Excluding Sequences in make_otu_table.py

11 views
Skip to first unread message

Marie

unread,
Jan 28, 2016, 3:48:51 AM1/28/16
to Qiime 1 Forum
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


testotu.txt
testfasta.fasta

Daniel McDonald

unread,
Jan 28, 2016, 6:43:34 PM1/28/16
to Qiime 1 Forum
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:


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

unread,
Jan 29, 2016, 2:35:01 AM1/29/16
to Qiime 1 Forum
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

Reply all
Reply to author
Forward
0 new messages