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  • #31
    Why would you want to convert the binary cns to acgt?

    Could you list your maq-steps, that would allow me to better understand
    what you are trying to achieve.

    Best
    -Jonathan

    Comment


    • #32
      first, i convert my fasta file into bfa
      than convert my fastq file into bfq
      after that i obtain the map file using bfa and bfq
      maq match alignment.map alignment.bfa alignment.bfq
      it has 3 runs at 126% each
      than once i obtain that
      i use
      maq assemble alignment.cns alignment.bfa alignment.map
      than it tells me that consensus file has been created and it is in binary format which i cannot view it.
      than i try to use maqindex -i -c alignment.cns alignment.map
      but it tells me that alignment.cns is failing therefore i need to do mapass2maq for the alignment.cns but it fails giving me an error of the failure of the alignment

      i tried multiple ways but i could not obtain any results
      thats where i actually stopped
      than i tried to use that to view the files in mapview but i still was not able to do anything.

      please let me know if you further want me to discuss it i tried to cover step by step, i hope this will allow you to see where i am making a mistake.

      thanks,

      K

      Comment


      • #33
        Those *should* be the very steps to success;

        For maqview/maqindex to work the cns needs to be binary (afaik),
        so... I'm currently out of ideas.

        could you paste the exact 'message' from maqindex?

        Best
        -Jonathan

        Comment


        • #34
          maqindex segmentation fault (seqid too large)

          Thanks every body for this community.

          I had experienced "segmentation fault" with maqindex 2.5 when trying to index .map files (1 solexa lane, 14,853,012 sequences, pair end, 36 bp).
          The reference genome is Sc288 (Yeast 12Mbp).

          I tried with mapview-2.6, commented out line 11 of const.h, and compiled.
          Everithing goes fine

          But when I did the following:
          $ maqindex -c s_8.consensus.cns -i s_8.map
          I had this:
          -- Indexing the alignment file 's_8.map' ... -- Found error seqid is too large 1549491744 >= 17 in notify -- maqmap_index.c:123 --
          Segmentation fault

          Can you help me to interpret this error?

          My Best.
          G.
          gabriele bucci

          Comment


          • #35
            maqindex segmentation fault (seqid too large)

            Thanks every body for this community.

            I had experienced "segmentation fault" with maqindex 2.5 when trying to index .map files (1 solexa lane, 14,853,012 sequences, pair end, 36 bp).
            The reference genome is Sc288 (Yeast 12Mbp).

            I tried with mapview-2.6, commented out line 11 of const.h, and compiled.
            Everithing goes fine

            But when I did the following:
            $ maqindex -c s_8.consensus.cns -i s_8.map
            I had this:
            -- Indexing the alignment file 's_8.map' ... -- Found error seqid is too large 1549491744 >= 17 in notify -- maqmap_index.c:123 --
            Segmentation fault

            Can you help me to interpret this error?

            My Best.
            G.
            gabriele bucci

            Comment


            • #36
              I tried to follow your directions when maqindex -i -c alignment.cns alignment.map
              I obtain
              -- Indexing the alignment file 'alignment.map' ... DONE!
              -- Indexing the alignment file 'alignment.cns' ... DONE!

              than i go on maqview -c alignment.cns alignment.map
              freeglut (maview) failed to open display ' '

              thanks,

              Comment


              • #37
                Originally posted by olus View Post
                Thanks every body for this community.

                I had experienced "segmentation fault" with maqindex 2.5 when trying to index .map files (1 solexa lane, 14,853,012 sequences, pair end, 36 bp).
                The reference genome is Sc288 (Yeast 12Mbp).

                I tried with mapview-2.6, commented out line 11 of const.h, and compiled.
                Everithing goes fine

                But when I did the following:
                $ maqindex -c s_8.consensus.cns -i s_8.map
                I had this:
                -- Indexing the alignment file 's_8.map' ... -- Found error seqid is too large 1549491744 >= 17 in notify -- maqmap_index.c:123 --
                Segmentation fault

                Can you help me to interpret this error?

                My Best.
                G.
                Sorry for the doubled posting...

                By the way, I solved my problem installing maqview-0.2.3.

                maqindex -i -c s_1.consensus.cns s_1.map
                -- Indexing the alignment file 's_1.map' ... DONE!
                -- Indexing the consensus file 's_1.consensus.cns' ... DONE!

                Thanks
                gabriele bucci

                Comment


                • #38
                  Originally posted by xuer View Post
                  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?
                  I was having segmentation fault both with maqview-0.2.5 and maqview-0.2.6.
                  I resolved installing 0.2.3.
                  Not sure it works also for you....

                  Cheers
                  gabriele bucci

                  Comment


                  • #39
                    Hi everyone I'm trying to install maqview but I think I have a problem.
                    Now I'm using cygwin, maq-0.7.1, maqview-0.2.5.

                    A part of the error message when I typed './autogen.sh' is below.

                    ---

                    $ ./autogen.sh
                    running: aclocal
                    3 [main] perl 1184 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
                    as parent(0x12B0000) != 0x1E10000
                    3 [main] perl 1184 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
                    as parent(0x12B0000) != 0x1E10000
                    3 [main] perl 2196 fork: child 1184 - died waiting for dll loading, errno 11
                    3 [main] perl 2196 fork: child 1184 - died waiting for dll loading, errno 11
                    5405969 [main] perl 2396 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
                    as parent(0x12B0000) != 0x1E10000
                    5405969 [main] perl 2396 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
                    as parent(0x12B0000) != 0x1E10000
                    5425460 [main] perl 2196 fork: child 2396 - died waiting for dll loading, errno 11
                    5425460 [main] perl 2196 fork: child 2396 - died waiting for dll loading, errno 11
                    11015791 [main] perl 3648 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
                    as parent(0x12B0000) != 0x1E10000
                    11015791 [main] perl 3648 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
                    as parent(0x12B0000) != 0x1E10000
                    11037204 [main] perl 2196 fork: child 3648 - died waiting for dll loading, errno 11
                    11037204 [main] perl 2196 fork: child 3648 - died waiting for dll loading, errno 11
                    16251520 [main] perl 848 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
                    as parent(0x12B0000) != 0x1E10000
                    16251520 [main] perl 848 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
                    as parent(0x12B0000) != 0x1E10000
                    16272947 [main] perl 2196 fork: child 848 - died waiting for dll loading, errno 11
                    16272947 [main] perl 2196 fork: child 848 - died waiting for dll loading, errno 11

                    Is there anybody who knows about this problem??

                    Comment


                    • #40
                      Installing maqview on cygwin on PC

                      Hello all! I am hoping someone out there can help me. I use a PC, but needed to run Maq and Maqview, so I installed cygwin and got Maq installed and usable. However, I am running into problems with Maqview. Everything looks good until I get to the 'make' command and I get a long string of stuff that ends in an error (this is just the last part):

                      /cygdrive/d/maqview/MainFrame.c:91: undefined reference to `_glutReshapeWindow'
                      /cygdrive/d/maqview/MainFrame.c:94: undefined reference to `_glutSetWindow'
                      MainFrame.o: In function `main':
                      /cygdrive/d/maqview/MainFrame.c:190: undefined reference to `_glutInit'
                      /cygdrive/d/maqview/MainFrame.c:204: undefined reference to `_glutInitDisplayMod
                      e'
                      /cygdrive/d/maqview/MainFrame.c:205: undefined reference to `_glutInitWindowSize
                      '
                      /cygdrive/d/maqview/MainFrame.c:206: undefined reference to `_glutInitWindowPosi
                      tion'
                      /cygdrive/d/maqview/MainFrame.c:207: undefined reference to `_glutCreateWindow'
                      /cygdrive/d/maqview/MainFrame.c:225: undefined reference to `_glutSetWindow'
                      /cygdrive/d/maqview/MainFrame.c:226: undefined reference to `_glutReshapeFunc'
                      /cygdrive/d/maqview/MainFrame.c:227: undefined reference to `_glutDisplayFunc'
                      /cygdrive/d/maqview/MainFrame.c:228: undefined reference to `_glutKeyboardFunc'
                      /cygdrive/d/maqview/MainFrame.c:229: undefined reference to `_glutSpecialFunc'
                      /cygdrive/d/maqview/MainFrame.c:240: undefined reference to `_glutMainLoop'
                      MainFrame.o: In function `main_display':
                      /cygdrive/d/maqview/MainFrame.c:72: undefined reference to `_glutSwapBuffers'
                      MainFrame.o: In function `main_reshape':
                      /cygdrive/d/maqview/MainFrame.c:95: undefined reference to `_glutPostRedisplay'
                      /cygdrive/d/maqview/MainFrame.c:95: undefined reference to `_glutPostRedisplay'
                      collect2: ld returned 1 exit status
                      make[1]: *** [maqview.exe] Error 1
                      make[1]: Leaving directory `/cygdrive/d/maqview'
                      make: *** [all] Error 2

                      Gah!!!!! Help!

                      Comment


                      • #41
                        "bus error" in maqindex

                        Hi everyone,

                        I still have the "bus error" problem when I tried to use maqindex command "maqindex -i all.map" . The error message showed as below:

                        -- Indexing the alignment file 'all.map' ... Bus error

                        My maqview is the latest version 0.2.6. When I used the previous version 0.2.5, no such bug showed up in the index process. I successfully finished indexing the map file and run maqview. But when I did a few click in the maqview window, an error with Bus error showed up and end the maqview automatically.

                        I use mac os x 10.5.8. Great thanks to any helpful comments!

                        Comment


                        • #42
                          Same problem but still no joy following the answer to the thread

                          Originally posted by Albert N View Post
                          Heeeelp!

                          I have some troubles triying to compile maqview-0.2.6 (sorry I'm a beginner).
                          Install file says: "To compile it, just run"./autogen.sh; ./configure; make"......but when I type ./autogen this is the output:
                          albert@mambara:~/maqview$ ./autogen.sh
                          running: aclocal
                          eval: 1: aclocal: not found
                          error: while running 'aclocal'

                          Somebody knows what am I doing wrong?
                          I had the same problem as Albert N. I followed the instructions in the thread. MaqView is trying to install and the initial configuration seems to go ok but I get the following error messages after I type "make", but I'm not sure what they mean:
                          g++ -g -O2 -o maqview read_cache.o view_goto.o view_panel.o gl_gui.o MainFrame.o btree.o maqmap_index.o zrio.o stdhashc.o cns_cache.o const.o adler32.o compress.o crc32.o deflate.o gzio.o inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o -lGL -lglut -lm
                          view_panel.o: In function `resetPickMatrixs':
                          /usr/local/bin/maqview/view_panel.c:270: undefined reference to `gluPickMatrix'
                          collect2: ld returned 1 exit status
                          make[1]: *** [maqview] Error 1
                          make[1]: Leaving directory `/usr/local/bin/maqview'
                          make: *** [all] Error 2

                          Any ideas?

                          Comment


                          • #43
                            SImilar problem in Maqview installation

                            Iam also getting the following error when typing in the "make" command as the last step to install the latest version of MAQVIEW, does anyone know what it means?

                            g++ -g -O2 -o maqview read_cache.o view_goto.o view_panel.o gl_gui.o MainFrame.o btree.o maqmap_index.o zrio.o stdhashc.o cns_cache.o const.o adler32.o compress.o crc32.o deflate.o gzio.o inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o -lGL -lglut -lm
                            view_panel.o: In function `resetPickMatrixs':
                            /usr/local/bin/maqview/view_panel.c:270: undefined reference to `gluPickMatrix'
                            collect2: ld returned 1 exit status
                            make[1]: *** [maqview] Error 1
                            make[1]: Leaving directory `/usr/local/bin/maqview'
                            make: *** [all] Error 2

                            Comment


                            • #44
                              Hi
                              I gave up on using maqview. Use this free tool instead, The Integrative Genomics Viewer (IGV).

                              Comment


                              • #45
                                integrative genome viewer

                                Hi I had a look at this but from what I could see I could only choose from the listed genomes? Mine wasn't in there and I couldn't see a way of uploading your own genome in there?

                                I'm aligning Illumina paired end reads for bacterial isolates against a related reference genome in MAQ, then trying to view the aligned reads against their reference genome, so that I can visually identify SNPs and the aligned reads. I was using a program called Tablet quite nicely until I updated to the latest version when I encountered problems with uploading my assembly.

                                Does anyone know of a program that could do similar? I'm giving up on Maqview unless a miracle happens!

                                Comment

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