sra-tools VS HomeBrew

Note that conda sra-tools does not support ARM (M chips use customized ARM architecture ) yet and the official repo also does not provide pre-compiled version for arm. You should be able to compile it from the source but YMMV. Similarly, STAR does not officially support ARM either but compilation on your own always worths a try.

According to this, the disk space required should be about 17 times the size of the accession (for both output files and tmp files). As can be seen below, I have >500GB of disk space. Yet, I receive this output:

Start with downloading SRA toolkit: https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-To...

Find some data of interest: https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[... (This searches SRA for human genome sequences on illumina with fastq files available)

Run fasterq-dump on the SRR (listed as "Runs" in the SRA page of your choice):

If you are okay with looking at already processed data, chdck out https://dee2.io/. Otherwise there is https://github.com/ncbi/sra-tools for getting fastq files (a cli tool) or https://github.com/saketkc/pysradb (python)

Fasterq-dump also doesnt play nice sometimes. By that I mean it causes problems like this https://github.com/ncbi/sra-tools/issues/383

In this case, you're missing software. Specifically, you're missing sra-tools. Fortunately, this is provided via Homebrew as sratoolkit. After installing that formula, you should be able to use the prefetch command.

Yeah, unfortunately this required key entry is by design for some reason (see more here https://github.com/ncbi/sra-tools/issues/291).

Before we start installing anything, if you are a Mac user, you need to install homebrew, a package manager for Mac that will help you install software quickly and easily from this article.

First, we are going to need Node.js. I use nodenv to manage multiple Node.js installations on my machine. The easiest way to install it on a Mac is to use Homebrew (check their Installation documentation if you’re on a different platform):

Homebrew - The Missing Package Manager for macOS (or Linux)

Homebrew is a highly popular package manager on macOS and Linux systems, enabling users to easily install, update, and uninstall command-line tools and applications. Its design philosophy focuses on simplifying the software installation process on macOS, eliminating the need for manual downloads and compilations of software packages.

Homebrew - package manager for linux-based OSs.

Package Manager: Homebrew

Hopping from one distro to another with a different package manager might require some time to adapt. Using a package manager that can be installed on most distro is one way to help you get to work faster. Flatpak is one of them; other alternative are Snap, Nix or Homebrew. Flatpak is a good starter, and if you have a bunch of free time, I suggest trying Nix.

Are you using SQLite that ships with macOS, or SQLite installed from homebrew?

I had a different problem in the past with the SQLite that ships with macOS, and have been using SQLite from homebrew since.

So if it’s the one that comes with macOS that gives you this problem that you are having, try using SQLite from homebrew instead.

https://brew.sh/

Before we begin, make sure you have Homebrew installed on your Mac. Homebrew is a package manager that makes it easy to install software and dependencies. You can install Homebrew by following the instructions on their website: https://brew.sh/

I’m on MacOS and erlang.org, elixir-lang.org, and postgresql.org all suggest installation via Homebrew, which is a very popular package manager for MacOS.