Excluding Sequences in make_otu_table.py

[Marie]

Hi,
I'm trying to remove the sequences contained in a fasta file from an OTU table using the -e option in make_otu_table.py. The command runs without errors, but the resulting OTU table still contains all of the original sequences - nothing is filtered out. I've double checked to make sure all of the sequence headers match exactly between the two files and tried running with simplified dummy files and still haven't had any success. Any thoughts on what the problem could be? Sample files are attached and the command is below.

Best regards,
Marie


make_otu_table.py -i testotu.txt -o testtable.biom -e testfasta.fasta

[Daniel McDonald]

Hi Marie,

I am mystified by this as well -- I'm going to open a bug on the QIIME tracker as it does seem like something unexpected is going on. Please find the issue here:

https://github.com/biocore/qiime/issues/2127

In the mean time, I think the easiest alternative is to filter the prior to OTU picking although that does of course have a compute expense associated with it.

Best,

Daniel

[Marie]

Hi Daniel,

Thanks for the quick reply - unfortunate that it wasn't an easy fix!  I'll keep an eye on the bug.

All best,

Marie