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  • SRA issue

    I am trying to use SRA to download public data SRR2129993. Running 'fastq-dump SRR2129993 -X 5 -Z' i get the output i expect - 5 spots read and write. So i assume that it is properly configured. But when i run 'prefetch --max-size 999Gb SRR2129993', i get the following error:

    Code:
    Maximum file size download limit is 1,047,527,424KB
    
    2016-04-07T13:00:45 prefetch.2.5.7: 1) Downloading 'SRR2129993'...
    2016-04-07T13:00:45 prefetch.2.5.7:  Downloading via http...
    2016-04-07T20:18:10 prefetch.2.5.7 int: incomplete while reading file within network system module - [url]http://sra-download.ncbi.nlm.nih.gov/srapub/SRR2129993:[/url] Cannot KFileRead
    2016-04-07T20:18:13 prefetch.2.5.7: 1) failed to download SRR2129993
    I.e. it started downloading and I saw that size of file was increasing, but suddenly error occured and it stopped. I have enough disk space to download it and have no i-net connection issues. Have anyone faced this problem before? Is there any way to download accession by parts - trying to get a whole file in a single run i get error in the middle of the proccess which remove all data downloaded, may be if i can download it by parts it wil solve my problems.

  • #2
    The file you want to download has an advertised size of about 133 GB. Do you really have this amount of free space on your local disk? By default, prefetch stores in your HOME directory.

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    • #3
      Originally posted by piet View Post
      The file you want to download has an advertised size of about 133 GB. Do you really have this amount of free space on your local disk? By default, prefetch stores in your HOME directory.
      I've changed default folder from /home to /data (i granted rights a+rw) where another partition is mounted with 5Tb free space. So I dont have free space issues as I wrote in initial post. I did it because I have only 99Gb on partition mounted to home. And by the way i've been screening free space on all paritions during download and havn't seen any issues.
      Last edited by m4merg; 04-08-2016, 09:27 AM.

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