Question: i can't find the SRR sample on NCBI FTP, such as SRR018260
0
gravatar for zhao03
14 months ago by
zhao0330
zhao0330 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 • 1.2k views
ADD COMMENTlink modified 14 months ago by JC11k • written 14 months ago by zhao0330

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

fastq-dump --split-spot --split-files --gzip -A SRR018260
ADD REPLYlink modified 14 months ago • written 14 months ago by SMK1.9k

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

ADD REPLYlink written 14 months ago by Mensur Dlakic6.5k
1
gravatar for genomax
14 months ago by
genomax89k
United States
genomax89k wrote:

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

ADD COMMENTlink written 14 months ago by genomax89k
1
gravatar for JC
14 months ago by
JC11k
Mexico
JC11k 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 14 months ago by JC11k
1
gravatar for ATpoint
14 months ago by
ATpoint38k
Germany
ATpoint38k 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 14 months ago • written 14 months ago by ATpoint38k
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