A question to those who have experience with MetaCache (metagenomic tool):

I have tried to build the MetaCache taxonomy from refseq (only bacteria), as described in the EXAMPLES here. However, the process turned out to be excruciatingly long, and I eventually gave up waiting after a week, reaching the progress of only 45%. I am using a 32-core server and the MetaCache seemed to make use of at least 16 cores, so I am puzzled by such slowness.

Is this normal behavior? Are there ways to do this faster or pre-built (relatively recent) databases? Is there a specific MetaCache forum, where I could pose a question to the developers?

MetaCache is a classifier in the Kraken mould. Here's the blurb.

Metagenomic shotgun sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments.


As a result, MetaCache consumes significantly less memory compared to the state-of-the-art read classifiers Kraken and CLARK while achieving highly competitive sensitivity and precision at comparable speed.

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    $\begingroup$ I don't use MetaCache but do other things that take days for building. While you note how many cores you have you did not note how much memory you have. The instructions note with default settings your system should have around 64GB of RAM Also they probably used as SSD drive, an HDD drive will take much longer. $\endgroup$
    – Guy Coder
    Aug 25, 2022 at 10:56
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    $\begingroup$ Maybe state the database size and RAM as the MetaCache abstract states, > "For example, using NCBI RefSeq draft and completed genomes with a total length of around 140 billion bases as reference, MetaCache’s database consumes only 62 GB of memory while both Kraken and CLARK fail to construct their respective databases on a workstation with 512 GB RAM." $\endgroup$
    – M__
    Aug 25, 2022 at 12:39
  • $\begingroup$ Perhaps consider Kraken2? $\endgroup$
    – M__
    Aug 29, 2022 at 14:18
  • $\begingroup$ @M__ Kraken2+Bracken work fine (perhaps because I am using a pre-existing downloaded index). I am interested specifically in MetaCache. $\endgroup$
    – Roger V.
    Aug 29, 2022 at 14:20


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