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Old 05-23-2013, 11:13 AM   #1
kelseyca
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Unhappy SRA -> FastQ, Problem with SRA toolkit?

Hello everyone!

I saw several other posts about this toolkit, but it seems most people ran into problems later on instead of during set up like I did.

I downloaded several .SRA data files from NCBI. I would like to convert them into .FastQ files, and then analyze them in Galaxy.

I downloaded the SRAtoolkit, and opened Command Prompt. However, when I try to change the directory to the folder where I extracted the tool kit ( cd C:\myname\Downloads\sratoolkit.2.3.2-5-win64\sratoolkit.2.3.2-5-win64\ ) I receive the following error: "The system cannot find the path specified."

What am I doing wrong? I have been trying everything I can think of for the past 2 hours. This is my first time doing anything like this and I'm sure I'm making a really simple mistake...

Thank you!
Kelsey
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Old 05-23-2013, 11:22 AM   #2
GenoMax
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This is an obvious question but I will ask. sratoolkit is only supported on 64-bit windows. Are you using some flavor of 64-bit windows(XP/7/8)?
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Old 05-23-2013, 11:27 AM   #3
kelseyca
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Quote:
Originally Posted by GenoMax View Post
This is an obvious question but I will ask. sratoolkit is only supported on 64-bit windows. Are you using some flavor of 64-bit windows(XP/7/8)?
Thank you for your prompt response! I am on Windows 7, 64-bit Operating System.
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Old 05-23-2013, 11:30 AM   #4
GenoMax
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Are you able to see the sratoolkit directory at the c:\myname\Downloads level via command prompt?
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Old 05-23-2013, 11:36 AM   #5
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I typed dir c:\myname\downloads and I see it there.

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Old 05-23-2013, 11:41 AM   #6
dpryan
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You need to unzip the file first.
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Old 05-23-2013, 11:42 AM   #7
GenoMax
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That file is still zipped.

You will have to unzip the file. Once you double click on the zip file there should be an "Extract all files" option at the top of the windows explorer window. Follow those prompts.
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Old 05-23-2013, 11:47 AM   #8
kelseyca
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Quote:
Originally Posted by GenoMax View Post
That file is still zipped.

You will have to unzip the file. Once you double click on the zip file there should be an "Extract all files" option at the top of the windows explorer window. Follow those prompts.
Thank you, both you. I can't believe I didn't realize that... Now I changed the directory, the change directory command worked, but when I try the next step "type 'perl configuration-assistant.perl' (without the quotation marks)" it says No such file or directory. I have perl installed on this computer. Should I reinstall it, could I maybe have the wrong version?

Thank you again, I have never used command prompt, perl, or any of these other programs before so please be patient with my simple questions.
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Old 05-23-2013, 11:49 AM   #9
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Run the sratookit.jar file (in the "bin" directory) using java instead. It should achieve the same result (of creating a local space where reference files downloaded from SRA for referenced-compression based files will be stored).

The perl script is also located in the "sratoolkit.2.3.2-5-win64\sratoolkit.2.3.2-5-win64\bin" directory. So you will have to cd into bin directory.

Last edited by GenoMax; 05-23-2013 at 11:52 AM.
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Old 05-23-2013, 11:51 AM   #10
kelseyca
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Quote:
Originally Posted by GenoMax View Post
Run the sratookit.jar file (in the "bin" directory) using java instead. It should achieve the same result (of creating a local space where reference files downloaded from SRA for referenced-compression based files will be stored).

The perl script is also located in the "bin" directory.
Should something happen when I run it? My screen flashes but nothing happens.
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Old 05-23-2013, 11:55 AM   #11
GenoMax
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Quote:
Originally Posted by kelseyca View Post
Should something happen when I run it? My screen flashes but nothing happens.
Do you have java installed and is "sratoolkit.jar" file showing up as "executable jar file"?

You should see this:
Attached Images
File Type: png Capture.PNG (14.8 KB, 9 views)

Last edited by GenoMax; 05-23-2013 at 11:57 AM.
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Old 05-23-2013, 11:55 AM   #12
kelseyca
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Quote:
Originally Posted by GenoMax View Post
Run the sratookit.jar file (in the "bin" directory) using java instead. It should achieve the same result (of creating a local space where reference files downloaded from SRA for referenced-compression based files will be stored).

The perl script is also located in the "sratoolkit.2.3.2-5-win64\sratoolkit.2.3.2-5-win64\bin" directory. So you will have to cd into bin directory.
Oh, I didn't do that. Let me try cd into the bin folder.
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Old 05-23-2013, 11:59 AM   #13
kelseyca
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Quote:
Originally Posted by GenoMax View Post
Do you have java installed and is "sratoolkit.jar" file showing up as "executable jar file"?
Yes to both. OK! I cd to the bin folder and the perl script went through. Now it is telling me "configuration is correct"! So it should work now, I guess?

I found a youtube tutorial so hopefully the rest of it is straight forward and I can figure out the conversion to fastq. Thank you so much, GenoMax! You are the best!
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