I am trying to use the remove.rare command to filter my .shared file my OTU frequency. I did this successfully on a previous analysis of this dataset, but now the command is returning an error message that I don’t understand:
mothur > remove.rare(shared=ALF_A_V6.final.subsample.fn.shared, label=0.03, nseqs=5000)
[ERROR]: Not enough variable pieces for shared.
[ERROR]: Could not open
The .shared file seems to be okay, and can be opened for other commands, like tree.shared. The only difference that I’m aware of between this and the previous .shared file is that this one is bigger (about 95K OTUs; the previous version was ~35K).