Question

Error during prefetch

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3.0 years ago

Princy ▴ 60

Please guide me, why this error is coming. I need to download SRA files.

Screenshot

Prefetch SRR SraToolkit NCBI • 1.2k views

ADD COMMENT • link updated 16 months ago by Ram 44k • written 3.0 years ago by Princy ▴ 60

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This command works perfectly fine for me using prefetch v2.11.0 and v2.8.2. Have you tried rerunning the command? Could be a network issue on your end

ADD REPLY • link 3.0 years ago by Philipp Bayer 8.7k

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Yes, I tried, but it did not work. So, I used ENA.

ADD REPLY • link 3.0 years ago by Princy ▴ 60

score 1 · Answer 1 · 2021-09-16

Maybe a connection problem, not unusual with NCBI. There is no need to bother with the NCBI Toolkits, you can get fastq files directly with links from e.g. sra-explorer.info

If you visit that website (which is a wrapper around the NCBI and ENI APIs) and enter your accession it will return several download links, e.g. these to get fastq directly:

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR704/004/SRR7046484/SRR7046484_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR704/004/SRR7046484/SRR7046484_2.fastq.gz

so simply do a wget or curl to get them:

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR704/004/SRR7046484/SRR7046484_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR704/004/SRR7046484/SRR7046484_2.fastq.gz