---
name: "load2db"
section: "1"
platform: "linux"
package: "augustus"
version: "3.5.0+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/load2db"
---

# load2db(1)

load genome sequences and extrinsic evidence hints into a MySQL database

## NAME

load2db - load genome sequences and extrinsic evidence hints into a MySQL database

## SYNOPSIS

**load2db** \[OPTIONS\] --species=*SPECIES* --dbaccess=*dbname,host,user,passwd* *inputfilename*

## DESCRIPTION

**load2db** is a tool to load genome sequences and extrinsic evidence hints into a MySQL database.\
 This database must be created before calling **load2db**.\
 When storing genomes/hints of multiple organisms call this program repeatedly for each one.

## OPTIONS

*inputfilename* refers to a genome file in FASTA format or a hints file in GFF format.

### Mandatory options

- **-s**, **--species**=*SPECIES*

  SPECIES is a name for your species and the same identifier as is used in the treefile and alnfile parameters to augustus.

- **-d**, **--dbaccess**=*dbname,host,user,passwd*

  dbname,host,user,passwd are the name of the SQL database, the host name or IP, the database user and password

### Additional options

**-c**, **--chunksize**=*size* (⇐ 1000000)

This option is only relevant when loading a sequence file.\
 The sequences in the input genome are split into chunks of this size so that subsequent retrievals of small sequence ranges do not require to read the complete - potentially much longer - chromosome. Default Value: 50000

- **-h**, **--help**

  Produce help message.

## EXAMPLE

```
  create database before calling load2db:
   $ mysql -u root -p
   > CREATE DATABASE vertebrates;
   > CREATE USER 'myuser'@'%' IDENTIFIED BY 'mypasswd'; /* or whatever the password code is*/
   > GRANT ALL ON vertebrates.* TO 'myuser'@'%' IDENTIFIED BY 'mypasswd';
  load2db --species=mouse --dbaccess=vertebrates,localhost,myuser,mypasswd mouse.fa
  load2db --species=mouse --dbaccess=vertebrates,localhost,myuser,mypasswd mouse.hints.gff
  load2db --species=human --dbaccess=vertebrates,localhost,myuser,mypasswd human.fa
  load2db --species=human --dbaccess=vertebrates,localhost,myuser,mypasswd human.hints.gff
```

## AUTHORS

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.