PGAP LTP issue and --auto-correct-tax

[arunprasanna83]

Hello, I assembled a genome with SPAdes --> checkM. CheckM showed it as Rhizobiales with 99.6% completeness. But ANI identified it as Altermonas.

I thought of trying RAPT in one go in local workstation.

./run_rapt.py -q R1.fq.gz,R2.fq.gz --organism "Alteromonas" --strain "AK250" -o RAFT_testout --auto-correct-tax -c 64

The number of contigs, N50 is same as SPAdes assembly. However, ANI report shows the following:

Submitted organism: Alteromonas (taxid = 226, rank = genus, lineage = Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Alteromonas/Salinimonas group) Predicted organism: Martelella lutilitoris (taxid = 2583532, rank = species, lineage = Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Aurantimonadaceae; Martelella)

Also, auto-correct-tax did not override the Alteromonas to Matelella in the final output.

The completeness is also low with 49.6%

Another question is: How to provide LTP prefix for PGAP?

Error: no LTP specified, locus tag prefix 'pgaptmp' will be used

I would like to provide a desired prefix.

Thanks in advance.