SRA "file unauthorized" specific dataset

Question

[justinjacobse]

Hi all,

I'm trying to download some files from GEO using the following code on a cluster:

#!/bin/bash

# Load modules
module load SRA-Toolkit/2.9.6-1-centos_linux64 # Load the SRA toolkit
# Get the fastq files       
fasterq-dump SRR11567291 -O /scratch/goettel_lab/Yoesefi_2022/'Data_fastq' -t /scratch/goettel_lab

However I get the following error (repeatedly)

2022-03-09T15:07:37 fasterq-dump.2.9.6 err: file unauthorized while opening file within network system module - Failed to    KNSManagerVMakeHttpFileInt('https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-hup-1/SRR011/11567/SRR11567291/SRR11567291.1' (130.14.250.26)) from '129.59.197.33'
2022-03-09T15:07:37 fasterq-dump.2.9.6 err: file unauthorized while opening file within network system module - error with https open 'https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-hup-1/SRR011/11567/SRR11567291/SRR11567291.1'
2022-03-09T15:07:37 fasterq-dump.2.9.6 err: invalid accession 'SRR11567291'

The file exists and when downloading other data using the same code (e.g. replace SRR11567291 by SRR12492863) no problems exist, so it seems specific to this dataset. Weirdly enough, some other accession numbers in the same dataset were downloaded successfully.

Does anyone know how to get around this error?

Thanks, Justin

Answer 1

[ATpoint]

Just enter the accessions at sra-explorer.info and get direct fastq download links. sra-tools tend to be...weird.

[justinjacobse]

Thanks, this particular dataset does not show (yet?) in SRA-explorer.

[GenoMax]

It is there. Got the following links from sra-explorer.info.

http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/091/SRR11567291/SRR11567291_1.fastq.gz
http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/091/SRR11567291/SRR11567291_2.fastq.gz

I have replaced ftp with http since most browsers don't do FTP any more.

Answer 2

[GenoMax]

This appears to be a new dataset (released last week). It may simply be a matter of "hold" not being released on this set if other files in this project are downloadable. You can write to SRA help desk for getting this corrected.

There is always the possibility that this is a "controlled access" dataset and you will need dbGAP application/access permission to get the data.

[justinjacobse]

Thanks GenoMax, I was hoping that "controlled access" would show on the GEO website, but I will double check the with SRA help desk and also see if there is a hold.

Answer 3

[justinjacobse]

For others that might run into similar issues, updating SRA toolkit to 3.0.0 fixed the problem.

[GenoMax]

Was that done based on an official response from NCBI SRA support or was it something you discovered on your own?