Comments (3)
First, please ignore if this was already fixed. I'm using amptk v1.1.4
, so not the most up to date...
I wanted to add that in the next step, after the *.biom.tmp
file is created and you append the metadata... In my system the default file name it was looking for to find the taxonomy table wasn't right:
The script looked for:
biom add-metadata -i Mangan.biom.tmp -o Mangan.biom --observation-metadata-fp Mangan.qiime.taxonomy.txt -m mangan.mappingFile.txt --sc-separated taxonomy --output-as-json
But there isn't any Mangan.qiime.taxonomy.txt
file. Instead, the default name is Mangan.otu_table.taxonomy.txt
. Once I swapped that manually it worked fine.
Cheers!
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Looks like amptk taxonomy
is expecting only tab delimited. So I guess I never saw this because I don't ever use csv -- I only added that as a request from Michelle.
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Michelle is such a trouble maker...
Easy fix anyhow. Thanks.
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