Question: i can't find the SRR sample on NCBI FTP, such as SRR018260
0
gravatar for zhao03
6 weeks ago by
zhao030
zhao030 wrote:

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"

rna-seq software error • 213 views
ADD COMMENTlink modified 6 weeks ago by JC8.2k • written 6 weeks ago by zhao030

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

fastq-dump --split-spot --split-files --gzip -A SRR018260
ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by SMK1.8k

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

ADD REPLYlink written 6 weeks ago by Mensur Dlakic520
1
gravatar for genomax
6 weeks ago by
genomax70k
United States
genomax70k wrote:

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

ADD COMMENTlink written 6 weeks ago by genomax70k
1
gravatar for JC
6 weeks ago by
JC8.2k
Mexico
JC8.2k wrote:

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.

ADD COMMENTlink written 6 weeks ago by JC8.2k
1
gravatar for ATpoint
6 weeks ago by
ATpoint21k
Germany
ATpoint21k wrote:

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)

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by ATpoint21k
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