---
tags: kraken2
title: 21-Jan-2022 kraken2 standard db
---
# 21-Jan-2022 kraken2 standard db
The way the error was addressed and how it was built is below, if wanting to do it. But the database I built with the code below can also just be downloaded from the last section. It's 56 GB when uncompressed.
[toc]
## Conda env
```bash
conda install -c conda-forge mamba
mamba create -n kraken2 -c conda-forge -c bioconda -c defaults kraken2=2.1.2
conda activate kraken2
```
## Addressing error
Running the standard build command was leading to an `rsync_from_ncbi.pl: unexpected FTP path (new server?)` error and killing the build program. There are a few issues on their github, [one stating](https://github.com/DerrickWood/kraken2/issues/292#issuecomment-689930681) they fixed it in an earlier version, but it still seems to be a problem. May be due to changes in NCBI messing with their program. But [this post](https://github.com/DerrickWood/kraken2/issues/226#issuecomment-942104929) had a tip that worked for me.
We need to modify the `rsync_from_ncbi.pl` script at line 46, changing "ftp" to "https".
In the active kraken2 conda environment, we can run this to edit the appropriate file:
```bash
nano -l ${CONDA_PREFIX}/libexec/rsync_from_ncbi.pl
```
That will open this in our terminal window:
<a href="https://i.imgur.com/JMZxKyC.png"><img src="https://i.imgur.com/JMZxKyC.png"></a>
We want to scroll down to line 46, and change this highlighted "ftp":
<a href="https://i.imgur.com/sUb9bsq.png"><img src="https://i.imgur.com/sUb9bsq.png"></a>
To be "https" like this:
<a href="https://i.imgur.com/6BQJ2O6.png"><img src="https://i.imgur.com/6BQJ2O6.png"></a>
Then to save, we want to press `ctrl+x`, it will ask if we want to "Save modified buffer?" or something similar at the bottom. Press `y` to save it, then press `return/enter` to save it under the same file name. Then we will have our normal prompt back and be ready to do the build.
## Building standard db
This was run on 21-Jan-2022
```bash
kraken2-build --standard --threads 32 --db kraken2-standard-21-Jan-2022
```
That took about 9.5 hours as run above. After it's done, we can run this to remove intermediate files and save a ton of space:
```bash
kraken2-build --clean --db kraken2-standard-21-Jan-2022/
# Database disk usage: 211G
# After cleaning, database uses 56G
```
Compressing:
```bash
tar -czvf kraken2-standard-21-Jan-2022.tar.gz kraken2-standard-21-Jan-2022/
```
## Download standard db built on 21-Jan-2022
Run the following if wanting to download the database built above.
```bash
curl -Lo kraken2-standard-21-Jan-2022.tar.gz https://figshare.com/ndownloader/files/33894434
tar -xzvf kraken2-standard-21-Jan-2022.tar.gz
```