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Old 09-07-2011, 08:25 PM   #1
Zergling
Junior Member
 
Location: Ontario

Join Date: Sep 2011
Posts: 1
Default fastq-dump runs indefinitely on windows

Hello,
I'm pretty new to the bioinformatics scene and I am trying to convert SRA data into fastq. I seem to be having no problems converting it on 64-bit ubuntu using the binary for CentOS x64 but whenever I try to do it on windows it runs indefinitely creating a file that keeps growing in size (I let it run to over 150 GB before letting it end the first time). The 3.9 GB sra file I converted on ubuntu became about 15.3 GB so there is definitely a problem.

I'm using sra toolkit 2.1.4 win32 when on windows (windows 7, 64 bit) and I'm getting the same results when running it through the cmd prompt and with MinGW. If anyone has an idea on what I might be wrong any help would be greatly appreciated. I would much prefer to convert files on windows so I don't have to keep switching operating systems to analyze the data after and the file increases in size much more rapidly on windows suggesting that it might be able to convert it faster if I can get it to convert properly

Thanks!
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