make.shared file for final.tx.list


I am running Mothur on my Mac and have no issues until I get to the Phylotype analysis. I am analyzing pyrosequencing 16S libraries. Everything seems fine with the processing and OTU analysis; however, when I get to the phylotype analysis I get an error that a sequence is in my list file but not my group file and that there are duplicates of this sequence in the list file. If I open both files, I see that this is not the case. I observe the sequence is present in the group file and there are not duplicate sequences in my list file. Has anyone encountered this issue and know how to get around it?


Thanks for reporting this issue. The phylotype command has a small bug that we will fix in the next release. The numOtus in the list file is one too high. Otus are clustered correctly, the count is just off. As a work around, you want to change decrease the number of otus by 1 in the final.tx.list file.

“1 62 GQY1XT001C296C,GQY1XT001BOB1X,GQY1XT001AT26X…” would become “1 61 GQY1XT001C296C,GQY1XT001BOB1X,GQY1XT001AT26X…”

I hope this helps,

Thank you! I did get this to work by decreasing the number.