Hi, I assembled my metagenomic sequences using SPAdes and then the resulting fasta file was mapped using DIAMOND to generate the .daa files. I created the DIAMOND database as suggested in the generic pipeline. After that when I meganize the .daa file with the mapping file nucl_acc2tax-Oct2017.abin, none of my sequences are assigned to a taxonomic group.
I’m not sure how to help you with your error - are you sure the meganizing step completed without errors?
But overall, for contigs or scaffolds I suggest to use LAST instead of Diamond.
The resulting maf file should be sorted and using sort-last-maf,
and converted to RMA with blast2rma providing it with the mapping files. Both available in MEGAN tools directory.