Crazy results

[spencer411]

I know this program is under development, but I am trying to id a bunch of species, and the results I am getting are all over the map. For example, I have a folder of isolates for which I was under the impression were all s. pseudintermedius, but when I run them using the following I get things like this:

sixess -d SILVA.gz 8050A_17.contigs.fa

I get: Top hit: CSCB01000016.56.1922
Description: >CSCB01000016.56.1922 Staphylococcus aureus
Species: Staphylococcus aureus

I also have a folder of reads that map 100% to the b. anthracis ames ancestor reference genome, and when I try those samples I get:

sixess -d SILVA.gz KNP_51.fa

Top hit: CFLJ01000066.3592.5030
Description: >CFLJ01000066.3592.5030 Streptococcus pneumoniae
Species: Streptococcus pneumoniae

Am I doing something wrong? I can't see how this program could possibly be this wrong, or maybe I'm that wrong? Nevertheless, I am pretty positive, at least about the b. anthracis samples, that it is definitely b. anthracis. Could this just be contamination? Some of these are coming out as Bacillus phocaeensis, and Bacillus cereus etc...

I know that both of my folders (anthracis and pseudintermedius) have pairwise ANIs way under 95%, and checkm also puts their contamination under 95%.

Just trying to figure out what is going on here, whether I have a bunch of wrong or contaminated samples from PIs who arent sure what they are doing, or whether this program has a lot more development to go, or whether I am an idiot and doing something wrong (this being the most likely scenario).

Any help is appreciated!