Question: Issue With Sra To Fastq Conversion
0
8.1 years ago by
Arpssss40
Arpssss40 wrote:

I have downloaded a SRA file from here. Now, I want to convert it into Fastq format.

So, what I did is following,

1) Download SRA Toolkit from here. (MS Windows 64 bit architecture - as I am using windows 7 64 bit)

2) Put SRA file on "sratoolkit.2.1.10-win64\bin"

3) Run command "fastq-dump SRR493095.sra"

However, I can't understand why it is giving error ?

Error is given here.

Can anybody help me why is this happening ?

sra fastq • 9.5k views
ADD COMMENTlink
modified 2.3 years ago by Biostar ♦♦ 20 • written 8.1 years ago by Arpssss40
2
8.1 years ago by
Leonor Palmeira3.7k
Liège, Belgium
Leonor Palmeira3.7k wrote:

First things first. This is how you should proceed:

1- Let's look at the generated error:

Path incorrect while opening manager


It also says:

failed SRR493095.sra


And you also learn that:

a report was generated into the file ...


2- What does this mean?

That "fastq-dump" cannot find your SRA file because you are telling him exactly where it is. You should probably call:

fastq-dump C:\Users\ArupGhosh\the\correct\path\to\this\file\SRR493095.sra

ADD COMMENTlink written 8.1 years ago by Leonor Palmeira3.7k

No. I have tried with absolute path also. Gives same issue, with http://pastebin.ca/2162892 output xml file.

ADD REPLYlink written 8.1 years ago by Arpssss40

This thread in SEQanswers (http://seqanswers.com/forums/showthread.php?t=13175) suggests a version problem between your toolkit and the one used to create the sra index.

Have you tried asking sra@ncbi.nlm.nih.gov for assistance as suggested in the error message?

ADD REPLYlink written 8.1 years ago by Leonor Palmeira3.7k

Thanks a lot. I am checking it.

ADD REPLYlink written 8.1 years ago by Arpssss40

You are correct. I tried with another .sra and downloaded current version of toolkit again. Works fine. Thanks.

ADD REPLYlink written 8.1 years ago by Arpssss40
2

Next time, before asking here, you should Google the error message you get. This is just what I did, and see, it solved your problem.

ADD REPLYlink written 8.1 years ago by Leonor Palmeira3.7k
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