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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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unmapped sequences during the first step of building the database #708

Open AzizHN opened 1 year ago

AzizHN commented 1 year ago

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

ADVANCMENT: I tried with fix_unmapped.py but the problem persists.

AzizHN commented 1 year ago

@DerrickWood @jenniferlu717 Thank you for your time !