Question

A problem with download SRA using SRA toolkit

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4.2 years ago

reza ▴ 300

I want to download the SRA using SRA toolkit, so I installed it using this guidance: https://github.com/ncbi/sra-tools/wiki/Building-and-Installing-from-Source

and then configured it using this guidance: https://github.com/ncbi/sra-tools/wiki/05.-Toolkit-Configuration

but when I used below command to download SRA:

prefetch Accession_number_of_SRA

I got the below message:

configuration not loaded: no vdb-config found
This sra toolkit installation has not been configured.
Before continuing, please run: vdb-config --interactive
For more information, see https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud/

Now I need your help to solve this problem.

SRAtoolkit NCBI SRA • 14k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 4.2 years ago by reza ▴ 300

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So did you run vdb-config --interactive?

ADD REPLY • link 4.2 years ago by ATpoint 82k

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Yes, this command is vdb-config -i (command for opening configuration window) actually. after configuration, this message will be repeated again and again

ADD REPLY • link 4.2 years ago by reza ▴ 300

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If you cannot get it to work, then obtain the SRA 'BioProject' ID, and search for this at the ENA (European Nucleotide Archive), where the FASTQ files are typically available for direct download.

ADD REPLY • link 4.2 years ago by Kevin Blighe 87k

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Hi ! I had the same issue. NCBI support told me that the problem is linked to the permissions. SRA toolkit need to have he permission to write and edit files in your environment. First set the permissions, then run vdb-config -I and then set it up and it is gonna work.

ADD REPLY • link 3.6 years ago by eynardrenaud • 0

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Did you do that, if so what did you do and what are the exact errors?

ADD REPLY • link 3.6 years ago by ATpoint 82k

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HIi, May you please let me know what are those permissions how can I set them? I am facing the same issue.

Looking forward to hearing from you.

Thank you!

ADD REPLY • link 3.6 years ago by ayesharafiq931 • 0

score 0 · Answer 1 · 2021-05-19

you need to configure the function before downloading the SRA data files. to config the function, make sure that you give a proper path or file location that contains a particular functions. Example: usually configure file will inside bin of the SRA toolkit. once you are inside the bin write ./vdb-config --interactive. this will open a dialogue box where you can enable the access.