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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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insufficient memory to build full kraken database requires at least 100gb of memory using mini db #196

Closed Ramanandan closed 9 years ago

Ramanandan commented 9 years ago

Dear Dr. Sergey Koren,

How do I install this full kraken database?

Can I download and placed it manually inside Utilities/DB?

Do we need 100GB of memory to download this full kraken database? or Do we need 100GB of memory to analyze our samples with the full kraken database?

insufficient memory to build full kraken database requires at least 100gb of memory using mini db

Cheers, Ram

skoren commented 9 years ago

Hi,

The default full Kraken database requires 100GB both to build and run efficiently. If you don't have 100GB, you would be unable to load it while running so downloading would not help: https://ccb.jhu.edu/software/kraken/MANUAL.html

Thus unless you have access to a machine with 100GB to run/build you would be unable to use the full Kraken DB.

Ramanandan commented 9 years ago

Thanks Dr. Sergey Koren, then I wont be able to work on full DB with my local machine (24GB ram) and work station (64 GB ram). Then I will try with our cluster which has 1000GB of ram. But I have to get many levels of permission :(.

skoren commented 9 years ago

The miniature database has reasonable sensitivity and specificity so before worrying about building the full DB, you can try analyzing your datasets with the miniDB and see how it performs.

avapirev commented 7 years ago

Hi, in the case of insufficient RAM for the whole Kraken DB on a certain machine, is there an option to point the pipeline to a different location where the full database resides. Just for reference, there are not that many clusters with 'fat' nodes where Kraken can be built by the users, only by the admins and this option is a bottleneck for many reserchers. Most HPC systems rely on many-core architectures and do not provide enough RAM for building Kraken. For using it - yes, not building though. Thank you.