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  • install bcl2fastq-1.8.4

    Hi everyone,

    I'm trying to install illumina's software bcl2fastq-1.8.4, but there are some problems that I can't resolve. Hope someone can help me.

    First, I installed it using "bcl2fastq-1.8.4.tar.bz2". It went smoothly when I did configure. But the problem came when I type make, like this:

    [root@localhost CASAVA-build]# make
    [ 0%] Unpacking merge.xslt
    [ 2%] Built target CASAVA_MERGE_XSLT
    [ 2%] Built target CASAVA_OPT
    [ 48%] Built target casava_common
    [ 53%] Built target casava_io
    [ 61%] Built target casava_alignment
    [ 64%] Built target casava_basecalling
    [ 74%] Built target casava_kagu
    [ 76%] Building CXX object c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/BclDemultiplexer.cpp.o
    /home/liumin/software/bcl2fastq/src/c++/lib/demultiplex/BclDemultiplexer.cpp: In member function ‘const casava::demultiplex::BclDemultiplexer::ClusterCorrectedBarcodeIndex casava::demultiplex::BclDemultiplexer::mapClusterBarcodes(unsigned int) const’:
    /home/liumin/software/bcl2fastq/src/c++/lib/demultiplex/BclDemultiplexer.cpp:65: error: no matching function for call to ‘bind(<unresolved overloaded function type>, boost::arg<1>&)’
    make[2]: *** [c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/BclDemultiplexer.cpp.o] Error 1
    make[1]: *** [c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/all] Error 2
    make: *** [all] Error 2

    Could someone tell me why this happen?

    And I also tried rpm method to install it. It gave me a message:

    [root@localhost software]# rpm -i bcl2fastq-1.8.4-Linux-x86_64.rpm
    error: Failed dependencies:
    perl(XML::Simple) is needed by bcl2fastq-1.8.4-1.x86_64

    But I already have this perl module (XML::Simple) in my server. Following list contain all perl modules:

    B::Flags -- 0.10
    Bio -- ???
    Carp -- 1.32
    Class:ata::Inheritable -- 0.08
    DBD::Multiplex -- 2.11
    DBD::mysql -- 4.024
    DBI -- 1.628
    DBI::Shell -- 11.95
    Data -- ???
    Devel::StackTrace -- 1.30
    Digest::SHA1 -- 2.13
    Exception::Class -- 1.37
    ExtUtils::MakeMaker -- 6.80
    IO::String -- 1.08
    IO::Tee -- 0.64
    IPC::Run -- 0.92
    List::Util -- 1.27
    Math:erivative -- undef
    Math::Spline -- 0.02
    Net:aemon -- 0.48
    OLE::Storage_Lite -- 0.19
    Opcodes -- 0.12
    Parse::RecDescent -- 1.967009
    Perl -- 5.10.1
    SVG -- 2.59
    Spreadsheet::WriteExcel -- 2.39
    Statistics:escriptive -- 3.0605
    Storable -- 2.45
    Sub::Uplevel -- 0.24
    Test:eep -- 0.110
    Test::Exception -- 0.32
    Test::Harness -- 3.29
    Test::NoWarnings -- 1.04
    Test::Simple -- 0.98
    Test::Tester -- 0.109
    Text::Reform -- 1.20
    Thread::Cancel -- 1.13
    Thread::Queue -- 3.02
    Thread::Semaphore -- 2.12
    Thread::Suspend -- 1.22
    XML-DOM -- ???
    XML:OM::XPath -- 0.14
    XML::LibXML -- 2.0106
    XML::NamespaceSupport -- 1.11
    XML::RegExp -- 0.04
    XML::SAX -- 0.99
    XML::SAX::Base -- 1.08
    XML::SAX::Expat -- 0.50
    XML::Simple -- 2.20
    XML::Twig -- 3.44
    XML::Writer -- 0.623
    XML::XPathEngine -- 0.14
    YAML -- 0.84
    threads -- 1.86
    threads::shared -- 1.43

    Could someone help me?
    Thank you very much!

    Min

  • #2
    The system is CentOS 6.4

    Comment


    • #3
      The compilation fails due to missing a function which looks like it is part of BOOST - do the install instructions mention that you should install BOOST first?

      Comment


      • #4
        Originally posted by maubp View Post
        The compilation fails due to missing a function which looks like it is part of BOOST - do the install instructions mention that you should install BOOST first?
        Hi Peter, thank you for your answer.
        But BOOST has been installed. You see,

        [root@localhost ~]# yum install boost
        Loaded plugins: fastestmirror, refresh-packagekit
        Loading mirror speeds from cached hostfile
        base | 3.7 kB 00:00
        extras | 3.4 kB 00:00
        updates | 3.4 kB 00:00
        Setting up Install Process
        Package boost-1.41.0-17.el6_4.x86_64 already installed and latest version
        Nothing to do

        So there might be some other problems.

        Comment


        • #5
          Have you installed the BOOST compiler header files etc using:
          Code:
          yum install boost-devel

          Comment


          • #6
            Originally posted by maubp View Post
            Have you installed the BOOST compiler header files etc using:
            Code:
            yum install boost-devel
            Yes, I have installed boost-devel.

            [root@localhost ~]# yum install boost-devel
            Loaded plugins: fastestmirror, refresh-packagekit
            Loading mirror speeds from cached hostfile
            Setting up Install Process
            Package boost-devel-1.41.0-17.el6_4.x86_64 already installed and latest version
            Nothing to do

            Comment


            • #7
              Hmm. The PDF instructions don't mention BOOST as a requirement when installing from source, so perhaps my guess from the error was wrong. They list:

              The following software is required to run bcl2fastq; check whether it has been installed:
              • GNU make (3.81 recommended)
              • Perl (>= 5.8)
              • libxslt
              • libxslt-devel
              • libxml2
              • libxml2-devel
              • gcc (4.0.0 or newer, except 4.0.2), with c++
              • ImageMagick
              • bzip2
              • bzip2-devel-zlib
              • zlib-devel
              However, they do provide a precompiled RPM file which would perhaps work on CentOS:
              This download contains the software, release notes, and user guide for the 1.8.4. version of the Bcl2FastQ conversion software. The Bcl2FastQ conversion software is a tool to handle bcl conversion and demultiplexing. Version 1.8.4 has added ability to mask multiple adapter sequences per read, has standard Illumina adapter sequences included in the bcl2fastq installation, and the stringency of the adapter masking feature is now configurable.
              Last edited by maubp; 10-26-2013, 04:15 AM. Reason: correction (see page 27 of PDF)

              Comment


              • #8
                See also this thread for bcl2fastq 1.8.3 which it is suggested (part of) boost is bundled with it:
                Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

                Comment


                • #9
                  Thank you very much.

                  I have installed all the softwares listed in the PDF document . I also tried RPM file.

                  [root@localhost software]# rpm -i bcl2fastq-1.8.4-Linux-x86_64.rpm
                  error: Failed dependencies:
                  perl(XML::Simple) is needed by bcl2fastq-1.8.4-1.x86_64

                  But I have installed this perl module. It is so weird. I just began to use Linux about two months ago. This makes me feel very confused.

                  Comment


                  • #10
                    Hi maubp, I re-configured the bcl2fastq. Although it said configuration was successful.

                    -- Found X11 header: /usr/include/X11/X.h
                    -- Found X11 library: /usr/lib64/libX11.so
                    -- Found LibXml2: /usr/lib64/libxml2.so
                    -- using compiler: gcc version 4.4.7
                    -- Adding the c++ library subdirectory: common
                    -- Adding the c++ library subdirectory: io
                    -- Adding the c++ library subdirectory: alignment
                    -- Adding the c++ library subdirectory: basecalling
                    -- Adding the c++ library subdirectory: kagu
                    -- Adding the c++ library subdirectory: demultiplex
                    -- Adding the c++ program subdirectory: bin
                    -- Adding the c++ program subdirectory: BaseCalls
                    -- Adding the c++ program subdirectory: Demultiplex
                    -- Found Doxygen: /usr/bin/doxygen
                    -- Doxygen: /usr/bin/doxygen. Dot: DOXYGEN_DOT_EXECUTABLE-NOTFOUND.
                    -- Creating Doxygen config file: /home/liumin/software/bcl2fastq/BUILD/c++/Doxyfile
                    -- Adding the verifyBoost dynamic link binary checker: verifyBoost
                    -- Found PTHREAD header: /usr/include/pthread.h
                    -- Found PTHREAD library: /usr/lib64/libpthread.so
                    -- pthread supported
                    -- Configuring done
                    -- Generating done
                    -- Build files have been written to: /home/liumin/software/bcl2fastq/BUILD
                    The build directory /home/liumin/software/bcl2fastq/BUILD was configured successfully

                    Type make at the top level of the root directory to build the BCL2FASTQ converter


                    during the process of configuration, there were many failure tests. I didn't noticed these before, because it ran very fast. I used printscreen to get a picture.

                    Could you please see it and maybe you can find the problem. Thanks!
                    Attached Files

                    Comment


                    • #11
                      I'd recommend using the boost distribution provided with bcl2fastq. Newer versions of boost may give problems. If you have installed boost on your system, then configure will use that installation. Compile the boost 1.44 from Illumina and make it known to configure.

                      It is always fun installing illumina (linux) software :-)

                      Comment


                      • #12
                        I had the same issue, and it was because of the boost library version.

                        go to the redist folder in the bcl2fastq distribution, and build boost 1.44 that comes in there. Then make sure that LD_LIBRARY_PATH and other system elements point to where boost is.

                        I finally compiled the thing

                        Now to see if I can make it work with my data...

                        Daniel

                        Comment


                        • #13
                          Unfortunately it doesn't work...
                          e.g. locs file are now clocs file, Assumes certain filenames that are different, etc... I don't think it was done for use with MiSeq.

                          Anyone has any experience with this??

                          Thanks,
                          Daniel

                          Comment


                          • #14
                            Did you check the manual that goes with it? Look at the options for the conversion/demultiplexing that should allow you to make the necessary adjustments (e.g. --positions-format clocs vs locs).

                            AFAIK it should work with MiSeq data (you would need the entire data folder). We use CASAVA regularly with MiSeq data and this is just a fraction of that package.

                            Comment


                            • #15
                              Yes, I'm reading the documentation from here:


                              It actually complains that the SampleSheet does not have the correct format:

                              configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls --output-dir Unaligned --positions-format .locs --no-eamss
                              "ERROR: Wrong number of fields in sample sheet (expected: 10, got 2: IEMFileVersion,4)"

                              Good to know someone is using the software for MiSeq... there's still hope then.

                              Thanks,
                              Daniel

                              Comment

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