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  • How to use MAQVIEW?

    Hi,
    I use this MAQVIEW command "./maqview alo1564.map", to display the alignment. but system replies:

    "freeglut (./maqview):unable to creat direct context rendering for window 'M.A.Q View'.
    This may hurt performance.
    Cannot open view on alo1564.map"


    Is there anyone know what wrong is?

  • #2
    Did you index the map with maqindex -c XXXX.cns YYYY.map ?

    Comment


    • #3
      Yes, I did.
      Also ran ./zrio make XXXXX.map

      Comment


      • #4
        I've had this error when trying to use a newer version of maqview to view .map files from older versions of maq.

        Comment


        • #5
          I got a "Segmentation fault" error when i tried
          ./maqindex -v input.map chrI:1-200

          or ./maqindex -i input.map.


          Is there anybody could help me?

          Comment


          • #6
            I tried running maqindex with maq output from versions 0.6.8 and 0.7.1, in either case there is a segmentation error

            %maqindex -i -c consensus.cns all.map
            -- Indexing the alignment file 'all.map' ... Segmentation fault

            Can anybody help?

            Comment


            • #7
              Jue has just uploaded a new maqview-0.2.5. This version works with 0.7.x. Sorry for the late update.

              Comment


              • #8
                You can use MapView to view any format alignment results.



                Now can be downloaded from our lab website.

                View short reads alignment

                input file:
                1. Reference sequence file and
                2. Eland , SOAP, MAQ, SeqMap ... any formated alignment results file

                MapView converts the input files to MSF format file.

                MapView loads the MSF file,then you can view the alignment and SNPs.

                Comment


                • #9
                  again maqview

                  I am sorry, is it because I made some mistake? with maqview -0.2.5, I got a blank window showing nothing sequence
                  after i close the window, I got a error:
                  freeglut_structure.c:439: fgEnumWindows: Assertion `fgState.Initialised' failed.

                  any one else have such problem ?

                  Comment


                  • #10
                    Hi
                    I just downloaded the latest MAQ and MAQviewer, and when I try to view my alignments, MAQview shuts down after few mouse clicks and scrolling with the message: "Bus error". Is there a limitation for the number of alignments that MAQview can handle ?

                    Comment


                    • #11
                      same for me, just downloaded and installed, and ran the maqdemo on phiX (~6kb)

                      new MAQ 7.1, new maqview 2.5

                      rhel5, 16Gb RAM

                      2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux

                      /MAQ_BWA/maqview/maqindex -i -c consensus.cns all.map
                      -- Indexing the alignment file 'all.map' ... Segmentation fault


                      Incidentally I segfault while trying to build indexes with SOAPalign for anything larger than ~15Mbases.

                      Comment


                      • #12
                        I too am getting a segmentation fault. It happens with all combinations of maqview 0.23/0.25 with maq 0.6/0.7.1

                        maqindex -i neg.map
                        -- Indexing the alignment file 'neg.map' ... Segmentation fault

                        This is on Centos 5.x, Xeon SMP 64 bit CPU, 64 GB RAM.

                        Comment


                        • #13
                          maqview freeglut error

                          Originally posted by ECO View Post
                          Did you index the map with maqindex -c XXXX.cns YYYY.map ?


                          Hello,

                          I am having similar issues like other users, i.e. get the following error message:


                          maqview s512.3diff.mapMerge
                          freeglut /maqview/bin/maqview: relocation error: /maqview/bin/maqview: symbol __fprintf_chk, version GLIBC_2.3.4 not defined in file libc.so.6 with link time reference


                          I have indexed my .map and .cns file as suggested by ECO.

                          The .map and .cns files are generated by the 0.7.1 version of maq and I am using the latest version of maqview, 0.2.5.


                          Thanks!
                          Anamika

                          Comment


                          • #14
                            Hi,

                            Did you get your problem solved? I am having the same problem...

                            Comment


                            • #15
                              I am having the same problem. Did you find a way to solve the problem?

                              Comment

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