Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Running qualimap fails:

    I tried to run qualimap: http://qualimap.bioinfo.cipf.es/.
    When using the command ./qualimap, I am always getting the following error message:

    ./qualimap Java memory size is set to 1200M Launching application... OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1024m; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 java: symbol lookup error: /home/xxx/Softwares/miniconda3/jre/lib/amd64/../../../lib/libX11.so.6: undefined symbol: xcb_wait_for_reply64

    What is the problem? Why doesn`t it work as it should? Is it a "java" problem or the file lixX11.so.6?

    I got the following answer via researchgate:

    "The symbol lookup error is a miniconda3 issue. The Java runtime environment (jre) therein has X11 libraries for managing windows to give a GUI when running a program from command line. Those libraries are looking for a specific set of libraries called XCB and not finding it. This tells me your miniconda3 environment is using Xlib instead of XCB, which makes sense (Xlib is a far more common and robust library than XCB, IMO).
    To fix this you should just need to get the XCB libraries added/updated to your miniconda's jre build."

    How may I do this?

  • #2
    I am not sure what the size of BAM file you are trying to use is but you could try adding the option "--java-mem-size=16G" to your qualimap command (Adjust RAM amount as needed). and see if that helps.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Exploring the Dynamics of the Tumor Microenvironment
      by seqadmin




      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
      07-08-2024, 03:19 PM
    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      06-25-2024, 06:43 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    26 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 09:45 AM
    0 responses
    201 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 08:54 AM
    0 responses
    212 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-02-2024, 03:00 PM
    0 responses
    193 views
    0 likes
    Last Post seqadmin  
    Working...
    X