Hello, I am trying to build a costumed database, including all reference genomes of fungi, bacteria, archaea, viruses, and Homo sapiens.
I am facing a problem in the first step: Creating sequence ID to taxonomy ID map. I had a message saying:
Found 10361157/19252012 targets, searched through 948300298 accession IDs..
lookup_accession_numbers: 8890855/19252012 accession numbers remain unmapped, see unmapped.txt in DB directory
Sequence ID to taxonomy ID map complete. [17m6. 413s]
I tried those 3 codes separately:
kraken2-build --build --db microbialDB/ --threads 3
kraken-build --build --db microbialDB/ --kmer-len 100 --threads 3
kraken2-build --build --threads 3 --fast-build --db microbialDB/ --kmer-len 100
But with all the 3 codes, the same thing happens. I always have unmapped sequences which can affect my taxonomic classification after.
Does anyone have an idea how to solve the problem? Thanks in advance
