biom convert ValueError: could not convert string to float:

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Brett

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Jun 9, 2016, 7:47:18 PM6/9/16
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Hello, 

I am assessing various methods of otu clustering with a mock community of known composition that I have sequenced. However, not all otu clustering methods generate a BIOM file as output. While trying to convert my .txt otu table to a .biom table with the "biom convert" script, I get the following error: ValueError: could not convert string to float: BY.MC.6.7_10814. I tried using QIIME labels without any decimals (e.g. BY_MC_6_7_10814), but received the same error. 

The command: biom convert -i uclust_filtered_otus.txt -o uclust_filtered_otus.biom --table-type="OTU table" --to-hdf5

The full error: attached

The .txt otu table: attached

Thanks in advance.  

-Brett 
biom_convert_error.txt
uclust_filtered_otus.txt

abir...@gmail.com

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Jun 10, 2016, 2:34:44 AM6/10/16
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Hi, Brett,
You mentioned that you're trying to convert an OTU table to biom format, and I see that you're passing in uclust_filtered_otus.txt, but, as far as I can tell from looking at the uploaded version of this file, it is not an OTU table.  When I look at it in a text editor, I don't see the standard grid of OTU id rows and sample id columns, with count values in each field; it looks more like a list of OTUs. Can you double-check your clustering method outputs and see if there's a file in the usual "classic" OTU table format that you could use instead?
Thanks,
Amanda

Brett

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Jun 10, 2016, 6:43:23 PM6/10/16
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Hi Amanda, 

I got it figured out; needed to pass the pick_otus.py result to make_otu_table.py. 

Thanks for getting back to me. 

Cheers, 

Brett
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