Unconfigured Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • m4merg
    Member
    • Jul 2014
    • 21

    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.
  • piet
    Member
    • Aug 2014
    • 21

    #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.

    Comment

    • m4merg
      Member
      • Jul 2014
      • 21

      #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.

      Comment

      Latest Articles

      Collapse

      • SEQadmin2
        Nine Things a Sample Prep Scientist Thinks About Before Sequencing
        by SEQadmin2


        I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

        Here are nine questions we think about, in roughly the order they matter, before...
        06-18-2026, 07:11 AM
      • SEQadmin2
        From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
        by SEQadmin2


        Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.


        The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
        ...
        06-02-2026, 10:05 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by SEQadmin2, 06-17-2026, 06:09 AM
      0 responses
      38 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 06-09-2026, 11:58 AM
      0 responses
      100 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 06-05-2026, 10:09 AM
      0 responses
      121 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 06-04-2026, 08:59 AM
      0 responses
      114 views
      0 reactions
      Last Post SEQadmin2  
      Working...