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  • Trinity and jellyfish problem

    Dear All,

    When using Trinity, the pl script suddenly stops:

    CMD: /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 766958445 both.fa
    Can't exec "/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin/jellyfish": No such file or directory at Trinity.pl line 1472.
    Error, cmd: /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 766958445 both.fa died with ret -1 at Trinity.pl line 1476.

    Does anybody have any idea why?

    Best wishes,

  • #2
    you don't have jellyfish installed properly.

    Did you execute the command 'make' inside the Trinity folder that you decompressed after downloading?

    Comment


    • #3
      Yes I have, Everything gets installed properly however the error is still there.
      Is there maybe a need to install jellyfish to?

      Comment


      • #4
        Does the jellyfish file exist at the location referenced? Can you verify that?

        Code:
        $ ls -lt /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin/jellyfish

        Comment


        • #5
          No
          bin file is empty
          $ ls -lt /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin
          total 0

          Comment


          • #6
            Originally posted by jevcampe View Post
            No
            bin file is empty
            $ ls -lt /home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish/bin
            total 0
            That does indicate that the plugin was not correctly compiled. Did you get any errors when you did the "make"? Can you try recompiling and post any errors you see.

            Comment


            • #7
              Before doing this i would like to ask this:
              Installing trinity is first unzipping the file followed by the command: make
              Are there other parts I need to compile?

              Comment


              • #8
                ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
                make[3]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/bcftools'
                make[3]: Entering directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/misc'
                make[3]: Nothing to be done for `lib'.
                make[3]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/misc'
                gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
                bam_tview.c:5:20: fatal error: curses.h: No such file or directory
                compilation terminated.
                make[2]: *** [bam_tview.o] Error 1
                make[2]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam'
                make[1]: *** [sam/libbam.a] Error 2
                make[1]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3'
                make: *** [all] Error 2

                errors

                Comment


                • #9
                  Originally posted by jevcampe View Post
                  Before doing this i would like to ask this:
                  Installing trinity is first unzipping the file followed by the command: make
                  Are there other parts I need to compile?
                  That is correct. I just verified that jellyfish gets built as part of the trinity compilation.

                  What OS are you using?

                  Comment


                  • #10
                    Originally posted by jevcampe View Post
                    ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
                    make[3]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/bcftools'
                    make[3]: Entering directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/misc'
                    make[3]: Nothing to be done for `lib'.
                    make[3]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam/misc'
                    gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
                    bam_tview.c:5:20: fatal error: curses.h: No such file or directory
                    compilation terminated.
                    make[2]: *** [bam_tview.o] Error 1
                    make[2]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam'
                    make[1]: *** [sam/libbam.a] Error 2
                    make[1]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3'
                    make: *** [all] Error 2

                    errors
                    You need to install "libncurses5-dev" library. If this is Ubuntu.

                    Comment


                    • #11
                      I'm using Linux version:
                      openSUSE 12.2 "mantis" - Kernel \r (\l)

                      Comment


                      • #12
                        Originally posted by jevcampe View Post
                        I'm using Linux version:
                        openSUSE 12.2 "mantis" - Kernel \r (\l)
                        Then the library is likely called "ncurses-devel". Install that.

                        Comment


                        • #13
                          Good old ncurses.
                          /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
                          Salk Institute for Biological Studies, La Jolla, CA, USA */

                          Comment


                          • #14
                            Hi all,

                            I have installed the package but the error still remains. However it looks that trinity has gone further compared to before.

                            -o bam2depth.o
                            gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
                            /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lcurses
                            collect2: error: ld returned 1 exit status
                            make[2]: *** [samtools] Error 1
                            make[2]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3/sam'
                            make[1]: *** [sam/libbam.a] Error 2
                            make[1]: Leaving directory `/home/marbiol/jelle/trinityrnaseq_r2013-02-25/trinity-plugins/rsem-1.2.3'
                            make: *** [all] Error 2

                            Comment


                            • #15
                              Did you install "ncurses" library as well?

                              Comment

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