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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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E-value of -1 #162

Open em9 opened 2 years ago

em9 commented 2 years ago

Hi,

I'm running phyloFlash v3.3b2 with default parameters, with the exception of -readlength. I noticed that the SSU rRNA assembly-based taxa output in the summary shows an E-value of -1. This is also the case in the test output online (https://hrgv.github.io/phyloFlash/test.phyloFlash.html).

Does this have to do with the parameters I am using, or is it in error?

Thanks!

kbseah commented 2 years ago

Thanks for catching this. It's not to do with the parameters you are using. Vsearch doesn't calculate an E-value for nucleotide alignments and sets it by default to -1. We should simply drop this column in the future.