Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • CummeRbund problem in R with segfault

    Hello guys, I am new to R an using it in Mac OSx which I started handling 4 months back. I am using cummeRbund to visualize my data outputs of the cuffdiff analysis and get an idea of the DE genes through different plots. I am unable to create the database after I load the library cummeRbund. When am executing the command cufflinks , it runs for a while and then stops with a segfault error and memory not mapped message. I tried to clear all the cache memory as well but still I am unable to fix it. I have to work on some data urgently and am stuck. It would be nice if you could suggest me something. I am not an expert in R so directly dealing with the diff_exp gene outputs of cuffdiff for creating the matrix and plots is being a bit cumbersome for me. Below are the errors am receiving. Please assist me.

    And then when I am calling the library of cummeRbund its is called but as I create the database with the output with readCuffLinks() the below error occurs. Please assist.

    Creating database ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/cuffData.db Reading Run Info File ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/run.info Writing runInfo Table Reading Read Group Info ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/read_groups.info Writing replicates Table Reading ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/gene_exp.diff

    * caught segfault * address 0x51a41311b, cause 'memory not mapped'

    Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection:

    It would be appreciable if you can give me some idea and help me out.

    Thanks,

  • #2
    Can you post the first few lines of your gene_exp.diff file? It may be something in there. I'll be happy to take a look...


    Loyal

    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, Yesterday, 06:37 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    50 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X