why does fasterq dump quit with error code 3 1406

Why Does Fasterq-Dump Quit With Error Code 3?

If you see the error message, “fasterq-dump quit with error code 3”, then there’s a good chance that you’re using a non-helix node. In this case, you need to run fasterq-dump on another node, such as a Helix node. If this does not fix the problem, you can use flag -split-3 to download paired reads.

Another possible solution is to use prefetch, which downloads temporary SRA files into $TMPDIR, usually /tmp. Alternatively, you can use the CACHE instead. The fasterq-dump function will print stdout to the console, which will show the start and end times of the download. You’ll need to modify your filename accordingly to prevent the error from reoccurring.

Another way to fix this error is to use trimgalore or fasterq-dump. These are the fastest available tools for analyzing SRA data. The former has been deprecated in favor of trimgalore, and the latter is a faster data dump. Trimgalore uses the local disk as a temporary directory. The second method uses a SRAtoolkit module and is not available for Windows. If you use fasterq-dump on a Windows system, you can simply use its Windows counterpart fastq-dump.

FASTQ-Dump requires SRA-accessions, which can eat up lots of disk space. However, this tool uses multi-threading and temporary files to speed up the extraction of FASTQ from the SRA. However, if you use the newer version, you need to add the flag –split-3 to avoid a single paired read. Previously, you might need to use the flag –skip-technical, but it’s no longer necessary with fasterq-dump.