A failure of the classification of a reference genome

[biotengwk]

Dear authors, @pchaumeil

Hi! I'm a post-doctor researcher from China and my name is Wenkai Teng. Just in these days I have tried to classify a group of genomes using GTDBtk (v2.4.0) with the latest reference database (GTDB release 220). However, a genome from GTDB r220 itself, with the ID RS_GCF_002158865.1, and classification as Comamonas_E serinivorans, could not be classified with the result:

'GCF_002158865.1 Unclassified Bacteria ... Insufficient number of amino acids in MSA (3.1%)'

My colleague tried this using the GTDBtk of another version and got the similar result. Could you please help me to check why that is?

Thanks in advance，

Wenkai Teng

[biotengwk]

I think I have found it.

When running prodigal for GCF_002158865.1, -g 11 should be used. However, -g 4 were used by GTDBtk.