Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Trinity installation error

    Hello! I want to run Trinity on a cluster. I typed 'make' and I got at the end the following errors. Could anyone help me and orient me? Thanks

    lib/misc.cc: In function 'std::string jellyfish::quote_arg(const std::string&)':
    lib/misc.cc:86: error: 'all_of' is not a member of 'std'
    make[3]: *** [lib/misc.lo] Error 1
    make[3]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins/jellyfish-2.1.3'
    make[2]: *** [all] Error 2
    make[2]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins/jellyfish-2.1.3'
    make[1]: *** [jellyfish] Error 2
    make[1]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins'
    make: *** [plugins] Error 2

  • #2
    See if this is applicable: https://www.biostars.org/p/105334/

    What version of GCC are you using?
    Last edited by GenoMax; 10-28-2014, 08:16 AM.

    Comment


    • #3
      More errors

      It worked!! Because I am working in a Cluster I had to module load gcc/4.9 but now I have this errors. Do you know what could be the problem?
      Thanks

      /usr/bin/ld: cannot find -lcurses
      collect2: error: ld returned 1 exit status
      make[3]: *** [samtools] Error 1
      make[3]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins/rsem-1.2.15/sam'
      make[2]: *** [sam/libbam.a] Error 2
      make[2]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins/rsem-1.2.15'
      make[1]: *** [rsem] Error 2
      make[1]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins'
      make: *** [plugins] Error 2

      Comment


      • #4
        You are missing the ncurses library. Check to see if there is a module for it.

        If you are planning to run this on a cluster then I would advise asking your cluster administrators to build a module for Trinity. That way they can take care of the dependencies and when you actually run your job there will be no issues with nodes not finding things, if your home directory is not available on all compute nodes.

        Comment


        • #5
          Hi!
          I asked the cluster administrators about a module for ncurses and this was his answer:

          You can find ncurses (lib, include) with

          module load os_extension/devel
          module show os_extension/devel

          echo $DEVEL_LIB_PATH
          echo $DEVEL_INC_PATH
          echo $DEVEL_INC

          So actually ncurses is in that module but I get the same error even after
          module load os_extension/devel

          Comment


          • #6
            Did you load the new GCC module along with the os_externsion/devel before compiling? What OS is your cluster using?

            Do you know if *curses-dev library is installed in that module?

            Try this code and you should see where it is trying to load curses from and if there are any errors:
            Code:
            $ ld -lcurses --verbose

            Comment


            • #7
              This is what I got:

              attempt to open /usr/x86_64-suse-linux/lib64/libcurses.so failed
              attempt to open /usr/x86_64-suse-linux/lib64/libcurses.a failed
              attempt to open /usr/local/lib64/libcurses.so failed
              attempt to open /usr/local/lib64/libcurses.a failed
              attempt to open /lib64/libcurses.so failed
              attempt to open /lib64/libcurses.a failed
              attempt to open /usr/lib64/libcurses.so failed
              attempt to open /usr/lib64/libcurses.a failed
              attempt to open /usr/x86_64-suse-linux/lib/libcurses.so failed
              attempt to open /usr/x86_64-suse-linux/lib/libcurses.a failed
              attempt to open /usr/lib64/libcurses.so failed
              attempt to open /usr/lib64/libcurses.a failed
              attempt to open /usr/local/lib/libcurses.so failed
              attempt to open /usr/local/lib/libcurses.a failed
              attempt to open /lib/libcurses.so failed
              attempt to open /lib/libcurses.a failed
              attempt to open /usr/lib/libcurses.so failed
              attempt to open /usr/lib/libcurses.a failed
              ld: cannot find -lcurses

              I loaded both modules. As for my OS

              LSB Version: core-2.0-noarch:core-3.2-noarch:core-4.0-noarch:core-2.0-x86_64:core-3.2-x86_64:core-4.0-x86_64:desktop-4.0-amd64:desktop-4.0-noarch:graphics-2.0-amd64:graphics-2.0-noarch:graphics-3.2-amd64:graphics-3.2-noarch:graphics-4.0-amd64:graphics-4.0-noarch
              Distributor ID: SUSE LINUX
              Description: SUSE Linux Enterprise Server 11 (x86_64)
              Release: 11
              Codename: n/a

              Linux lxa191 3.0.101-0.35-default #1 SMP Wed Jul 9 11:43:04 UTC 2014 (c36987d) x86_64 x86_64 x86_64 GNU/Linux

              Comment


              • #8
                I just solved my problem.
                I modify the Makefile in
                trinityrnaseq_r20140717/trinity-plugins/rsem-1.2.15/sam

                I change the two lines:
                LIBPATH= -L/lrz/sys/os_extension/SLES11SP3/devel_03Jul2014/usr/lib64
                LIBCURSES= -lncurses

                Thank you for all the help!!!

                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
                49 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