I’ve had problems with discrepant data in my name and group files. First, when I get to the pre-cluster command, I’m getting a discrepancy between the two files file that’s shutting me down. It seems I’m missing something. My final fasta and names files prior to pre-cluster are:
Your groupfile at that point is:
Which implies that you’ve somehow trimmed your group file as you proceeded. How? My group file at that point is the one I created at the very beginning, using the merge.files and make.groups commands.
I DID figure out a work-around – to wait to make my groups and merge my reads just prior to preclustering. Problem is then I have to redo my alignment, filtering and screening. I’d imagine the net effect is just as though I created three separate alignments in Sequencher and then brought them together.
Then, a similar problem pops up when I generate my phylotypes. I started by using the taxonomy I generated when I first classified, and the name file equivalent to your final.names. I get “[ERROR]: … is not in your namefile, please correct.”
My workaround was to reclassify my final fasta and name files and the last group file. It seems to have worked, but in both cases, I think there must be a more reasonable, less Byzantine way to proceed.
Finally, a smaller (?) problem: when I classify my philotypes, I input: classify.otu(list=218.a2.a3.final.an.list, name=218.a2.a3.final.names, taxonomy=218.a2.a3.final.pds.wang.taxonomy, label=1)
For some reason, I get back:
Your file does not include the label 1. I will use 0.07.
Output File Names: