Hi,

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 341

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 this???

I will really appreciate you help. Thanks in advance

Asun