Question: How can i download multiple SRA data by using windows 10?
0
gravatar for Ali Syed
9 months ago by
Ali Syed0
Ali Syed0 wrote:

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
  
rna-seq next-gen • 503 views
ADD COMMENTlink modified 9 months ago by Arnaud Ceol850 • written 9 months ago by Ali Syed0

Can you give the SRA number that is not working, then I check if it is a general thing or on your side.

ADD REPLYlink written 9 months ago by ATpoint32k
0
gravatar for ATpoint
9 months ago by
ATpoint32k
Germany
ATpoint32k wrote:

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)

ADD COMMENTlink written 9 months ago by ATpoint32k

@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.

ADD REPLYlink modified 9 months ago • written 9 months ago by Carambakaracho2.0k

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.

ADD REPLYlink written 9 months ago by ATpoint32k

Even better, install the Windows Subsystem for Linux and install a linux distribution of your choice.

ADD REPLYlink written 9 months ago by jared.andrews075.3k

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.

ADD REPLYlink written 9 months ago by Ali Syed0

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.

ADD REPLYlink written 9 months ago by archana.bioinfo87180

Thanks... Actually i am already using my lab Linux server.. and accessing with SSH shell...

ADD REPLYlink written 9 months ago by Ali Syed0
0
gravatar for Arnaud Ceol
9 months ago by
Arnaud Ceol850
Milan, Italy
Arnaud Ceol850 wrote:

On windows, the easiest way is to use docker: see https://hub.docker.com/r/ncbi/sra-toolkit for instance.

ADD COMMENTlink written 9 months ago by Arnaud Ceol850

thanks.. but its not working.. all old versions there...

ADD REPLYlink written 9 months ago by Ali Syed0
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