Integrate external clustering results

Commands in mothur
1

Hi,

I am trying to integrate the results of ESPRIT-TREE into mothur but I am running into some issues. The reason I am using ESPRIT-TREE is that the average neighbor algorithm in mothur does not work because the sequences are not similar enough to create a good alignment.

I try to integrate the results with the make.shared command:

make.shared(list=esprittree.list,group=MothurChimeraUchime_default/sfffile.shhh.merge.good.pick.groups,label=0.03)

I created a file that looks like a mothur List file (http://www.mothur.org/wiki/List_file). I also replaced the sequence names with the list in the names file from the uchime step, otherwise I am getting a lot of these messages:

[ERROR]: ICLCB7401ASWFQ is in your groupfile and not your listfile. Please correct.

But even with the sequence IDs from the names file in the list file I still get these warnings which I checked with this command:

cat esprittree.list | tr '\t' '\n' | tr ',' '\n' | grep ICLCB7401ASWFQ
ICLCB7401ASWFQ

I made the OTUs in the List file comma separated and the cluster members tab separated, which I guess is correct. Any suggestions on this approach and what could be going wrong?

2

If you send your listfile to mothur.bugs@gmail.com, I can take a look.

3

Hi Mattias,
I took a look at your list file, and the issue you are having is caused by the incorrect number of OTUs. The list file starts with 0.03 12390 ICLCB7402IAUWE … but when I count I find 926792 OTUs. Mothur stops reading the OTUs after it reaches 12390, so the OTUs after that point are not included.
Kindly,
Sarah