Chimera detection --uchime_ref unexpected behaviour

[nvucic]

Hello,

I've been using --uchime_ref to identify chimeras providing a list of reference sequences in FASTA format. I noticed that vsearch does not report match with highest score when there are large number of sequences (~5k) between second best and best match in cases where second match comes first in the FASTA file. I could provide test data if necessary.

Can you suggest any kind of workarund or fix for this?

Best, Nemanja