Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #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.

    Comment


    • #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.

      Comment


      • #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?

          Comment


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

            Comment


            • #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

                Comment


                • #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).

                  Comment


                  • #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

                    Latest Articles

                    Collapse

                    • seqadmin
                      Recent Developments in Metagenomics
                      by seqadmin





                      Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...
                      09-23-2024, 06:35 AM
                    • seqadmin
                      Understanding Genetic Influence on Infectious Disease
                      by seqadmin




                      During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.

                      Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...
                      09-09-2024, 10:59 AM

                    ad_right_rmr

                    Collapse

                    News

                    Collapse

                    Topics Statistics Last Post
                    Started by seqadmin, 10-02-2024, 04:51 AM
                    0 responses
                    12 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 10-01-2024, 07:10 AM
                    0 responses
                    20 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 09-30-2024, 08:33 AM
                    0 responses
                    25 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 09-26-2024, 12:57 PM
                    0 responses
                    18 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X