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  • #16
    I found that other thread, saying that the format is complicated,
    so there is no such table.

    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc



    I'm having problems with files >4GB and wanted to test it
    on a partially downloaded file first

    I have to split the large files, so they work with my programs.
    It's also faster, better for testing, dealing with 4GB files is tedious.

    I doubt that sra-tools will work with such splitted files
    Last edited by gsgs; 08-21-2013, 03:47 AM.

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    • #17
      OK, I tried to download the file to my external drive, it took 5.5h ,
      until an error message was displayed that the file couldn't be copied.

      Then I searched my main HD and found that it was put into a temporary file
      which had 4631463048 Bytes, so apparently >4GB is possible on my
      main drive but not on the external one.
      (Windows XP, computer bought in 2010 or 2011)


      I made a copy of that temporary file to another file on the maindrive,
      then I closed the error window, and indeed, the temporary file was
      deleted, but luckily I had the copy.
      As expected I can't copy that file to the external drive nor can I access it
      with any of my programs.
      But DOS-commands copy,type,find do work.

      So, I need a program that splits the big file into 2 smaller files, that can be assessed.

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      • #18
        If you are using 32-bit windows XP (which you likely are) this may not be possible. What kind of format do you have on your external drive? You may need NTFS for files > 4GB.

        Comment


        • #19
          Ah, yeah, I expect that the SRA format is pretty non-trivial from the various discussions of it. Honestly, if your computer is having issues with files ~4GB then you might just be better off using someone else's (though check if the drive is NTFS formatted), particularly if you're stuck on windows. Got a labmate with a Mac?

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          • #20
            I cannot just switch to Win64, since I need all my old programs
            that were written on 16bit or 32bit

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            • #21
              Originally posted by gsgs View Post
              I cannot just switch to Win64, since I need all my old programs
              that were written on 16bit or 32bit
              It should be possible to use those on the 64-bit windows (you could also run a VM and 32-bit windows, if you find an absolute need for it).

              Comment


              • #22
                I found downloaded,unzipped,copied
                sra decrypt for Win 32

                but I get the error:

                C:\1918>vdb-decr tu1
                2013-08-21T19:04:59 vdb-decr.2.3.2 err: encryption key not found while opening m
                anager within virtual file system module - unable to obtain a password
                2013-08-21T19:04:59 vdb-decr.2.3.2: exiting: RC(rcVFS,rcMgr,rcOpening,rcEncrypti
                onKey,rcNotFound) (2615479768)


                they didn't say in the paper or at the NCBI download page
                that I need a password

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                • #23
                  Your life would be much easier if you just used a computer that could download and convert the whole file from SRA using fastq-dump. Just borrow someone's laptop instead of trying to reinvent the wheel (particularly since this this particular wheel has terrible documentation).

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                  • #24
                    you won't believe me, but I really need all these old programs that
                    that no longer work with these big files
                    and often give other problems with Win64
                    A utility to split the files looks so much easier.
                    Of course, I wrote such an utility decades ago, really simple,
                    but compiled with 16bit --> don't work.
                    A 64-bit compiler might help, at least to run a few of my programs
                    on 64-bit. But remembering how much trouble it was to install and
                    understand my 16-bit compiler (GCC3.2,DJGPP) in 2002 ...

                    Comment

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