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  • BFAST - Help

    Hello,

    I am trying to align Solid reads that map uniquely to the C. Elegans genome. I have a fastq file that has 4 lines for each read that are 50 bases in length. The reads are in color space (0-3). I have very little programming experience outside of writing simple perl scripts and am very new to next generation sequencing.

    I have successfully used bowtie in the past to align reads to the human genome from Solexa data, but for some reason, I am having difficulty getting started with the latest version of BFAST. I have been reading the manual for a couple hours, which seems straightforward, but I think that there are some installation steps that I need to execute before creating the index and matching the reads.

    I am working on a linux system. Could someone please tell me the commands that I need to enter to install BFAST? I entered the command, ./configure and got a response, but I think there are some additional steps that remain for the installation process.

    Thanks,
    cutcopy11

  • #2
    Originally posted by cutcopy11 View Post
    Hello,

    I am trying to align Solid reads that map uniquely to the C. Elegans genome. I have a fastq file that has 4 lines for each read that are 50 bases in length. The reads are in color space (0-3). I have very little programming experience outside of writing simple perl scripts and am very new to next generation sequencing.

    I have successfully used bowtie in the past to align reads to the human genome from Solexa data, but for some reason, I am having difficulty getting started with the latest version of BFAST. I have been reading the manual for a couple hours, which seems straightforward, but I think that there are some installation steps that I need to execute before creating the index and matching the reads.

    I am working on a linux system. Could someone please tell me the commands that I need to enter to install BFAST? I entered the command, ./configure and got a response, but I think there are some additional steps that remain for the installation process.

    Thanks,
    cutcopy11
    Try:
    ./configure
    make
    make install

    If you need more help, post here or the bfast help mailing list: [email protected].

    Comment


    • #3
      Thanks for the quick response.

      After performing the "./configure" and "make" commands, the "make install" command gave the following output:

      ~/Desktop/bfast-0.6.1c$ make install
      Making install in bfast
      make[1]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
      make[2]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
      test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
      /usr/bin/install -c 'bfast' '/usr/local/bin/bfast'
      /usr/bin/install: cannot create regular file `/usr/local/bin/bfast': Permission denied
      make[2]: *** [install-binPROGRAMS] Error 1
      make[2]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
      make[1]: *** [install-am] Error 2
      make[1]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
      make: *** [install-recursive] Error 1

      Is this a problem? I see that the Bfast program is available now.

      -Clayton

      Comment


      • #4
        Originally posted by cutcopy11 View Post
        Thanks for the quick response.

        After performing the "./configure" and "make" commands, the "make install" command gave the following output:

        ~/Desktop/bfast-0.6.1c$ make install
        Making install in bfast
        make[1]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
        make[2]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
        test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
        /usr/bin/install -c 'bfast' '/usr/local/bin/bfast'
        /usr/bin/install: cannot create regular file `/usr/local/bin/bfast': Permission denied
        make[2]: *** [install-binPROGRAMS] Error 1
        make[2]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
        make[1]: *** [install-am] Error 2
        make[1]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
        make: *** [install-recursive] Error 1

        Is this a problem? I see that the Bfast program is available now.

        -Clayton
        Take a look at the line that says "Permission denied". Looks like you need to contact your cluster or computer administrator since you don't have sufficient privileges on the computer/cluster.

        Comment


        • #5
          Originally posted by cutcopy11 View Post
          Thanks for the quick response.

          After performing the "./configure" and "make" commands, the "make install" command gave the following output:

          ~/Desktop/bfast-0.6.1c$ make install
          Making install in bfast
          make[1]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
          make[2]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
          test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
          /usr/bin/install -c 'bfast' '/usr/local/bin/bfast'
          /usr/bin/install: cannot create regular file `/usr/local/bin/bfast': Permission denied
          make[2]: *** [install-binPROGRAMS] Error 1
          make[2]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
          make[1]: *** [install-am] Error 2
          make[1]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
          make: *** [install-recursive] Error 1

          Is this a problem? I see that the Bfast program is available now.

          -Clayton
          Come on Nils (or Nils-bot), we can do better:

          1. After configure and make, your binaries/software is ready to use.
          Just point your PATH env variable to /home/cweaver/Desktop/bfast-0.6.1c/bfast and you are good to go.

          2. During configuring specify another location to install the software:

          $ mkdir $HOME/local
          $ configure --prefix=$HOME/local
          $ make
          $ make install

          bfast will be placed in $HOME/local/bin

          Good luck.
          -drd

          Comment


          • #6
            Troble installin bfast

            I am getting the following error when I run make. Can anybody offer any advice? I am on a linux fedora 64 bit amazon cloud machine. Thanks for any help!



            make all-recursive
            make[1]: Entering directory `/mnt/vol3/simulations/bfast'
            Making all in bfast
            make[2]: Entering directory `/mnt/vol3/simulations/bfast/bfast'
            gcc -Wall -g -O2 -pthread -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lz -lm
            aflib.o: In function `AFILE_afwrite':
            /mnt/vol3/simulations/bfast/bfast/aflib.c:241: undefined reference to `BZ2_bzwrite'
            aflib.o: In function `AFILE_afread':
            /mnt/vol3/simulations/bfast/bfast/aflib.c:185: undefined reference to `BZ2_bzRead'
            /mnt/vol3/simulations/bfast/bfast/aflib.c:192: undefined reference to `BZ2_bzReadGetUnused'
            /mnt/vol3/simulations/bfast/bfast/aflib.c:199: undefined reference to `BZ2_bzReadClose'
            /mnt/vol3/simulations/bfast/bfast/aflib.c:207: undefined reference to `BZ2_bzReadOpen'
            aflib.o: In function `AFILE_afclose':
            /mnt/vol3/simulations/bfast/bfast/aflib.c:150: undefined reference to `BZ2_bzWriteClose'
            aflib.o: In function `AFILE_afdopen':
            /mnt/vol3/simulations/bfast/bfast/aflib.c:125: undefined reference to `BZ2_bzWriteOpen'
            /mnt/vol3/simulations/bfast/bfast/aflib.c:115: undefined reference to `BZ2_bzReadOpen'
            aflib.o: In function `AFILE_afopen':
            /mnt/vol3/simulations/bfast/bfast/aflib.c:52: undefined reference to `BZ2_bzReadOpen'
            /mnt/vol3/simulations/bfast/bfast/aflib.c:62: undefined reference to `BZ2_bzWriteOpen'
            collect2: ld returned 1 exit status
            make[2]: *** [bfast] Error 1
            make[2]: Leaving directory `/mnt/vol3/simulations/bfast/bfast'
            make[1]: *** [all-recursive] Error 1
            make[1]: Leaving directory `/mnt/vol3/simulations/bfast'
            make: *** [all] Error 2

            Comment


            • #7
              You are missing the includes and libraries for the bzip2 library.
              Try this:

              Code:
              $ sudo yum install bzip2 bzip2-devel bzip2-libs
              and try again.
              -drd

              Comment


              • #8
                Hi..
                I am experiencing the same problem in Ubuntu and not able to install the package libraries also..
                kindly help me out..

                Thanks

                Comment


                • #9
                  Originally posted by Venkat View Post
                  Hi..
                  I am experiencing the same problem in Ubuntu and not able to install the package libraries also..
                  kindly help me out..

                  Thanks
                  Why are you unable to install the packages? Please be much more descriptive about what you tried and what is not working.

                  Comment


                  • #10
                    I tried to compile the packages..
                    but its says

                    make all-recursive
                    make[1]: Entering directory `/host/bfast+bwa-0.6.4e'
                    Making all in bfast
                    make[2]: Entering directory `/host/bfast+bwa-0.6.4e/bfast'
                    gcc -Wall -g -O2 -pthread -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o bwtindex.o bwt_gen.o QSufSort.o is.o bwtmisc.o bwaseqio.o bwtio.o utils.o util.o bntseq.o bwt.o bwtgap.o stdaln.o bwtaln.o occ_results.o bwtbfast2_aux.o bwtbfast_aux.o bwtbfast2.o bwtbfast.o aflib.o Main.o -lpthread -lz -lz -lm
                    aflib.o: In function `AFILE_afwrite':
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:241: undefined reference to `BZ2_bzwrite'
                    aflib.o: In function `AFILE_afread':
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:185: undefined reference to `BZ2_bzRead'
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:192: undefined reference to `BZ2_bzReadGetUnused'
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:199: undefined reference to `BZ2_bzReadClose'
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:207: undefined reference to `BZ2_bzReadOpen'
                    aflib.o: In function `AFILE_afclose':
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:150: undefined reference to `BZ2_bzWriteClose'
                    aflib.o: In function `AFILE_afdopen':
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:125: undefined reference to `BZ2_bzWriteOpen'
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:115: undefined reference to `BZ2_bzReadOpen'
                    aflib.o: In function `AFILE_afopen':
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:52: undefined reference to `BZ2_bzReadOpen'
                    /host/bfast+bwa-0.6.4e/bfast/aflib.c:62: undefined reference to `BZ2_bzWriteOpen'
                    collect2: ld returned 1 exit status
                    make[2]: *** [bfast] Error 1
                    make[2]: Leaving directory `/host/bfast+bwa-0.6.4e/bfast'
                    make[1]: *** [all-recursive] Error 1
                    make[1]: Leaving directory `/host/bfast+bwa-0.6.4e'
                    make: *** [all] Error 2

                    some bzip files are missing
                    I installed the bzip libraries and still getting same errors..

                    Comment


                    • #11
                      Did you install the bzip2 developers packages?

                      Comment


                      • #12
                        I have installed the available bzip2 dev packages too..still am not getting it..

                        Comment


                        • #13
                          Could you run the configure script again "./configure" and post your output? Thanks for your patience.

                          Comment


                          • #14
                            It works!!

                            I have configured the file and installed but did not set the path initially so..not aware where it has been installed..?
                            Many Thanks.

                            Comment


                            • #15
                              Hi,
                              I can't install bfast in Ubuntu. Thanks for any help.

                              After ./configure

                              checking for a BSD-compatible install... /usr/bin/install -c
                              checking whether build environment is sane... yes
                              checking for a thread-safe mkdir -p... /bin/mkdir -p
                              checking for gawk... gawk
                              checking whether make sets $(MAKE)... yes
                              checking build system type... x86_64-unknown-linux-gnu
                              checking for gcc... gcc
                              checking whether the C compiler works... yes
                              checking for C compiler default output file name... a.out
                              checking for suffix of executables...
                              checking whether we are cross compiling... no
                              checking for suffix of object files... o
                              checking whether we are using the GNU C compiler... yes
                              checking whether gcc accepts -g... yes
                              checking for gcc option to accept ISO C89... none needed
                              checking for style of include used by make... GNU
                              checking dependency style of gcc... gcc3
                              checking how to run the C preprocessor... gcc -E
                              checking for grep that handles long lines and -e... /bin/grep
                              checking for egrep... /bin/grep -E
                              checking for ANSI C header files... yes
                              checking for sys/types.h... yes
                              checking for sys/stat.h... yes
                              checking for stdlib.h... yes
                              checking for string.h... yes
                              checking for memory.h... yes
                              checking for strings.h... yes
                              checking for inttypes.h... yes
                              checking for stdint.h... yes
                              checking for unistd.h... yes
                              checking minix/config.h usability... no
                              checking minix/config.h presence... no
                              checking for minix/config.h... no
                              checking whether it is safe to define __EXTENSIONS__... yes
                              fatal: Not a git repository (or any of the parent directories): .git
                              checking for BZ2_bzRead in -lbz2... no
                              checking for an ANSI C-conforming const... yes
                              checking for stdlib.h... (cached) yes
                              checking for GNU libc compatible malloc... yes
                              checking for stdlib.h... (cached) yes
                              checking for GNU libc compatible realloc... yes
                              checking for pow in -lm... yes
                              checking for gzread in -lz... yes
                              checking for floor... yes
                              checking for pow... yes
                              checking for sqrt... yes
                              checking for strchr... yes
                              checking for strdup... yes
                              checking for strpbrk... yes
                              checking for strstr... yes
                              checking for strtok_r... yes
                              checking for int8_t... yes
                              checking for int32_t... yes
                              checking for int64_t... yes
                              checking for uint8_t... yes
                              checking for uint32_t... yes
                              checking for uint64_t... yes
                              checking size of short int... 2
                              checking size of int... 4
                              checking size of long int... 8
                              checking for ANSI C header files... (cached) yes
                              checking limits.h usability... yes
                              checking limits.h presence... yes
                              checking for limits.h... yes
                              checking for stdint.h... (cached) yes
                              checking for stdlib.h... (cached) yes
                              checking for string.h... (cached) yes
                              checking sys/time.h usability... yes
                              checking sys/time.h presence... yes
                              checking for sys/time.h... yes
                              checking for unistd.h... (cached) yes
                              checking float.h usability... yes
                              checking float.h presence... yes
                              checking for float.h... yes
                              checking zlib.h usability... yes
                              checking zlib.h presence... yes
                              checking for zlib.h... yes
                              checking bzlib.h usability... no
                              checking bzlib.h presence... no
                              checking for bzlib.h... no
                              checking fcntl.h usability... yes
                              checking fcntl.h presence... yes
                              checking for fcntl.h... yes
                              checking for inline... inline
                              configure: creating ./config.status
                              config.status: creating Makefile
                              config.status: creating bfast/Makefile
                              config.status: creating butil/Makefile
                              config.status: creating scripts/Makefile
                              config.status: creating tests/Makefile
                              config.status: creating config.h
                              config.status: config.h is unchanged
                              config.status: executing depfiles commands

                              After make

                              make all-recursive
                              make[1]: Вход в каталог `/media/share/bfast-0.6.4e'
                              Making all in bfast
                              make[2]: Вход в каталог `/media/share/bfast-0.6.4e/bfast'
                              gcc -DHAVE_CONFIG_H -I. -I.. -Wall -g -O2 -pthread -MT MatchesReadInputFiles.o -MD -MP -MF .deps/MatchesReadInputFiles.Tpo -c -o MatchesReadInputFiles.o MatchesReadInputFiles.c
                              In file included from MatchesReadInputFiles.c:10:
                              aflib.h:6: fatal error: bzlib.h: Нет такого файла или каталога
                              compilation terminated.
                              make[2]: *** [MatchesReadInputFiles.o] Ошибка 1
                              make[2]: Выход из каталога `/media/share/bfast-0.6.4e/bfast'
                              make[1]: *** [all-recursive] Ошибка 1
                              make[1]: Выход из каталога `/media/share/bfast-0.6.4e'
                              make: *** [all] Ошибка 2

                              Comment

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