bitscore and evalue after running qiime feature-classifier classify-consensus-vsearch

[Hiromi]

Hi all,

I am new using Qiime2, so I am sorry if I repeat a question in the forum. I have searched but couldn't find something similar.

I am using Qiime2 v2023.9. I run qiime feature-classifier classify-consensus-vsearch, the classification was really good, but after visualizing the outputs of "--o-search-results" the bitscores are all 0 and evalues -1, and I wonder if there must be an error in my results then.

qiime feature-classifier classify-consensus-vsearch
--i-query Query_seq/filtered-seq-VV_ITS2-229-215.qza
--i-reference-reads Ref_seq/Local/Local_ITS2_VV_seq_derep.qza
--i-reference-taxonomy Ref_Tax/Local/Local_ITS2_VV_taxa_derep.qza
--p-maxaccepts 4
--p-perc-identity 0.97
--p-min-consensus 0.97
--p-query-cov 0.97
--p-top-hits-only True
--p-strand plus
--p-maxhits 10
--o-classification Taxonomy_VV_ITS2_local_vsearch_4979797_Trueplus.qza
--o-search-results Top_hits_VV_ITS2_local_vsearch_4979797_Trueplus.qza

I will really appreaciate your help.

Kind regards,

Hiromi

[colinbrislawn (Colin J Brislawn)]

@Hiromi

the bitscores are all 0 and evalues -1, and I wonder if there must be an error in my results then.

Nope, your results are okay! Those columns are only used by blast

From the vsearch manual:

Warning, vsearch uses global pairwise alignments, not blast’s seed-and-extend algorithm. Therefore, some common blast output values (alignment start and end, evalue, bit score) are reported differently.
...

11. evalue: expectancy-value (not computed for nucleotide alignments).
    Always set to -1.
12. bits: bit score (not computed for nucleotide alignments). Always set to 0.

[Hiromi]

I totally missed that part
Thank you so much!

[colinbrislawn (Colin J Brislawn)]

Thank you for bringing this to our attention!

This is known behavior for vsearch, but we could improve its presentation within Qiime2.

GitHub x-ref