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  • 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

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