If you’re getting a “Fasterq-dump quit with error code 3” message while running it on a compute node, the problem could be caused by memory. The quickest way to fix this problem is to rerun the command on a different node, like Helix. Then, you can download the data using the flag -split-3. After this operation, you should be able to view the results in a new tab.
If the error code occurs while processing FastQ files, you may have to change the format in which it’s stored. If you want to process them in your own software, you should first use ENA, a tool that provides direct download links to FastQ files and md5 sums. Fastq-dump also allows you to split and compress the files in gzip. Depending on your configuration settings, you can use either format.
If you’re running Windows, you should avoid using fasterq-dump as this application isn’t available for your platform. However, if you need to perform a SRA dump, you should use fastqDump instead. You can download the files in advance using prefetch, which downloads the SRA files to the temporary location $TMPDIR. The path to SRAtoolkit functions is also available for fasterq-dump.
FASTQ-Dump is designed to work with SRA-accessions created with NCBI Sequence Read Archive Toolkit. It contains two fields, namely experiment accession and run accession. The experiment accession represents study metadata, while the library accession is the actual data of the sequencing experiment. It is important to install the SRA toolkit version 2.10.8 before running FASTQ-dump.