I have tried Prefetch to download SRA accession list:
D:\Ali\Tools\sartoolkit.2.9.6-win64\bin\prefetch.exe —option-file C:\Users\Ali\Desktop\SRA_Acc_List.txt
but this gives error
2019-07-03T02:00:13 prefetch.2.9.3 err: path not found while resolving tree within virtual file system module - '/C/Users/Ali/Desktop/SRA_Acc_List.txt
•
written
by
Ali Syed •
Do yourself a favor and install Linux on a Virtual Machine and then consider following: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
@OP: While ATpoint's solution might read like a lot of work, it is quite elegant. Other options are on the SRA download manual. Keep in mind it is highly likely you'll need Linux or access to a Linux server at some point in time.
What you should also check is if the files are restricted. If so given you have applied for access, you have to be inside the directory specified in vdb-config for the restricted data. If it doesn't work don't hestimate to mail the NCBI help desk, they have to sort it out given they provide this annoying sra format and this toolkit which throws errors all the time.
Even better, install the Windows Subsystem for Linux and install a linux distribution of your choice.
Thanks for kind advice sir,, Actually i have to download bulk of data, and transfer directly to the FASTQ format.. Previously i used Prefetch and ASPERA in linux server.. but now they both are not useful. so i switched to windows 10.
You can install Ubuntu 18 on your windows 10 side by side and it doesn't require anything else. It is very easy to install and installation will take a few minutes. I am using this for large data set analysis and never faced any issues.
Just go to Microsoft store and search for Ubuntu and get it whatever version you like. You can use Linux easily here.
Thanks... Actually i am already using my lab Linux server.. and accessing with SSH shell...
On windows, the easiest way is to use docker: see https://hub.docker.com/r/ncbi/sra-toolkit for instance.
thanks.. but its not working.. all old versions there...
Log in to answer this question.
Can you give the SRA number that is not working, then I check if it is a general thing or on your side.