Jellyfish version problem Kraken

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5.5 years ago

owenz ▴ 20

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

kraken jellyfish • 1.5k views

ADD COMMENT • link 5.5 years ago by owenz ▴ 20

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

ADD REPLY • link 5.5 years ago by owenz ▴ 20

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

ADD REPLY • link 5.5 years ago by GenoMax 141k

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

https://www.ccb.jhu.edu/software/kraken/dl/minikraken_20171019_8GB.tgz

https://www.ccb.jhu.edu/software/kraken2/dl/minikraken2_v1_8GB.tgz

ADD REPLY • link 5.5 years ago by h.mon 35k

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