Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • using snappy java in picard tools

    Hey,

    I have a problem using picard-tools on large files. It tells me that I don't have snappyjava in java.library.
    I'm not so familiar with java. Can anyone please point me on how to fix this.
    I've already come across this:

    Download picard for free. A set of tools for working with high-throughput sequencing data. A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team


    documentation, but don't really get.
    I'm on a mac os x 10.6.8

    Thank you for your help!

  • #2
    A quick fix is to run "java -Dsnappy.disable=true -jar ...", which will disable snappy, making Picard slower. But at least you don't have to run around trying to get snappy installed correctly!

    Comment


    • #3
      Thanks for the quick fix, that works for me. Although really slow

      Comment


      • #4
        Snappy comes distributed with the most recent versions of picard-tools (v1.53 - http://sourceforge.net/projects/picard/files/)
        It's in the top-level directory by itself. The remaining picard jar files are in a sub-directory.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-27-2024, 06:37 PM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-27-2024, 06:07 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        53 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        69 views
        0 likes
        Last Post seqadmin  
        Working...
        X