Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Segmentation Fault 11, cuffdiff 2.2.1

    I used homebrew to download cufflinks 2.2.1 and the related packages to replicate the Cole-Trapnell paper from 2012 and have run into an issue on step 5. I was using boost 1.58 but then saw the warning that there is an issue with boost 1.56 and above so I uninstalled it and tried the boost155 package but I still keep getting segmentation fault 11. I am running this on my Mac OSX, 8gb of RAM, with 14.08 gb of disk space available. Any help would be much appreciated! I am very new to all of this.

    cuffdiff -o diff_out -b /usr/local/Cellar/my_rnaseq_exp/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa -p 8 -L C1,C2 -u /usr/local/Cellar/my_rnaseq_exp/merged_asm/merged.gtf \./C1_R1_thout/accepted_hits.bam,./C1_R2_thout/accepted_hits.bam,./C1_R3_thout/accepted_hits.bam \./C2_R1_thout/accepted_hits2.bam,./C2_R2_thout/accepted_hits.bam,./C2_R3_thout/accepted_hits.bam

  • #2
    I was also facing the exact same problem of segmentation fault 11 with cufflinks 2.2.1 and struggled hard to fix it. I am also a mac user and installed it from brew. At last, I found Mac OS X and its higher versions does not include X11(Xquartz). Installation of this tool suddenly fixed my problem. Now, Cufflink is working perfectly.

    Comment


    • #3
      This error can also be due to insufficient memory.

      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
      51 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