Hi Mathilde,

Thank you for reporting this issue.

Both the time used and the lack of any results for most of the sequences look very strange. I have therefore tried to reproduce your efforts and downloaded the SINTAX_COI_v5.1.0ref.fasta file from the https://github.com/terrimporter/CO1Classifier repository.

It seems like the problem is related to masking of the sequences in the database. By default, vsearch applies "soft masking" to the sequences in the databases. That means that all lower case letters are masked and not used during the initial stage of sequence comparison. It is described in the manual, but it is not mentioned for the sintax command, so we need to improve the documentation. Perhaps it should not even be applied by default for this command. Since the database seems to only contain lower case letters for the nucleotide symbols, all of the sequences are masked, leaving no results.

I am sorry that you have wasted 13 days of computation time (times 40 cpus) with this. The good news is that this problem can be easily resolved by including the --dbmask none option on the command line. When I did this with 10710 randomly subsampled sequences from the same database, the whole run completed in under 10 minutes using 8 threads and less than 6GB memory on my Macbook. And the results looked reasonable.

For a future release of vsearch we should consider:

• Update documentation regarding soft-masking and sintax
• Should soft-masking be applied at all (by default) for the sintax command?
• Should a warning be issued when detecting fully masked sequences in the query or database, in general?

Hi Torbjørn,

thank you very much for your quick response, explanation, and for running the test, it was very insightful ! I'm glad this is such an easy fix, because I was planning to use vsearch with sintax for all my databases.

Best wishes,
Mathilde Salamon