Unable to proceed to analysis following MiSeqSOP

mothur bugs
1

Hi all,

I have some problems trying analyse my 16S data using mothur. I’ve been following MiSeq SOP step by step until “Analysis”, in which I skipped the error rate because I dont have mock samples in my trial.

When I input rename.file in Analysis, I don’t have stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.phylip.tre. Additionally, stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.shared, and stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.0.03.cons.taxonomy in the SOP are different from what I have after following SOP. The files I have are stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.unique_list.shared and stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.unique_list.0.03.cons.taxonomy

Can anyone help me with the problem please? Did I make a mistake somewhere?

Thank you!

2

Those are the correct files. You likely used the different cluster/cluster.split path. The tre file would have been generated at https://mothur.org/wiki/MiSeq_SOP#Phylogenetic

3

Thank you very much Pat! I’ve found the problem. There were 60 samples and it took forever to generate the tree file. I’ve waited 3 hrs and then Mothur crashed. Won’t be able to complete the tree file.