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  • #46
    Originally posted by harlock0083 View Post
    -Chenyao

    Are you getting a segmentation fault? On your processed hits?
    Exactly, If I only used .bam file, that's what I get:
    -----------------------
    You are using Cufflinks v1.0.3, which is the most recent release.
    [08:53:42] Inspecting reads and determining fragment length distribution.
    > Processed 82462 loci. [*************************] 100%
    Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
    > Map Properties:
    > Total Map Mass: 902937.00
    > Read Type: 38bp single-end
    > Fragment Length Distribution: Truncated Gaussian (default)
    > Default Mean: 200
    > Default Std Dev: 80
    [08:54:12] Assembling transcripts and estimating abundances.
    > Processing Locus chr1:3040607-3040643 [ ] 0%Segmentation fault

    -------------------

    If I add the reference genome, that's what I get:
    --------------------------------------
    > Processed 25678 loci. [*************************] 100%
    Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
    > Map Properties:
    > Total Map Mass: 902937.00
    > Read Type: 0bp single-end
    > Fragment Length Distribution: Truncated Gaussian (default)
    > Default Mean: 200
    > Default Std Dev: 80
    [08:58:26] Estimating transcript abundances.
    > Processing Locus 18:3266353-3327517 [************************ ] 99%Segmentation fault

    Notably, the first one can get the right read,but still get fault in the last step

    Comment


    • #47
      Could you list your system specs, linux distribution, and steps you took to compile boost and samtools. Also use the "-v" option on your test run to see if you can see where the error occurs.

      Comment


      • #48
        Originally posted by harlock0083 View Post
        Could you list your system specs, linux distribution, and steps you took to compile boost and samtools. Also use the "-v" option on your test run to see if you can see where the error occurs.
        I have the problem when installing boost,which can not be detected, so I use "sudo get" as Tiger suggested, and it "configure" well, but I can not "make" successfully. I though maybe because of I wrongly pointed the path of boost. After I change the path, the cufflinks successfully make.

        I use "-v" option, the error is:
        Inspecting bundle 2:180323949-180330541 with 0 reads
        Inspecting bundle 2:180332494-180377413 with 0 reads
        Inspecting bundle 2:180392668-180444704 with 0 reads
        Inspecting bundle 2:180444821-180453438 with 0 reads
        Inspecting bundle 2:180459967-180476985 with 0 reads
        Inspecting bundle 2:180500918-180511605 with 0 reads
        Inspecting bundle 2:180553047-180559335 with 0 reads

        Map Properties:
        > Total Map Mass: 712614.00
        > Read Type: 0bp single-end
        > Fragment Length Distribution: Truncated Gaussian (default)
        > Default Mean: 200
        > Default Std Dev: 80
        0 ReadHits still live
        Found 177 reference contigs
        Total map density: 712614.000000
        [15:23:19] Estimating transcript abundances.
        Segmentation fault
        ----------------------
        Any thoughts?

        Comment


        • #49
          who can help me?

          Comment


          • #50
            Hi Chenyao,

            I ran cufflinks on a research dataset. The output is below:

            You are using Cufflinks v1.0.3, which is the most recent release.
            [11:59:07] Inspecting reads and determining fragment length distribution.
            > Processed 71057 loci. [*************************] 100%
            Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
            > Map Properties:
            > Total Map Mass: 2534201.50
            > Read Type: 75bp single-end
            > Fragment Length Distribution: Truncated Gaussian (default)
            > Default Mean: 200
            > Default Std Dev: 80
            [11:59:47] Assembling transcripts and estimating abundances.
            > Processed 71057 loci. [*************************] 100%

            Even though, the warning is still present, I didn't get segmentation fault.

            Comment


            • #51
              Could't make cufflinks

              Hello all!
              I am trying to install Cufflinks in a 64b ubuntu-linux machine and I am having lots of problems. I have install boost in usr/local as the guide in the cufflink web says but when I tried to make this is what I get:

              sandra@sandra-VirtualBox:~/cufflinks-0.9.3$ sudo make
              make all-recursive
              make[1]: se ingresa al directorio «/home/sandra/cufflinks-0.9.3»
              Making all in src
              make[2]: se ingresa al directorio «/home/sandra/cufflinks-0.9.3/src»
              g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/home/sandra/boost_1_48_0/include -I/usr/local/include -o cufflinks -L/home/sandra/boost_1_48_0/lib -L/usr/local/lib cufflinks.o libcufflinks.a libgc.a -lbam -lz
              cufflinks.o: In function `sleep<boost::date_time::subsecond_duration<boost:osix_time::time_duration, 1000l> >':
              /usr/include/boost/thread/pthread/thread_data.hpp:138: undefined reference to `boost::this_thread::sleep(boost:osix_time:time const&)'
              cufflinks.o: In function `thread_data_base':
              /usr/include/boost/thread/pthread/thread_data.hpp:67: undefined reference to `vtable for boost::detail::thread_data_base'
              cufflinks.o: In function `thread<void (*)(const RefSequenceTable&, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*), boost::reference_wrapper<const RefSequenceTable>, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*>':
              /usr/include/boost/thread/detail/thread.hpp:293: undefined reference to `boost::thread::start_thread()'
              cufflinks.o: In function `assemble_hits(BundleFactory&, BiasLearner*)':
              /home/sandra/cufflinks-0.9.3/src/cufflinks.cpp:953: undefined reference to `boost::thread::~thread()'
              cufflinks.o: In function `sleep<boost::date_time::subsecond_duration<boost:osix_time::time_duration, 1000l> >':
              /usr/include/boost/thread/pthread/thread_data.hpp:138: undefined reference to `boost::this_thread::sleep(boost:osix_time:time const&)'
              cufflinks.o: In function `assemble_hits(BundleFactory&, BiasLearner*)':
              /home/sandra/cufflinks-0.9.3/src/cufflinks.cpp:953: undefined reference to `boost::thread::~thread()'
              cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::reset(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*)':
              /usr/include/boost/thread/tss.hpp:105: undefined reference to `boost::detail::set_tss_data(void const*, boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)'
              cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              cufflinks.o: In function `at_thread_exit<void (*)()>':
              /usr/include/boost/thread/detail/thread.hpp:521: undefined reference to `boost::detail::add_thread_exit_function(boost::detail::thread_exit_function_base*)'
              cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              cufflinks.o: In function `~thread_data':
              /usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
              /usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
              cufflinks.o.rodata._ZTIN5boost6detail11thread_dataINS_3_bi6bind_tIvPFvRK16RefSequenceTableP9HitBundleP11BiasLearnereP8_IO_FILESC_SC_ENS2_5list7INS_17reference_wrapperIS5_EENS2_5valueIS8_EENSI_ISA_EENSI_IeEENSI_ISC_EESM_SM_EEEEEE[typeinfo for boost::detail::thread_data<boost::_bi::bind_t<void, void (*)(RefSequenceTable const&, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*), boost::_bi::list7<boost::reference_wrapper<RefSequenceTable const>, boost::_bi::value<HitBundle*>, boost::_bi::value<BiasLearner*>, boost::_bi::value<long double>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*> > > >]+0x10): undefined reference to `typeinfo for boost::detail::thread_data_base'
              libcufflinks.a(common.o): In function `~thread_specific_ptr':
              /usr/include/boost/thread/tss.hpp:79: undefined reference to `boost::detail::set_tss_data(void const*, boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)'
              libcufflinks.a(assemble.o): In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >:perator->() const':
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              libcufflinks.a(assemble.o): In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
              libcufflinks.a(assemble.o):/usr/include/boost/thread/tss.hpp:84: more undefined references to `boost::detail::get_tss_data(void const*)' follow
              collect2: ld devolvió el estado de salida 1
              make[2]: *** [cufflinks] Error 1
              make[2]: se sale del directorio «/home/sandra/cufflinks-0.9.3/src»
              make[1]: *** [all-recursive] Error 1
              make[1]: se sale del directorio «/home/sandra/cufflinks-0.9.3»
              make: *** [all] Error 2



              What is happening?
              Thanks for any help!
              Sandra

              Comment


              • #52
                Hey Sandra ,
                I am facing the same issue as you did. How did you install cufflinks after this error.? Although I am installing cufflinks 1.3.0.
                Any help is much appreciated.
                Thanks,
                Himanshu Sharma.

                Comment


                • #53
                  Hello all,
                  Is there anyone who knows the solution to this problem. Please help me .
                  Thanks.

                  Comment


                  • #54
                    Hello,
                    Finally I couldn't make it so I was working in galaxy instead. Hope anyone will reply this post, but if not, just take a look at the web: https://main.g2.bx.psu.edu/

                    Comment


                    • #55
                      There's a problem with the linker either not being able to find some/all of the boost library or the linking being done in an order wherein something is being linked before a dependency. Frankly, the easiest way to install cufflinks is to just download the binary.

                      Comment


                      • #56
                        Hi all,

                        I have installed successfully from source code, here is the step:
                        1. install boost (boost_1_47_0)
                        2. install samtools
                        3. install eigen
                        4. install cufflinks (cufflinks-2.1.1)
                        ./configure --with-boost=/path/to/lib/boost_1_47_0/ --prefix=/path/to/cufflinks-2.1.1/ --with-bam=/path/to/bam/ --with-eigen=/path/to/Eigen/ --with-boost-libdir=/path/to/lib/boost_1_47_0/include/ --with-boost-thread=/path/to/lib/boost_1_47_0/lib/libboost_thread.so

                        NOTE: /path/to/bam/ directory contain the following directories:
                        include/bam
                        include/Eigen #the subdirectory of eigen after uncompressed eigen package
                        lib/libbam.a

                        Explaination of the error message:
                        The thread package in the include//boost/thread directory cann't be compiled successfully by cufflinks, so we can use the compiled library when we install boost.
                        Last edited by pengchy; 04-17-2013, 05:34 PM. Reason: add version information

                        Comment


                        • #57
                          I have been working on trying to build cufflinks for the past few days and so far I keep getting stuck with the same error
                          checking for boostlib >= 1.47.0... configure: error: We could not detect the boost libraries (version 1.47 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.

                          I have installed
                          1. boost_1_53_0
                          2. samtools(samtools-0.1.19)
                          3. eigen (eigen-eigen-2249f9c22fe8)
                          4. install cufflinks (cufflinks-2.1.1)


                          for boost I did the following:
                          ./bootstrap.sh
                          ./b2
                          The Boost C++ Libraries were successfully built!
                          The following directory should be added to compiler include paths:
                          /home/mrmary/ngs/applications/boost_1_53_0
                          The following directory should be added to linker library paths:
                          /home/mrmary/ngs/applications/boost_1_53_0/stage/lib

                          I continued forward with this command.
                          ./bjam --prefix=/home/mrmary/ngs/applications/boost_1_53_0
                          --toolset=gcc link=static runtime-link=static stage install

                          then i went cd'ed into my cufflinks directory and entered the following
                          ./configure --prefix=/home/mrmary/ngs/applications/cufflinks-2.1.1 --with-boost=/home/mrmary/ngs/applications/boost_1_53_0 --with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so --with-bam=/usr/local/include/bam --with-eigen=/usr/local/include/Eigen

                          when that didn't work I modified the command a little and tried again

                          ./configure --prefix=/home/mrmary/ngs/applications/cufflinks-2.1.1 --with-boost=/home/mrmary/ngs/applications/boost_1_53_0/stage/lib --with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so --with-bam=/usr/local/include/bam --with-eigen=/usr/local/include/Eigen


                          any help would be god send at this point. Much thanks and regards

                          Dave

                          Comment


                          • #58
                            try specify:
                            --with-boost-libdir=/path/to/lib/boost_1_47_0/include/

                            Comment


                            • #59
                              Thanks Pengchy for answering I really appreciate it

                              This is what I tried again:

                              ./configure
                              --prefix=/home/mrmary/ngs/applications/cufflinks-2.1.1/
                              --with-boost-libdir=/home/mrmary/ngs/applications/boost_1_53_0/
                              --with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so
                              --with-bam=/usr/local/include/bam/
                              --with-eigen=/usr/local/include/Eigen/

                              Im a little confused when I ran the ./b2 command to build boost I got the following recommendations:

                              The following directory should be added to compiler include paths:
                              /home/mrmary/ngs/applications/boost_1_53_0
                              The following directory should be added to linker library paths:
                              /home/mrmary/ngs/applications/boost_1_53_0/stage/lib

                              Im not sure where I should add the include paths and what path --with-boost-libdir is asking for

                              Thanks anyone and everyone who reads this

                              Dave

                              Comment


                              • #60
                                Dave: Where exactly did you install boost libraries? Are they in "/usr/local" or in your home directory?

                                You may have already seen the instructions here: http://cufflinks.cbcb.umd.edu/tutorial.html#inst Depending on where you installed the boost libraries add that path using " --with-boost=/path/to/boost"

                                Here are a couple of threads for reference: http://seqanswers.com/forums/showthread.php?t=19805 and http://seqanswers.com/forums/showthread.php?t=14224

                                Comment

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