# SRA-Toolkit Faster Download and Extract Reads in FASTQ: fasterq-dump: command not found
**URL:** https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605
**Category:** Uncategorized
**Tags:** devops-administration, galaxy-local
**Created:** [January 28, 2024, 1:43pm UTC](https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605 "2024-01-28T13:43:28Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@KaunoSeptintasFortas](https://help.galaxyproject.org/u/KaunoSeptintasFortas)
#### Post date: [January 28, 2024, 1:43pm UTC](https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605/1 "2024-01-28T13:43:28Z")
Hello, I am installed and configured SRA-Toolkit on local galaxy server.
After running script, I have got error:
Downloading accession: SRR27174817…
/home/biodata/galaxy/database/jobs\_directory/000/435/tool\_script.sh: line 62: fasterq-dump: command not found.
Maybe you know what is wrong?
If I install sra-tools via sudo apt it works perfectly
---
### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [January 31, 2024, 6:59pm UTC](https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605/2 "2024-01-31T18:59:50Z")
Welcome, @KaunoSeptintasFortas
> [@KaunoSeptintasFortas](#):
>
> Downloading accession: SRR27174817…
> /home/biodata/galaxy/database/jobs\_directory/000/435/tool\_script.sh: line 62: fasterq-dump: command not found.
The “not found” error message means the environment that the job is running in has a configuration problem. The root issue is usually some dependency problem (not installed, or has incorrect permissions).
You can install tools directly in the Galaxy application and check the box to use dependencies resolvers (Admin → Tool Management) or you can batch the work with helper scripts (example → [Hands-on: Hands-on: Galaxy Tool Management with Ephemeris / Galaxy Server administration](https://training.galaxyproject.org/training-material/topics/admin/tutorials/tool-management/tutorial.html)).
Resources
> [@Private Galaxy Servers](https://help.galaxyproject.org/t/private-galaxy-servers/10861/1):
>
> ### Local Galaxy
>
> A local Galaxy server is a choice for personal use, and can be scaled to support multiple users.
>
> Your service can be hosted publicly or privately. Connect to local, institutional, or commercial cloud computing resources and customize your usage policies.
>
> 💻 Local Galaxy
>
> - Training Network [Galaxy server administration training](https://training.galaxyproject.org/training-material/topics/admin/)
> - Technical Documentation [Galaxy releases, plus Admin and Development docs](https://docs.galaxyproject.org)
> - Open-source code base [GalaxyProject Github repositories](https://github.com/galaxyproject)
---
### Author:  [@KaunoSeptintasFortas](https://help.galaxyproject.org/u/KaunoSeptintasFortas)
#### Post date: [January 31, 2024, 7:22pm UTC](https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605/3 "2024-01-31T19:22:16Z")
Hello, the problem was in dependence version (actually problem was in bad quality of galaxy management). SRA-Toolkit wants dependence version does not existing on galaxy toolshed. I spend this problem changing dependence version in toolkit code.
The more I use galaxy the more I think it is better not to use galaxy…
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### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [January 31, 2024, 7:37pm UTC](https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605/4 "2024-01-31T19:37:38Z")
Hi @KaunoSeptintasFortas
Reproducibility always has some cost/benefit trade offs! But I’m glad that you were able to get this working, and maybe your comments about the how-to will help others 🙂
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### Author:  [@KaunoSeptintasFortas](https://help.galaxyproject.org/u/KaunoSeptintasFortas)
#### Post date: [January 31, 2024, 9:13pm UTC](https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605/5 "2024-01-31T21:13:07Z")
Actually, it is not history of reproducibility, just one more case to think about proper Galaxy support. It is OK po pay for it and have quality service than have random service with random support 🙂
Now I am fighting with Galaxy Annovar and I am shure I will fail again ☹
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### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [January 31, 2024, 11:06pm UTC](https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605/6 "2024-01-31T23:06:03Z")
Hi @KaunoSeptintasFortas
**Annovar** is no longer available. Why? The original tool author doesn’t want it to be available open source. They may have left the wrapper in the Tool Shed, and that version worked with just one genome (hg19) with earlier Galaxy versions but not likely with current versions. I don’t know the status beyond that and we’ve removed it from the public servers.
If it still interests you, you should contact the tool author directly to see if they will offer a site license for private use and maybe some custom advice for getting more genomes supported, or even hg19 again, plus help with any wrapper updates that may be needed.
As for paying for support, the core team releases everything – all software and all computational infrastructure at public servers – for free with zero monetization. That means others can offer pay-for-service flavors, and they do!
Review here for all of the choices we know about.
> [@Private Galaxy Servers](https://help.galaxyproject.org/t/private-galaxy-servers/10861/1):
>
> ## Private Galaxy server
>
> [**Public Galaxy servers**](https://help.galaxyproject.org/t/10860/) are a convenient choice for researchers world wide.
>
> Need more? Consider setting up a **private Galaxy server** where you can control the resources.
>
> Selected choices are below, please see the **Galaxy Directory** for all.
>
> 🚀 [Galaxy Platform Directory: Servers, Clouds, and Deployable Resources - Galaxy Community Hub](https://galaxyproject.org/use)
And, if the configuration for a stand-alone server seems to include more than you need, we do offer a free Docker version to consider. Same page as the two before but I’ll quote here directly.
> [@Private Galaxy Servers](https://help.galaxyproject.org/t/private-galaxy-servers/10861/1):
>
> ### Docker Galaxy
>
> Much comes pre-configured, and common administrative tasks are simpler to implement and maintain. Be sure to review the repository’s README for these custom instructions.
>
> 🐋 Docker Galaxy
>
> - [Galaxy Docker - Galaxy Community Hub](https://galaxyproject.org/use/galaxy-docker/)
And finally, there are many Matrix chats you can visit for one-off administrative questions. These reach the developers directly, both core team and community contributors. We are organized into **Working Groups** and the resources for all can be found here, including the chats. → [Galaxy Working Groups | Galaxy Hub](https://galaxyproject.org/community/wg/)
Update 2026: For updated methods, please see 🎓 [https://galaxyproject.github.io/training-material/topics/variant-analysis/](https://galaxyproject.github.io/training-material/topics/variant-analysis/) and [ANNOVAR alternative](https://help.galaxyproject.org/t/annovar-alternative/3373)
---
### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [March 17, 2026, 4:43am UTC](https://help.galaxyproject.org/t/sra-toolkit-faster-download-and-extract-reads-in-fastq-fasterq-dump-command-not-found/11605/7 "2026-03-17T04:43:54Z")