-taxOnly seems to discard some sequences

[ingeborgklara]

Hello,

I am running lotus2 only for taxonomy assignment of ITS1 sequences (so -taxOnly) (which is great! works super fast). I assumed that the output file would contain the same number of sequences as the input file, but with taxonomic assignments. However, not all sequences make it through taxonomy assignment. I have already tried adding other options to make sure none of my sequences are discarded, but it does not change. Is there an additional quality check happening during taxonomy assignment that I am not aware of?

I use the following code:

lotus2 -taxOnly ~seqtab.nochimITS.fasta -refDB ~/sh_refs_qiime_ver10_99_s_all_04.04.2024.fasta -tax4refDB ~/sh_taxonomy_qiime_ver10_99_s_all_04.04.2024.txt -taxAligner lamda -lulu 0 -ITSx 0 -clustering 7 -deactivateChimeraCheck 1 -buildPhylo 0 -backmap_id 1 -verbosity 3 -keepOfftargets 1 keepUnclassified 1 -keepTmpFiles 1 -redoTaxOnly 1