taxonomy problems

Commands in mothur
1

After I get the steps done:

mothur > system(mv stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.taxonomy stability.an.cons.taxonomy)

I opened the file “stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.taxonomy” and compared to “stability.an.cons.taxonomy”. The first two OTU IDs are exchanged. Why?
Otu00001 632009 Bacteria(100);“Proteobacteria”(100);Gammaproteobacteria(100);“Enterobacteriales”(100);Enterobacteriaceae(100);unclassified(100);
Otu00002 798397 Bacteria(100);“Bacteroidetes”(100);Flavobacteria(100);“Flavobacteriales”(100);Flavobacteriaceae(100);Elizabethkingia(100);

Otu00001 798397 Bacteria(100);“Bacteroidetes”(100);Flavobacteria(100);“Flavobacteriales”(100);Flavobacteriaceae(100);Elizabethkingia(100);
Otu00002 632009 Bacteria(100);“Proteobacteria”(100);Gammaproteobacteria(100);“Enterobacteriales”(100);Enterobacteriaceae(100);unclassified(100);

They should be the same. Am I right?

2

If I had to guess, the two files you are looking at are from different runs of the data and because there’s a bit of randomness the ordering got switched. If you look at your shared file, how many sequences are in OTUs 1 and 2?

Pat

3

Hi Pat, thanks so much for replying this post. The .shared file showed:
That is, 632009 for OTU1 and 798397 for OTU2

stability.an.cons.taxonomy showed:
Otu00001 798397 Bacteria(100);“Bacteroidetes”(100);Flavobacteria(100);“Flavobacteriales”(100);Flavobacteriaceae(100);Elizabethkingia(100);
Otu00002 632009 Bacteria(100);“Proteobacteria”(100);Gammaproteobacteria(100);“Enterobacteriales”(100);Enterobacteriaceae(100);unclassified(100);

This is something bothering me now: It is not consistent. Why?

I agree that, I did not run through all of these analysis in one run. I know that I quit mothur in the middle of analysis because I headed back home and I rerun it.
But they are from the same batch of data. If it is true, different run affects the OTU assignments, I will worry about it.
I will try to complete all of the run in one time and have another look and let you know what I get!

Thank you again for your replying.

4

You could run “set.seed(1)” as the first command in the pipeline and that should give you the same results each time you run the pipeline.

Pat