Filtering sequencing error

[maysa1 (maysa)]

Hello,

I am trying to figure out how many ASVs I have for Streptococcus genus and if I really have different species of Streptococcus or I just call the organism twice?I tried to filtering the sequencing to just include Streptococcus so I can blast them and compare the species.
I have two questions:
1- I run the following code and got an error that "All features were filtered, resulting in an empty collection of feature sequences. " what’s wrong with the code?

qiime taxa filter-seqs \
–i-sequences rep-seqs1.qza
–i-taxonomy taxonomy.qza
–p-include “k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae ;g__Streptococcus”
–o-filtered-sequences sequences-of-streptococcus.qza

2- Is there another way to ensure that I have different species since ASVs have no meaningful IDs?

Best,
Maysa

[Nicholas_Bokulich]

@maysa1

" All features were filtered, resulting in an empty collection of feature sequences. " what’s wrong with the code?

your filtering criteria are probably too strict. Even minor spelling errors in here (or spaces or invisible characters, etc) could cause this to fail:

@maysa1

–p-include “k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae ;g__Streptococcus”

Maybe instead use --p-include g__Streptococcus

Good luck!