Mothur.exe stops working when I attempt a make.shared comman

I’m having huge hassles lately. I am attempting to pull out different species of bacteria for strain otu analysis. I first attempted it with (get.lineage command) betaproteobacteria and got lovely results. I then did it again for Spirochaete. Everything works beautifully until I type in
“make.shared(, group=final.pick.groups, label=0.03)”
at which point I am told that mothur.exe has stopped working and the program is closed. The only difference that I can identify is that in the case of the Beta’s, there were 55 sequences left whereas the Spirochaetes were left with only 11 sequences before the make.shared command was used. Any help with this would be hugely helpful!!!


Sam Waterworth - MSc student, Rhodes University, South Africa

Can you post the commands you ran from get.lineage through make.shared as well as the version of mothur you are using?

I have downloaded “silva.seed_v119.align” . Can I use it in “align.seqs” and “classify.seqs”? Is it necessary for me to change name as “silva.seed_v119.fasta”? Compared with RDP and gg database,which is better for classifying our sequences?

could you create a new thread for this question instead of tacking it on to the end of a very old thread?