i can't find the SRR sample on NCBI FTP, such as SRR018260

Question

[zhao03]

I used FTP to search SRR018260 that i want to download, however, SRR018260 sample can't be found. is the website error? or i should download from other website. thank you for your answers.

FTP: https://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/ SRR018260 on NCBI: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR018260

i tried to download by prefetch.2.9.3 -v SRR064286, there was error to come, "transfer incomplete while reading file within network system module - Cannot KStreamRead: https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR064286/SRR064286.2"

[AK]

Can you try fastq-dump? I was able to download SRR018260 by:

fastq-dump --split-spot --split-files --gzip -A SRR018260

[Mensur Dlakic]

Lots of useful info about downloading SRA files can be found here and here.

Answer 1

[GenoMax]

You can find the fastq files at EBI-ENA SRR018260. In future use ENA where possible to get fastq files.

Answer 2

[JC]

A few weeks ago I have a similar case, so I reported to the NCBI staff who responded:

This location became unsustainable long time ago and is not maintained. New data were not added for years. You need to use SRA Toolkit for downloading SRA data. Please refer to the Download guide: https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/

So, you cannot trust the FTP server, use sratoolkit or ENA.

Answer 3

[ATpoint]

Don't download via that ftp server. Use SRAtoolkit or directly get fastq files from the ENA. For a tutorial on both see: Fast download of FASTQ files from the European Nucleotide Archive (ENA)