mothur

Make.shared is not generating a list file

I was hoping to experiment with ASV analysis with one of my data sets.

Apologies if I am misunderstanding the process, but following the Miseq SOP under Preparing for Analysis > ASVs I understood that I could start with the count file I generated after running pre.cluster and removing chimeras during my OTU analysis.

The Miseq SOP suggests running the following:

mothur > make.shared(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table)

However, it appears that make.shared requires a label, so my command was as follows:

mothur > make.shared(count=asursb.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table, label=ASV)

This outputs a shared file and a map file, whereas the SOP suggests that it should output a shared file and a list file.

I took a look at the make.shared wiki page, which suggests that using the command above should generate a shared file, with no mention of a list file or map file.

So I’m kind of stumped as to how to generate the asv.list file required for the next step.

While searching the forum for help on this issue, I did come across this topic, where, for all intents and purposes, the user ran the same command as I did, and did generate a list file.

I’m sure I have just done something stupid. Any ideas?

Using mothur v1.43.0 on macOS Mojave 10.14.6

The unique method in the cluster command places each sequence in the count file into its own OTU.

mothur > cluster(count=final.count_table, method=unique) - create asv list file

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