I tried to use MALT to perform metagenomic classification analysis on a viral custom database that I set up using malt-build. When I check the output rma6 file on MEGAN, I found some reference genomes are assigned to wrong taxonomy ID. For example, here is the taxonomy ID showed in rma6 file,
>AY007505.3|tax|28037::288 -> the taxid belongs to bacteria >AJ302074.2|tax|1313::33 -> the taxid belongs to bacteria
But then I check the viruses.accession2taxid file I used for building the custom database, they are correct and looks as the following:
AY007505 AY007505.3 157924 32441581 AJ302074 AJ302074.2 120574 20067966
It seems that some of reference genomes are assigned to completely wrong taxid. Is it because my accession to taxid format is wrong or ? Here I also attached my command how to build the database.
malt-build -J-Xmx50G -i ./*.fasta.gz --sequenceType DNA --index viral -a2t viruses.accession2taxid -t 2
BTW, the version of MALT I used is 0.6.1
Thank you for helping in advance!