt --to-tsv --table-type=‘OTU table’ --header-key taxonomy

Luca