Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Segmentation fault, cuffdiff

    Greetings,

    I am trying to run cuffdiff and at each attempt am met with the message "Segmentation fault".

    I have seen at least two posts from users who encountered the same message, but have not seen any replies addressing this problem.

    I would greatly appreciate any assistance.

    Many thanks!

  • #2
    I am also encountering the same problem. It would be great if someone can suggest a solution to this.

    Thanks in advance.

    Comment


    • #3
      At what point in the process does the fault occur? What is the output that surrounds it?

      Please PM me if you have a (preferably small) dataset that exhibits this issue and you're willing to upload it for me to recreate the error.

      Comment


      • #4
        Hi,
        Thank you for your response.

        Here is the command that I am using:

        cuffdiff -o ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

        Each *.sam file is ~50G so not sure if I can upload them.

        Best Regards
        Nirmala

        Comment


        • #5
          Where in the process is it when it crashes?

          Comment


          • #6
            It stops immediately giving a segmentation fault error

            Comment


            • #7
              in cuffdiff, the -o option should be followed by the results output directory, not by the transcript gtf file. try deleting -o in your command:
              cuffdiff -o ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

              Comment


              • #8
                Sorry it was a typo in my previous post. Here's the command:

                cuffdiff -o cuffDiffOutput ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

                Comment


                • #9
                  I just find out that the output directory must not already exist when you run the cuffdiff command. If it's already there cuffdiff will give segmentation fault. cuffdiff will create it.
                  Last edited by gzhao; 04-18-2011, 09:02 AM.

                  Comment


                  • #10
                    Originally posted by gzhao View Post
                    I just find out that the output directory must not already exist when you run the cuffdiff command. If it's already there cuffdiff will give segmentation fault. cuffdiff will create it.

                    You are right. I got same issue in version v1.0.1 after I run cuffmerge, but at first I thought it is some issue with the merged tanscripts.gtf.

                    Comment


                    • #11
                      If the folder name for -o i cuffdiff is long, I also got same error message. I used a shorter name worked fine.

                      Comment


                      • #12
                        same problem - can't fix

                        I'm using cuffdiff for the first time and got the segmentation fault error. Someone suggested it might be a memory issue but I'm using a MacPro 16G RAM and 8 cores so I don't think that's it. As for the output file thing as suggested by gzhao and Ishen, I removed that option altogether (as well as all other options) so output should be in the default directory. Still doesn't work. I've tried using both Cufflinks 2.2.0 and 2.2.1.
                        Any help will be greatly appreciated.

                        Comment


                        • #13
                          I got the same problem but it turns out I didn't include the label option. Maybe you can try with the -L commend

                          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
                          12 views
                          0 likes
                          Last Post seqadmin  
                          Started by seqadmin, Yesterday, 06:07 PM
                          0 responses
                          10 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
                          68 views
                          0 likes
                          Last Post seqadmin  
                          Working...
                          X