I am trying to analyse my eukaryotic metagenome data using yours workflow
for windshield splatter analysis. But I find several problems:


1- it is related to "draw phylogeny", this tool fails always for most of my
samples, reporting the error: incorrect tree structure. Tree string position


2- It is related with the "summarize taxonomy" step. I this case I obtain
results but the number of counts are too high compared with the original
reads. My samples are small, around 8000 reads and the counts obtained are
more that 200000 for some phyla. I guess this is not ok, as far as I
understand from your paper than counts are equivalent to reads, am I right?


3- another strange thing is the fact that the number of sequences increase
after run the step for select the high quality segments. Any reason for


I will really appreciate you help. Thanks in advance




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