Question: Jellyfish version problem Kraken
gravatar for owenz
2.2 years ago by
owenz10 wrote:

I installed Kraken on Linux and was about to build the bacterial db. Unfortunately, the Jellyfish version installed was 2.2.8 which is not compatible with Kraken.

I uninstalled this version and tried to install the necessary 1.1.11 version through apt. Unfortunately it was not retrieved.

I download the tar.gz and tried to change the PATH variable but when I tried to enter the Kraken build command, it was still not effecting.

Could this also be a problem with Kraken and the threads required? What should be the ideal thread count?

Thanks in advance

jellyfish kraken • 610 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by owenz10

The problem now seems to be to limit hash size on a 32gb Ram PC. What should be ideal?

ADD REPLYlink written 2.2 years ago by owenz10

Find other hardware with more RAM? There is really no substitute for lack of adequate RAM.

ADD REPLYlink written 2.2 years ago by GenoMax94k

Both Kraken and Kraken2 provide a "MiniKraken" pre-built database, including bacterial, archaeal, and viral genomes:

ADD REPLYlink written 2.2 years ago by h.mon32k
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