Filtering sequencing error


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?


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

Maybe instead use --p-include g__Streptococcus

Good luck!

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.