<p>A question to those who have experience with <a href="https://github.com/muellan/metacache#detailed-installation-instructions" rel="nofollow noreferrer">MetaCache (metagenomic tool)</a>:</p>
<p>I have tried to build the MetaCache taxonomy from refseq (only bacteria), <a href="https://github.com/muellan/metacache/blob/master/docs/mode_build.txt" rel="nofollow noreferrer">as described in the EXAMPLES here</a>. 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.</p>
<p>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?</p>
<hr />
<p><a href="https://academic.oup.com/bioinformatics/article/33/23/3740/4083578" rel="nofollow noreferrer">MetaCache</a> is a classifier in the Kraken mould. Here's the blurb.</p>
<blockquote>
<p>Metagenomic shotgun sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments.</p>
</blockquote>
<p>...</p>
<blockquote>
<p>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.</p>
</blockquote>

CC BY-SA 4.0
2022-08-25T10:56:49.823Z
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](https://en.wikipedia.org/wiki/Solid-state_drive) drive, an [HDD](https://en.wikipedia.org/wiki/Hard_disk_drive) drive will take much longer.
Guy Coder
CC BY-SA 4.0
2022-08-25T12:39:56.527Z
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."
M__
CC BY-SA 4.0
2022-08-29T14:18:45.033Z
Perhaps consider `Kraken2`?
M__
CC BY-SA 4.0
2022-08-29T14:20:09.667Z
@M__ Kraken2+Bracken work fine (perhaps because I am using a pre-existing downloaded index). I am interested specifically in MetaCache.
Roger V.
<database><software-installation><public-dataset>
Building database for MetaCache takes extremely long
# Building database for MetaCache takes extremely long

(Asked by: username_0 on 2022-08-25)

A question to those who have experience with [MetaCache (metagenomic tool)](https://github.com/muellan/metacache#detailed-installation-instructions):

I have tried to build the MetaCache taxonomy from refseq (only bacteria), [as described in the EXAMPLES here](https://github.com/muellan/metacache/blob/master/docs/mode_build.txt). 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](https://academic.oup.com/bioinformatics/article/33/23/3740/4083578) 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.

**Tags:** database, software-installation, public-dataset
> **Comments:**
> **username_1**: 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](https://en.wikipedia.org/wiki/Solid-state_drive) drive, an [HDD](https://en.wikipedia.org/wiki/Hard_disk_drive) drive will take much longer.  
> **username_2**: 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."  
> **username_2**: Perhaps consider `Kraken2`?  
> **username_0**: @M__ Kraken2+Bracken work fine (perhaps because I am using a pre-existing downloaded index). I am interested specifically in MetaCache.  

---

## 0 answers

