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  • roko-t
    replied
    I had the confusing trouble at the installing for Hiseq v4 but I solved it. (^^)
    In my case it was because of the Boost library version and the incompatibility with gcc in my default environment on Linux.

    The following version set is NG.
    Boost C++ library v 1.55.0 or v 1.44.0
    gcc 4.8.1, with c++

    The following version set is OK !!
    Boost C++ library v 1.44.0
    gcc 4.6.2, with c++

    We need to set the following environment variables to use specified Boost and gcc for configuring the build.
    CC
    CXX

    BOOST_ROOT #location of the boost library
    BOOST_INCLUDEDIR #location of the include directory of boost
    BOOST_LIBRARYDIR #location of the lib directory of boost

    *For details, refer to "configure help".
    $ bcl2fastq-1.8.4/src/configure --help
    Last edited by roko-t; 07-23-2014, 04:36 PM.

    Leave a comment:


  • dsobral
    replied
    Thanks. I'm continuing this in the other thread:
    Bridged amplification & clustering followed by sequencing by synthesis. (Genome Analyzer / HiSeq / MiSeq)


    Daniel

    Leave a comment:


  • GenoMax
    replied
    Originally posted by dsobral View Post
    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
    I am going to let you go through what I posted in the new thread you started. Let us work through that thread since your problem is no longer about installation. We can fix the samplesheet easily.

    Once you respond to the questions in the other thread we can continue.

    Leave a comment:


  • dsobral
    replied
    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

    Leave a comment:


  • GenoMax
    replied
    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.

    Leave a comment:


  • dsobral
    replied
    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

    Leave a comment:


  • dsobral
    replied
    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

    Leave a comment:


  • sklages
    replied
    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 :-)

    Leave a comment:


  • min1204
    replied
    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

    Leave a comment:


  • min1204
    replied
    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.

    Leave a comment:


  • maubp
    replied
    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

    Leave a comment:


  • maubp
    replied
    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)

    Leave a comment:


  • min1204
    replied
    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

    Leave a comment:


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

    Leave a comment:


  • min1204
    replied
    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.

    Leave a comment:

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