How to download SRA files

You can download .sra files using SRA Toolkit.

Install SRA Toolkit

Download the latest version of SRA Toolkit from here. In this post, I downloaded the sratoolkit.2.10.5-mac64.tar file for macOS and unpack the SRA Toolkit (Options: x = extract, v = verbose, f = file).

tar -xvf sratoolkit.2.10.5-mac64.tar

sratoolkit.2.10.5-mac64/bin/prefetch SRR5721625

When I ran the above command on macOS Catalina (version 10.15.3), I got the following error:

“sratools.2.10.5” cannot be opened because the developer cannot be verified.

Click the “Cancel” button to close the error message window. Go to System Preferences > Security & Privacy > General, and click the “Allow Anyway” button right to the "sratools.2.10.5" was blocked from use because it is not from an identified developer. message.

When I ran sratoolkit.2.10.5-mac64/bin/prefetch command again, I saw macOS cannot verify the developer of “sratools.2.10.5”. Are you sure you want to open it? message. I clicked the “Open” button. But another file (vdb-config.2.10.5) was blocked for the same reason. I repeated the similar things until it finally worked.

The default download directory is Users/[user name]/ncbi/public/sra in macOS.

Another options

Go to System Preferences > Security & Privacy > Privacy, and select “Developer Tools.” Allow And then restart

Or you can install using homebrew:
brew install -v sratoolkit

Download SRA files using sratoolkit

You can use the prefetch utility in the SRA Toolkit to download SRA data and any required reference sequences in a single operation. Prefetch can be used on single data file or to batch download several at a time.

# Download a single file
sratoolkit.2.10.5-mac64/bin/prefetch SRR5721625

# Download multiple files
sratoolkit.2.10.5-mac64/bin/prefetch SRR5721625 SRR5721626

# Download all of the files listed in the SraAccList.txt file
sratoolkit.2.10.5-mac64/bin/prefetch --option-file SraAccList.txt

### SraAccList.txt ###

Convert SRA files to FASTQ files

# Paired-end
fastq-dump -I --split-files SRR5721625.sra

In this case, the output files are SRR5721625_1.fastq and SRR5721625+2.fastq.

If you are familiar with Docker, you can use NCBI’s Docker image:

docker run --rm -v "$(pwd)":/data -w /data ncbi/sra-tools fastq-dump --split-files SRR5721625.sra --gzip

Also, you can use multi-threaded fasterq-dump. You can specify the number of thread by -e. Note that unlike fastq-dump, there is no --gzip|--bizp2 option (as of 2021/05/02), so you may want to compress your files after they have been written (link).

docker run --rm -v "$(pwd)":/data -w /data ncbi/sra-tools fasterq-dump SRR5721625.sra -e 10

gzip *.fastq

# Or you can use pigz
pigz *.fastq



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