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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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Kraken2 database built not properly but without error #328

Open t-walter opened 3 years ago

t-walter commented 3 years ago

Hello,

I am trying to build standard kraken2 database. I have used the default command: kraken2-build --standard --threads 8 --db kraken_standard The database is created without any errors but I suppose that it is not built properly. After running classification I obtain taxonomic assignment for only about 0.04% of reads, all of them being assigned to human.

As a comparison I performed classification with MiniKraken2_v2_8GB database obtaining much more results (most of them being bacterial or archeal classifications). Also the hash.k2d file is smaller (4.6 GB) in case of my standard db then minikraken db. I have tried building smaller db with the following commands: kraken2-build --download-taxonomy --db kraken_custom kraken2-build --download-library archaea --db kraken_custom kraken2-build --build --threads 8 --db kraken_custom After running classification, no reads were assigned at all (100% unclassified).

Maybe it could matter that I am using conda installation of kraken2.

Could you advise me what could be the source of the problem and how to solve it?

Thanks in advance!

Tomek

jenniferlu717 commented 3 years ago

I would need more information. What is the sample that you are using?

What is the output from your kraken2-build commands?