I was recently asked about percentages of sequences removed from each sample that classified as chloroplast/mitochondria. I checked the log output for the run, I thought I remembered that terminal output gave percentages of lineage removed for each sample, but it looks like that is not or no longer printed to the log output. Is there an easier way than calculating percentages from files before and after remove.lineage? Or what version of mother can I go back to so that I can run the command and see the percentage of sequences removed on on the terminal? Or am I imagining that it ever did that in the first place?
I don’t recall that ever being there. I would look at the output from classify.seqs to find the number of those groups you removed from the analysis.
I think I was thinking of % chimeras, that shows up in the terminal feed but doesn’t get printed to the log. I did make.share from the count_table file before and after remove.linage, and count.groups to compare them. Was surprised to find kind of a big difference between two processes for leaf endophytes, although the two groups had similar amounts of bacterial sequences after filtering, there was definitely a lot more plant sequence in one set of samples. Good to know!