Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Bcl2Fastq 1.8.3 install error on Ubuntu 12.04LTS: "No support for bzip2 compression"

    Hi,

    I was trying to install the CASAVA Bcl2Fastq 1.8.3 package on my Ubuntu Server 12.04LTS. First, I encountered the same "No support for gzip compression" discussed in the following thread:
    http://seqanswers.com/forums/showthread.php?t=11106
    Follow the solution in the thread, I solve the problem by:
    Code:
    sudo ln -s /usr/lib/x86_64-linux-gnu/libpthread* /usr/lib
    sudo ln -s /usr/lib/x86_64-linux-gnu/libz.so /usr/lib
    However, now I get another similar error: "No support for bzip2 compression".
    I am wondering if there is any way to solve this?

    Here is the detailed install log:

    Code:
    administrator@Epizyme2:/tmp/bcl2fastq-1.8.3-build$ sudo ${SOURCE}/src/configure --prefix=${INSTALL} --verbose
    [sudo] password for administrator: 
    cmake version "cmake version 2.8.4" is already installed at /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake
    nothing to be done
    Using installed /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake
    Source  directory: /tmp/bcl2fastq-1.8.3/src
    Prefix  directory: /usr/local/bcl2fastq-1.8.3
    Exec    directory: 
    Binary  directory: 
    Lib     directory: 
    Libexec directory: 
    Include directory: 
    Data    directory: 
    Doc     directory: 
    Man     directory: 
    Build   directory: /tmp/bcl2fastq-1.8.3-build
    Cmake  executable: /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake
    
    Running on: Linux Epizyme2 3.2.0-29-generic #46-Ubuntu SMP Fri Jul 27 17:03:23 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
    Configuring the build directory with:
        /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake -H"/tmp/bcl2fastq-1.8.3/src" -B"/tmp/bcl2fastq-1.8.3-build" -G"Unix Makefiles" -DCASAVA_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DBoost_DEBUG:BOOL=ON
    
    -- The C compiler identification is GNU
    -- The CXX compiler identification is GNU
    -- Check for working C compiler: /usr/bin/gcc
    -- Check for working C compiler: /usr/bin/gcc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- install      prefix: /usr/local/bcl2fastq-1.8.3
    -- install exec prefix: .
    -- install     bin dir: ./bin
    -- install     lib dir: ./lib/bcl2fastq-1.8.3
    -- install libexec dir: ./libexec/bcl2fastq-1.8.3
    -- install include dir: include/bcl2fastq-1.8.3
    -- install    data dir: share/bcl2fastq-1.8.3
    -- install     doc dir: doc/bcl2fastq-1.8.3
    -- install     man dir: man
    -- Verifying target directories access
    -- Creating external tools in subdirectory opt
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:461 ] Boost not in cache
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:464 ] _boost_TEST_VERSIONS = 1.46.0;1.46;1.45.0;1.45;1.44.0;1.44
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:466 ] Boost_USE_MULTITHREADED = TRUE
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:468 ] Boost_USE_STATIC_LIBS = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:470 ] Boost_USE_STATIC_RUNTIME = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:472 ] Boost_ADDITIONAL_VERSIONS = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:474 ] Boost_NO_SYSTEM_PATHS = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:537 ] Declared as CMake or Environmental Variables:
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:539 ]   BOOST_ROOT = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:541 ]   BOOST_INCLUDEDIR = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:543 ]   BOOST_LIBRARYDIR = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:545 ] _boost_TEST_VERSIONS = 1.46.0;1.46;1.45.0;1.45;1.44.0;1.44
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:598 ] Include debugging info:
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:600 ]   _boost_INCLUDE_SEARCH_DIRS = C:/boost/include;C:/boost;/boost/include;/boost;/sw/local/include
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:602 ]   _boost_PATH_SUFFIXES = boost-1_46_0;boost_1_46_0;boost-1_46;boost_1_46;boost-1_45_0;boost_1_45_0;boost-1_45;boost_1_45;boost-1_44_0;boost_1_44_0;boost-1_44;boost_1_44
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:737 ] guessed _boost_COMPILER = -gcc
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:747 ] _boost_MULTITHREADED = -mt
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:790 ] _boost_RELEASE_ABI_TAG = -
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:792 ] _boost_DEBUG_ABI_TAG = -d
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:835 ] _boost_LIBRARY_SEARCH_DIRS = Boost_INCLUDE_DIR-NOTFOUND/lib;Boost_INCLUDE_DIR-NOTFOUND/../lib;Boost_INCLUDE_DIR-NOTFOUND/stage/lib;C:/boost/lib;C:/boost;/boost/boost___/lib;/boost/boost__/lib;/boost/lib;/boost;/sw/local/lib
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for DATE_TIME_LIBRARY_RELEASE: boost_date_time-gcc-mt-;boost_date_time-gcc-mt;boost_date_time-mt-;boost_date_time-mt;boost_date_time
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for DATE_TIME_LIBRARY_DEBUG: boost_date_time-gcc-mt-d-;boost_date_time-gcc-mt-d;boost_date_time-mt-d-;boost_date_time-mt-d;boost_date_time-mt;boost_date_time
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for FILESYSTEM_LIBRARY_RELEASE: boost_filesystem-gcc-mt-;boost_filesystem-gcc-mt;boost_filesystem-mt-;boost_filesystem-mt;boost_filesystem
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for FILESYSTEM_LIBRARY_DEBUG: boost_filesystem-gcc-mt-d-;boost_filesystem-gcc-mt-d;boost_filesystem-mt-d-;boost_filesystem-mt-d;boost_filesystem-mt;boost_filesystem
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for IOSTREAMS_LIBRARY_RELEASE: boost_iostreams-gcc-mt-;boost_iostreams-gcc-mt;boost_iostreams-mt-;boost_iostreams-mt;boost_iostreams
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for IOSTREAMS_LIBRARY_DEBUG: boost_iostreams-gcc-mt-d-;boost_iostreams-gcc-mt-d;boost_iostreams-mt-d-;boost_iostreams-mt-d;boost_iostreams-mt;boost_iostreams
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for PROGRAM_OPTIONS_LIBRARY_RELEASE: boost_program_options-gcc-mt-;boost_program_options-gcc-mt;boost_program_options-mt-;boost_program_options-mt;boost_program_options
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for PROGRAM_OPTIONS_LIBRARY_DEBUG: boost_program_options-gcc-mt-d-;boost_program_options-gcc-mt-d;boost_program_options-mt-d-;boost_program_options-mt-d;boost_program_options-mt;boost_program_options
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for REGEX_LIBRARY_RELEASE: boost_regex-gcc-mt-;boost_regex-gcc-mt;boost_regex-mt-;boost_regex-mt;boost_regex
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for REGEX_LIBRARY_DEBUG: boost_regex-gcc-mt-d-;boost_regex-gcc-mt-d;boost_regex-mt-d-;boost_regex-mt-d;boost_regex-mt;boost_regex
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for SERIALIZATION_LIBRARY_RELEASE: boost_serialization-gcc-mt-;boost_serialization-gcc-mt;boost_serialization-mt-;boost_serialization-mt;boost_serialization
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for SERIALIZATION_LIBRARY_DEBUG: boost_serialization-gcc-mt-d-;boost_serialization-gcc-mt-d;boost_serialization-mt-d-;boost_serialization-mt-d;boost_serialization-mt;boost_serialization
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for SYSTEM_LIBRARY_RELEASE: boost_system-gcc-mt-;boost_system-gcc-mt;boost_system-mt-;boost_system-mt;boost_system
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for SYSTEM_LIBRARY_DEBUG: boost_system-gcc-mt-d-;boost_system-gcc-mt-d;boost_system-mt-d-;boost_system-mt-d;boost_system-mt;boost_system
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for THREAD_LIBRARY_RELEASE: boost_thread-gcc-mt-;boost_thread-gcc-mt;boost_thread-mt-;boost_thread-mt;boost_thread
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for THREAD_LIBRARY_DEBUG: boost_thread-gcc-mt-d-;boost_thread-gcc-mt-d;boost_thread-mt-d-;boost_thread-mt-d;boost_thread-mt;boost_thread
    -- Could NOT find Boost
    Unable to find the Boost header files. Please set BOOST_ROOT to the root directory containing Boost or BOOST_INCLUDEDIR to the directory containing Boost's headers.
    -- Boost 1.44.0 not found. Boost will be built from the distribution...
    Decompressing /tmp/bcl2fastq-1.8.3/src/../redist/boost_1_44_0.tar.gz
    Building Boost.Jam with toolset gcc... tools/jam/src/bin.linuxx86_64/bjam
    Unicode/ICU support for Boost.Regex?... not found.
    Backing up existing Boost.Build configuration in project-config.jam.5
    Generating Boost.Build configuration in project-config.jam...
    
    Bootstrapping is done. To build, run:
    
        ./bjam
        
    To adjust configuration, edit 'project-config.jam'.
    Further information:
    
       - Command line help:
         ./bjam --help
         
       - Getting started guide: 
         http://www.boost.org/more/getting_started/unix-variants.html
         
       - Boost.Build documentation:
         http://www.boost.org/boost-build2/doc/html/index.html
    
    Performing configuration checks
    
        - has_icu builds           : no
    
    Component configuration:
    
        - date_time                : building
        - filesystem               : building
        - graph                    : not building
        - graph_parallel           : not building
        - iostreams                : building
        - math                     : not building
        - mpi                      : not building
        - program_options          : building
        - python                   : not building
        - random                   : not building
        - regex                    : building
        - serialization            : building
        - signals                  : not building
        - system                   : building
        - test                     : not building
        - thread                   : building
        - wave                     : not building
    
    ...patience...
    ...patience...
    ...found 17154 targets...
    boost-1_44_0 installed successfully
    -- Successfuly built boost 1.44.0 from the distribution package...
    -- Check if the system is big endian
    -- Searching 16 bit integer
    -- Looking for sys/types.h
    -- Looking for sys/types.h - found
    -- Looking for stdint.h
    -- Looking for stdint.h - found
    -- Looking for stddef.h
    -- Looking for stddef.h - found
    -- Check size of unsigned short
    -- Check size of unsigned short - done
    -- Using unsigned short
    -- Check if the system is big endian - little endian
    -- Looking for floorf
    -- Looking for floorf - found
    -- Looking for round
    -- Looking for round - found
    -- Looking for roundf
    -- Looking for roundf - found
    -- Looking for powf
    -- Looking for powf - found
    -- Looking for erf
    -- Looking for erf - found
    -- Looking for erf
    -- Looking for erf - found
    -- Looking for erfc
    -- Looking for erfc - found
    -- Looking for erfc
    -- Looking for erfc - found
    -- Found ZLIB  header: /usr/include/zlib.h
    -- Found ZLIB library: /usr/lib/libz.so
    -- gzip compression supported
    CMake Error at cmake/cxxConfigure.cmake:84 (message):
      No support for bzip2 compression
    Call Stack (most recent call first):
      c++/CMakeLists.txt:33 (include)
    
    
    -- Configuring incomplete, errors occurred!
    Couldn't configure the project:
    
    /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake -H"/tmp/bcl2fastq-1.8.3/src" -B"/tmp/bcl2fastq-1.8.3-build" -G"Unix Makefiles"  -DCASAVA_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DBoost_DEBUG:BOOL=ON
    
    Moving CMakeCache.txt to CMakeCache.txt.removed

  • #2
    ln -s /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/libbz2.so

    However I wasn't able to compile BclToFastq on Ubuntu 12.10 because of an incompatibility between the gcc version 4.7.2 and the lib boost supplied in BclToFastq.

    I got around this by running alien on the BclToFastq supplied rpm and installing the new deb using dpkg - only as a one off hack though, I've got a CentOS cluster here now where it's properly compiled/installed.

    Comment


    • #3
      worked

      Thank you frozenlyse!

      "ln -s /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/libbz2.so" solved this problem!

      However, some more errors appeared after this. After installing some Perl Modules and "xsltproc" package, I finally made Bcl2Fastq 1.8.3 work on Ubuntu 12.04

      I think I should also have CentOS installed on one of our servers in the future
      Last edited by slees; 01-29-2013, 07:40 PM.

      Comment


      • #4
        The system is centOS 6.4

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Current Approaches to Protein Sequencing
          by seqadmin


          Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
          04-04-2024, 04:25 PM
        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 04-11-2024, 12:08 PM
        0 responses
        25 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        28 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        24 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        52 views
        0 likes
        Last Post seqadmin  
        Working...
        X