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Old 08-16-2013, 12:25 PM   #1
cement_head
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Location: Oxford, Ohio

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Posts: 199
Default sra to Fastq files

Hello,

I don't understand how to use fastq-dump. All I get is errors.

Code:
$ ./fastq-dump -A SRR638709 SRR638709.sra 
2013-08-16T20:23:37 fastq-dump.2.3.2 err: name not found while resolving tree within virtual file system module - failed to open 'SRR638709.sra'
What am I doing wrong?

Thanks
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Old 08-16-2013, 02:27 PM   #2
GenoMax
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Have you tried

Code:
$ ./fastq-dump  /full_path_to/SRR638709.sra
Several people have posted that providing full path to the SRA file seems to work due to some quirk in fastq-dump code.
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Old 08-19-2013, 06:40 AM   #3
cement_head
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Default

Quote:
Originally Posted by GenoMax View Post
Have you tried

Code:
$ ./fastq-dump  /full_path_to/SRR638709.sra
Several people have posted that providing full path to the SRA file seems to work due to some quirk in fastq-dump code.
Partially worked. One thing (that wasn't obvious) was that one must copy the SRA file to the working directory (the BIN directory) and then run the *.jar file. LEAVE the window open.

Now, one can run the fastq-dump script and it should work.

Then it worked for me (Ubuntu 12.04.2 LTS AMD64).

- ch
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