sra to Fastq files

[cement_head]

Hello,

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

$ ./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

[GenoMax]

Have you tried

$ ./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.

[cement_head]

Have you tried

$ ./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