Question: Jellyfish version problem Kraken
gravatar for owenz
7 months 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 • 237 views
ADD COMMENTlink modified 7 months ago • written 7 months 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 7 months ago by owenz10

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

ADD REPLYlink written 7 months ago by genomax68k

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

ADD REPLYlink written 7 months ago by h.mon25k
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