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  • problem installing Pindel

    I have been trying to install pindel 0.2.4t on my Mac OS X 7.5 and I get an error message.

    bash-3.2$ less INSTALL
    bash-3.2$ ./INSTALL /Users/davidkowbel/samtools-0.1.19/
    path is now: /Users/davidkowbel/samtools-0.1.19/
    make -C src pindel
    parameter.cpp:26:10: fatal error: 'omp.h' file not found
    #include <omp.h>
    ^
    1 error generated.
    pindel.cpp:28:10: fatal error: 'omp.h' file not found
    #include <omp.h>
    ^
    1 error generated.
    parameter.cpp:26:10: fatal error: 'omp.h' file not found
    #include <omp.h>
    ^
    1 error generated.
    pindel.cpp:28:10: fatal error: 'omp.h' file not found
    #include <omp.h>
    ^
    1 error generated.
    c++ -Wall -g -c -O3 -fopenmp -I/Users/davidkowbel/samtools-0.1.19/ pindel.cpp -o pindel.o
    clang: warning: argument unused during compilation: '-fopenmp'
    pindel.cpp:28:10: fatal error: 'omp.h' file not found
    #include <omp.h>
    ^
    1 error generated.
    make[1]: *** [pindel.o] Error 1
    make: *** [pindel] Error 2

    Creating pindel2vcf utility...
    pindel2vcf created.

    Creating sam2pindel utility...
    sam2pindel created.
    mv: rename src/pindel to ./pindel: No such file or directory

    Pindel successfully compiled. The pindel executable can be found in this directory.
    I have installed Xcode 4.6 . I don't know why the header file omp.h cannot be found?

  • #2
    your compiler does not have library set up correctly.

    try gcc compiler



    I had the same issue when I upgraded my xcode. installing gcc compiler solves this.

    Comment


    • #3
      update from the experts in my institute

      "Yep. I'd probably use that, someone on biostars suggests using the homebrew version. The issue is indeed that LLVM/clang does not currently support OpenMP and so you need to fall back to GCC"

      "GCC is now maintained in homebrew-versions, with major version
      number in formula name as suffix. Please tap using:
      $ brew search gcc
      brew tap homebrew/versions

      and then install GCC based on its version, e.g., 'brew install gcc47'."

      Comment


      • #4
        After use samtools sam2pindel then I execute Pindel. Here is what I get ....

        $ pindel -f [PATH]/human_g1k_v37.fasta -p [PATH]/pindel/input_pindel.txt -c 17:41,194,312-41,279,500 -o [PATH]/pindel/EI17_Pindel
        Pindel version 0.2.4t, August 13 2012.
        Processing chromosome: 1
        Skipping chromosome: 1
        Processing chromosome: 2
        Skipping chromosome: 2
        Processing chromosome: 3
        Skipping chromosome: 3
        Processing chromosome: 4
        Skipping chromosome: 4
        Processing chromosome: 5
        Skipping chromosome: 5
        Processing chromosome: 6
        Skipping chromosome: 6
        Processing chromosome: 7
        Skipping chromosome: 7
        Processing chromosome: 8
        Skipping chromosome: 8
        Processing chromosome: 9
        Skipping chromosome: 9
        Processing chromosome: 10
        Skipping chromosome: 10
        Processing chromosome: 11
        Skipping chromosome: 11
        Processing chromosome: 12
        Skipping chromosome: 12
        Processing chromosome: 13
        Skipping chromosome: 13
        Processing chromosome: 14
        Skipping chromosome: 14
        Processing chromosome: 15
        Skipping chromosome: 15
        Processing chromosome: 16
        Skipping chromosome: 16
        Processing chromosome: 17
        Chromosome Size: 81195210
        NumBoxes: 60004 BoxSize: 3373

        Looking at chromosome 17 bases 41194312 to 41279500.
        getReads 17 101195210
        Scanning and processing reads anchored in 17
        last one: 0 and UPCLOSE= 0

        The last read Pindel scanned:
        @PC-LABO-NGS-MIS_25:1:1103:23265:10796
        TAAGGGTGGGTAGGTTTGTTGGTATCCTAGTGGGTGAGGGGTGGCTTTGGAGTTGCAGTTGATGTGTGATAGTTGAGGGTTGATTGCTGTACTTGCTTGTAAGCATGGGGGGGGGGGGTTTTGATGGGGTTTGGGTTTTTATGT
        + chrM 16129 254 220 patient

        Number of reads in current window: 0, + 0 - 0
        Number of reads where the close end could be mapped: 0, + 0 - 0
        Percentage of reads which could be mapped: + 0.00% - 0.00%

        No reads found in [PATH]/input_pindelbis.txt
        There are no reads for this bin.
        Loading genome sequences and reads: 0 seconds.
        Mining, Sorting and output results: 0 seconds.
        Do you have any idea?

        Thank you in advance for your help

        Comment


        • #5
          your reference genome has no "chr" while I saw chrM in your file. please notice that chr1 != 1

          Comment


          • #6
            Originally posted by KaiYe View Post
            your compiler does not have library set up correctly.

            try gcc compiler



            I had the same issue when I upgraded my xcode. installing gcc compiler solves this.
            Thanks. That did the job!

            Comment


            • #7
              Did you guys modify the makefile in any way? i did a brew install of gcc48, and have now modified the makefile in src with $(CXX)=g++-4.8 but still the same error
              Last edited by Jeromek; 08-28-2014, 03:28 AM.

              Comment


              • #8
                Hi,

                I'm trying to run the demo files in pindel
                /home/nina/linux/tools/pindel-m/pindel -f simulated_reference.fa -i simulated_config.txt -o output

                but it gave me error message:
                /home/nina/linux/tools/pindel-m/pindel: error while loading shared libraries: libhts.so.1: cannot open shared object file: No such file or directory

                Is there a way to install the missing library?

                I've tried
                sudo make install libhts.so.1

                It shows
                mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/lib/pkgconfig
                install -p -m 644 libhts.so /usr/local/lib/libhts.so.1.2.1
                ln -sf libhts.so.1.2.1 /usr/local/lib/libhts.so
                ln -sf libhts.so.1.2.1 /usr/local/lib/libhts.so.1
                sed -e 's#@includedir@#/usr/local/include#g;s#@libdir@#/usr/local/lib#g;s#@PACKAGE_VERSION@#1.2.1#g' htslib.pc.in > /usr/local/lib/pkgconfig/htslib.pc
                chmod 644 /usr/local/lib/pkgconfig/htslib.pc
                install -p bgzip htsfile tabix /usr/local/bin
                install -p -m 644 htslib/*.h /usr/local/include/htslib
                install -p -m 644 libhts.a /usr/local/lib/libhts.a
                install -p -m 644 htsfile.1 tabix.1 /usr/local/share/man/man1
                install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/man5
                make: Nothing to be done for `libhts.so.1'.

                Thx!!

                Comment


                • #9
                  @wyll: See the last line here https://github.com/genome/pindel/blo...README_INSTALL

                  Comment


                  • #10
                    I've actually read that line over and over again for some time, but still wasn't able to understand it. Now that I go back and read again, I think I know how to type the command now. You have to add the rest of the command after ./pindel silly me...
                    @GenoMax: Thanks a bunch =D

                    Comment

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