Count.groups discrepancy?

Hi, I’m importing the output from DADA2 fungal ASVs into mothur for clustering, classification and general tidy up.
So far, I’ve edited the ASV file to imitate a shared mothur file, then used count.seqs to produce a count.table. However, when using count.groups on the original shared file and the produced count.table, I noticed a discrepancy in the count value of the first sample in count.table and also missing entries (usually the last two samples).
Shouldn’t the count values be the same? This seems like a minor glitch but it invalidates my import procedure… Is there an alternative?

I think I know what caused the problem: there were “empty” samples with 0 sequence counts in the original shared file. When taken out, the count.seqs procedure worked fine and there was no discrepancy between the shared file and the count.table…

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This is actually rather serious: having checked past projects, there are quite a few projects affected with now doubtful output, I’ve got an absolutely livid PI, my position is in question - and why didn’t I spot this error earlier?

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