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  • wigToBigWig error

    Hello,

    Trying to use the script 'wigToBigWig' for the obvious and I keep receiving a floating point exception error. Can't seem to find the cause. Has anyone encountered this before?

    John

  • #2
    Originally posted by JohnK View Post
    Hello,

    Trying to use the script 'wigToBigWig' for the obvious and I keep receiving a floating point exception error. Can't seem to find the cause. Has anyone encountered this before?

    John
    Can you post the exact command you are executing?
    I've never been into wigToBigWig errors, except for chromosome sizes :-) but there's the -clip options for that

    d

    Comment


    • #3
      Originally posted by dawe View Post
      Can you post the exact command you are executing?
      I've never been into wigToBigWig errors, except for chromosome sizes :-) but there's the -clip options for that

      d
      #!/bin/bash

      #$-cwd
      #$-V
      #$ -l huge_mem
      #$ -l mem=24G


      ~/wigToBigWig ./chrchr2/j.wig ./mm9.size.bld ./chrchr2/test.bw


      The error I receive is such:

      /opt/gridengine/default/spool/compute-4-0/job_scripts/17246: line 9: 30495 Floating point exception~/wigToBigWig ./chrchr2/j.wig ./mm9.size.bld ./chrchr2/j.bw

      Comment


      • #4
        *the huge mem was me just trying different things.

        Comment


        • #5
          Originally posted by JohnK View Post
          #!/bin/bash

          #$-cwd
          #$-V
          #$ -l huge_mem
          #$ -l mem=24G


          ~/wigToBigWig ./chrchr2/j.wig ./mm9.size.bld ./chrchr2/test.bw


          The error I receive is such:

          /opt/gridengine/default/spool/compute-4-0/job_scripts/17246: line 9: 30495 Floating point exception~/wigToBigWig ./chrchr2/j.wig ./mm9.size.bld ./chrchr2/j.bw
          Whoa... Never happened to me... Just to know:
          1- which CFLAGS have been used to compile wigToBigWig? (not -O3 I hope)
          2- how big is the wig? are you sure it is "kent compilant" ?

          what does

          Code:
          qacct -j 17246
          says (assuming 17246 is the $JOBID for your gridengine scheduler)?

          d

          Comment


          • #6
            Originally posted by dawe View Post
            Whoa... Never happened to me... Just to know:
            1- which CFLAGS have been used to compile wigToBigWig? (not -O3 I hope)
            2- how big is the wig? are you sure it is "kent compilant" ?

            what does

            Code:
            qacct -j 17246
            says (assuming 17246 is the $JOBID for your gridengine scheduler)?

            d
            this is the result from qacct -j $id

            ru_isrss 0
            ru_minflt 697
            ru_majflt 0
            ru_nswap 0
            ru_inblock 0
            ru_oublock 0
            ru_msgsnd 0
            ru_msgrcv 0
            ru_nsignals 0
            ru_nvcsw 49
            ru_nivcsw 1
            cpu 0
            mem 0.000
            io 0.000
            iow 0.000
            maxvmem 0.000

            i removed the track header lines, so i just have the raw .wig information like such:

            3000076 -1
            3000436 -1
            3000437 -1
            3000441 -1
            3000466 -1
            3000482 -1
            3000545 -1
            3000549 -1
            3000637 -1
            3000650 -1


            here's an 'od -c' to show the character usage:

            0000000 3 0 0 0 0 7 6 - 1 \n 3 0 0 0 4
            0000020 3 6 - 1 \n 3 0 0 0 4 3 7 - 1
            0000040 \n 3 0 0 0 4 4 1 - 1 \n 3 0 0 0
            0000060 4 6 6 - 1 \n 3 0 0 0 4 8 2 -
            0000100 1 \n 3 0 0 0 5 4 5 - 1 \n 3 0 0
            0000120 0 5 4 9 - 1 \n 3 0 0 0 6 3 7
            0000140 - 1 \n 3 0 0 0 6 5 0 - 1 \n 3 0
            0000160 0 0 6 5 6 - 1 \n 3 0 0 0 6 7 8
            0000200 - 1 \n 3 0 0 0 8 1 4 - 1 \n 3
            0000220 0 0 0 8 2 4 - 1 \n 3 0 0 0 9 6
            0000240 2 - 1 \n 3 0 0 1 0 0 7 - 1 \n
            0000260 3 0 0 1 0 3 8 - 1 \n 3 0 0 1 2
            0000300 4 1 - 1 \n 3 0 0 1 3 6 3 - 1
            0000320 \n 3 0 0 1 4 8 3 - 1 \n 3 0 0 1
            0000340 4 8 6 - 1 \n 3 0 0 2 2 2 6 -


            just a line by line separated by a whitespace char.

            Comment


            • #7
              Originally posted by dawe View Post
              Whoa... Never happened to me... Just to know:
              1- which CFLAGS have been used to compile wigToBigWig? (not -O3 I hope)
              2- how big is the wig? are you sure it is "kent compilant" ?

              what does

              Code:
              qacct -j 17246
              says (assuming 17246 is the $JOBID for your gridengine scheduler)?

              d
              I thought it was already compiled from the ucsc repository here:

              http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

              the find chromosome start/stop worked for me.

              the .wig file is approximately 3.7M.

              Comment


              • #8
                Originally posted by JohnK View Post
                I thought it was already compiled from the ucsc repository here:

                http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

                the find chromosome start/stop worked for me.

                the .wig file is approximately 3.7M.
                I've asked because I usually download their sources and compile on my own (and had issues with optimization flags).
                So, the binary is fine, gridengine doesn't report anything strange (except that the job has barely started), the wig is little and compilant (besides, I don't think you'll need to request 24 Gb to SGE to process a 4Mb wig file...)... I guess you'll have to run gdb to figure this out...

                Comment


                • #9
                  Originally posted by dawe View Post
                  I've asked because I usually download their sources and compile on my own (and had issues with optimization flags).
                  So, the binary is fine, gridengine doesn't report anything strange (except that the job has barely started), the wig is little and compilant (besides, I don't think you'll need to request 24 Gb to SGE to process a 4Mb wig file...)... I guess you'll have to run gdb to figure this out...
                  I believe I got the fix. Anyway, I downloaded the John Kent source tree package 'jksource.zip' and had it installed:

                  http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

                  No more floating point exception. You were right on about the compiling issues I believe.

                  Comment

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