Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Trinity segmentation fault

    Hi there,

    I would like to use the transcript assembler Trinity to assemble RNAseq data while using a reference genome as a guide. I aligned my reads on the reference genome with Tophat, sorted the obtained bam file and then used the following command:

    Code:
    ~/Software/Trinityrnaseq-v2.6.6/Trinity --genome_guided_bam accepted_hits_sorted.bam --genome_guided_max_intron 32000 --max_memory 10G --CPU 10 &
    The command returns a Segmentation fault error without any further details
    Can someone help me with this please?
    thanks!

  • #2
    That 10G is a guide (I assume you took that from the example command line). What size is your BAM file? You may need to assign more RAM for this job.

    Comment


    • #3
      Originally posted by GenoMax View Post
      That 10G is a guide (I assume you took that from the example command line). What size is your BAM file? You may need to assign more RAM for this job.
      Hi there,

      thanks for your e-mail. I do not think it is a matter of amount of memory. The bam file is under 100 Mb, very small actually. Also Trinity version I am using is the latest. I really can not understand what is going on. Any ideas?
      thanks a lot

      Comment


      • #4
        Have you run trinity with other data successfully? if not test it with something else. Did you compile the program yourself?

        Comment


        • #5
          Yes it returns a segmentation fault also with other paired end data. I compiled directly with the make command as stated in the manual. It fails also if I provide only arguments --left and --right.
          Actually I just checked the installation with make test_trinity and this failed with the following message

          Code:
          #######################################################
          ##  Run Trinity to Generate Transcriptome Assemblies ##
          #######################################################
          
          ../../Trinity --seqType fq --max_memory 2G \
                        --left reads.left.fq.gz \
                        --right reads.right.fq.gz \
                        --SS_lib_type RF \
                        --CPU 4 
          ./runMe.sh: line 11: 42124 Segmentation fault      ../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4
          make[1]: *** [test] Error 139
          make[1]: Leaving directory 
          make: *** [test_trinity] Error 2

          thanks

          Comment


          • #6
            Ok. So it is your compiler that may be the problem. What version of GCC did you use to compile this? You may need to use a newer version.

            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