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  • TGICL using

    Hello everyone:

    when I use the tgicl, I encounter a problem :
    "Process terminated with an error, at step 'Initialization'! "

    my command line is : ./tgicl -F ~/tmp/test.fa

    The error in file err_tgicl_test.fa.log as follows:
    >>> --- Initialization [/home/zhuy/tmp/test.fa] started at Apr 24 13:52:54 2012
    tgicl.nozmsort.pl running options:
    tgicl.nozmsort.pl /home/zhuy/tmp/test.fa
    Standard log file: tgicl_test.fa.log
    Error log file: err_tgicl_test.fa.log
    Using 1 CPUs for clustering and assembly
    Path is : /home/zhuy/bin/RNA/denovo_2.0/tgicl/bin:/home/zhuy/bin/RNA/denovo_2.0/tgicl:/home/zhuy/local/perl/bin:/home/zhouzh/lib/jdk1.6.0_23/bin:/home/zhuy/
    -= Rebuilding /home/zhuy/tmp/test.fa indices =-
    Error at cdbfasta /home/zhuy/tmp/test.fa

    Process terminated with an error, at step 'Initialization'!
    tgicl.nozmsort.pl (/home/zhuy/tmp/test.fa) encountered an error at step Initialization
    Working directory was /home/zhuy/bin/RNA/denovo_2.0/tgicl.

    Thank you !

  • #2
    Is your fasta file correct? Maybe you can post the first few entries.It seems that indexing your sequences failed (cdbfasta).

    Comment


    • #3
      Thank you, sklages!

      I think my fasta file is all right, and it can be normally formatdb.

      Also, I change another fasta file coming from NCBI Genome database, but the error still exist.

      Comment


      • #4
        What error message do you get when you execute

        Code:
        cdbfasta /home/zhuy/tmp/test.fa
        It might be that cdbfasta doesn't like your fasta file, even though BLAST formatdb can handle it. Try to modify the identifiers in your fasta file (first I'd make sure that the first space-delimited part is unique, since this is the default identifier used by cdbfasta) and run the cdbfasta utility manually, outside of tgicl, until it accepts your fasta file.

        Comment


        • #5
          Thank you for your advice, arvid!

          When I type '/home/zhuy/bin/cdbfasta test.fa',

          bash: /home/zhuy/bin/cdbfasta: No such file or directory. This is maybe the reason,

          but the file 'cdbfasta' is existing, and the file permission is: -wxr-xr-x, the path'/home/zhuy/bin/' is also included in my $PATH.

          I don't known why has this problem?

          Comment


          • #6
            Please type the following commands:
            Code:
            ls -al /home/zhuy/bin/cdbfasta
            ls -al /home/zhuy/bin/RNA/denovo_2.0/tgicl/bin/cdbfasta
            and report the output. The error you've posted says that cdbfasta doesn't exist there... I'd guess that you find the cdbfasta executable in /home/zhuy/bin/RNA/denovo_2.0/tgicl/bin, according to the TGICL log in your first post. If it's in $PATH (as well indicated in the log), just typing "cdbfasta" should be enough. ~/bin/ is typically in $PATH, but you can check this with
            Code:
            echo $PATH

            Comment


            • #7
              What linux are you using?

              If the binary is really present, try

              ldd /home/zhuy/bin/cdbfasta
              and see if the linux loader is found ...

              I had such kind of problems with custom made linux and some pre-compiled binaries (years ago though).

              Comment


              • #8
                Originally posted by sklages View Post
                What linux are you using?

                If the binary is really present, try

                and see if the linux loader is found ...

                I had such kind of problems with custom made linux and some pre-compiled binaries (years ago though).
                My linux is : "Linux version 2.6.32-21-generic, Ubuntu 10.04"

                When I type "ldd /home/zhuy/bin/cdbfasta"
                -------- not a dynamic executable

                but type "file /home/zhuy/bin/cdbfasta", it shows:
                "ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.2.5, stripped"

                I don't know what this mean?

                Thank you !

                Comment


                • #9
                  Originally posted by zhuyan View Post
                  My linux is : "Linux version 2.6.32-21-generic, Ubuntu 10.04"

                  When I type "ldd /home/zhuy/bin/cdbfasta"
                  -------- not a dynamic executable

                  but type "file /home/zhuy/bin/cdbfasta", it shows:
                  "ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.2.5, stripped"

                  I don't know what this mean?

                  Thank you !

                  That's strange.

                  I get:

                  Code:
                  bin $ file cdbfasta 
                  cdbfasta: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), 
                  dynamically linked (uses shared libs), for GNU/Linux 2.2.5, stripped
                  
                  bin $ ldd cdbfasta
                      linux-gate.so.1 =>  (0xffffe000)
                      libm.so.6 => /project/mariux32/i686/tools/lib/libm.so.6 (0xf773b000)
                      libc.so.6 => /project/mariux32/i686/tools/lib/libc.so.6 (0xf75dc000)
                      /lib/ld-linux.so.2 (0xf7761000)
                  What is the output of arvids proposed commands (ls)?

                  Comment


                  • #10
                    Code:
                    $ ls -al /home/zhuy/bin/cdbfasta
                    -rwxr-xr-x 1 zhuy zhuy 113180 2012-04-24 11:21 /home/zhuy/bin/cdbfasta

                    $ ls -al /home/zhuy/software/TGICL-2.1/bin/cdbfasta
                    -rwxr-xr-x 1 zhuy zhuy 113180 2010-11-13 02:23 /home/zhuy/software/TGICL-2.1/bin/cdbfasta
                    It looks normal !

                    Comment


                    • #11
                      Originally posted by zhuyan View Post
                      Code:


                      It looks normal !
                      Indeed it does... I have no idea why it won't run on your machine... Maybe the executable got corrupted somehow. You could try to unpack the installation archive again and reinstall it. Otherwise I'd try to contact the authors (might be tricky since it is quite old).

                      Comment


                      • #12
                        Hmm, now we have just another 'cdbfasta'? (Which apparently has been built/installed on 2010-11-13). So what happens when you type :

                        which cdbfasta
                        ldd /home/zhuy/software/TGICL-2.1/bin/cdbfasta
                        /home/zhuy/software/TGICL-2.1/bin/cdbfasta test.fa

                        Comment


                        • #13
                          I unpack the installation archive again and re-install it.
                          $ /home/zhuy/bin/cdbfasta
                          bash: /home/zhuy/bin/cdbfasta: Accessing a corrupted shared library

                          $ ldd /home/zhuy/bin/cdbfasta
                          not a dynamic executable
                          It looks as if there are something wrong with my library files.

                          Comment


                          • #14
                            Try to re-install the shared libraries cdbfasta is relying on (see post #9) with the Ubuntu package manager (in case you have corrupted something with a manual installation)... or you might want to try to run it on a machine with an older Linux distro, or a RedHat-type one (like Fedora or CentOS). I've been able to successfully run TGICL on Fedora 14-16 and CentOS 5.x (didn't try on 6.x, yet).
                            Last edited by arvid; 04-25-2012, 11:12 PM.

                            Comment


                            • #15
                              Originally posted by zhuyan View Post
                              I unpack the installation archive again and re-install it.
                              It looks as if there are something wrong with my library files.
                              What is "/home/zhuy/software/TGICL-2.1/bin/cdbfasta"?

                              When I download the current TGICL, extract the files and run:

                              Code:
                              $ ldd ./cdbfasta
                                  linux-gate.so.1 =>  (0xffffe000)
                                  libm.so.6 => /project/mariux32/i686/tools/lib/libm.so.6 (0xf76e4000)
                                  libc.so.6 => /project/mariux32/i686/tools/lib/libc.so.6 (0xf7585000)
                                  /lib/ld-linux.so.2 (0xf770a000)
                              I do get an output. I can even run that tool without error.

                              This is a pretty up-to-date linux system. What ditribution are you using?

                              Comment

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