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  • Burrows-Wheeler Alignment Tool Make Error

    Good morning,

    I am having trouble with 'making' bwa. Below I posted my code and my error messages. Any help would be much appreciated.

    My commands:
    #gets the newest version from sourceforge
    wget http://sourceforge.net/projects/bio-...r.bz2/download -O bwa.tar.bz2

    #unpacks the tarball
    tar -xjf bwa.tar.bz2
    cd bwa-0.7.3a

    #makes bwa
    make

    My errors:
    jmwhitha@Linux-OptiPlex-755:~/bwa-0.7.3a$ make
    gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
    gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
    gcc -c -g -Wall -O2 -DHAVE_PTHREAD ksw.c -o ksw.o
    In file included from ksw.c:28:0:
    /usr/lib/gcc/i686-linux-gnu/4.7/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"
    ksw.c:44:2: error: unknown type name ‘__m128i’
    ksw.c: In function ‘ksw_qinit’:
    ksw.c:67:11: error: ‘__m128i’ undeclared (first use in this function)
    ksw.c:67:11: note: each undeclared identifier is reported only once for each function it appears in
    ksw.c:67:19: error: expected expression before ‘)’ token
    ksw.c: In function ‘ksw_u8’:
    ksw.c:110:2: error: unknown type name ‘__m128i’
    ksw.c:126:2: warning: implicit declaration of function ‘_mm_set1_epi32’ [-Wimplicit-function-declaration]
    ksw.c:127:2: warning: implicit declaration of function ‘_mm_set1_epi8’ [-Wimplicit-function-declaration]
    ksw.c:133:3: warning: implicit declaration of function ‘_mm_store_si128’ [-Wimplicit-function-declaration]
    ksw.c:140:3: error: unknown type name ‘__m128i’
    ksw.c:141:3: warning: implicit declaration of function ‘_mm_load_si128’ [-Wimplicit-function-declaration]
    ksw.c:142:3: warning: implicit declaration of function ‘_mm_slli_si128’ [-Wimplicit-function-declaration]
    ksw.c:150:4: warning: implicit declaration of function ‘_mm_adds_epu8’ [-Wimplicit-function-declaration]
    ksw.c:151:4: warning: implicit declaration of function ‘_mm_subs_epu8’ [-Wimplicit-function-declaration]
    ksw.c:153:4: warning: implicit declaration of function ‘_mm_max_epu8’ [-Wimplicit-function-declaration]
    ksw.c:177:5: warning: implicit declaration of function ‘_mm_movemask_epi8’ [-Wimplicit-function-declaration]
    ksw.c:177:5: warning: implicit declaration of function ‘_mm_cmpeq_epi8’ [-Wimplicit-function-declaration]
    ksw.c:183:3: warning: implicit declaration of function ‘_mm_srli_si128’ [-Wimplicit-function-declaration]
    ksw.c:183:3: warning: implicit declaration of function ‘_mm_extract_epi16’ [-Wimplicit-function-declaration]
    ksw.c: In function ‘ksw_i16’:
    ksw.c:227:2: error: unknown type name ‘__m128i’
    ksw.c:243:2: warning: implicit declaration of function ‘_mm_set1_epi16’ [-Wimplicit-function-declaration]
    ksw.c:255:3: error: unknown type name ‘__m128i’
    ksw.c:259:4: warning: implicit declaration of function ‘_mm_adds_epi16’ [-Wimplicit-function-declaration]
    ksw.c:261:4: warning: implicit declaration of function ‘_mm_max_epi16’ [-Wimplicit-function-declaration]
    ksw.c:265:4: warning: implicit declaration of function ‘_mm_subs_epu16’ [-Wimplicit-function-declaration]
    ksw.c:281:5: warning: implicit declaration of function ‘_mm_cmpgt_epi16’ [-Wimplicit-function-declaration]
    make: *** [ksw.o] Error 1

    Thank you and God bless,
    Jason

  • #2
    The latest bwa requires SSE2. If you are working with an old machine, use 0.5.x.

    Comment


    • #3
      That's very helpful! Thank you! Can you tell me where I can get the right package? Does SSE2 have a different name on sourceforge? Does it come in one of these libraries?
      libraries:

      - libatlas-base-dev
      #- libatlas-dev
      - libblas-dev
      - liblapack-dev
      - libeigen3-dev
      - libc6-dev
      - libzip-dev
      - libbz2-dev
      - zlib1g-dev
      - libcurl4-openssl-dev
      - libgsl0-dev
      - libgsl0ldbl
      - gsl-bin
      - mime-support
      - libncurses5-dev
      - libpcre3-dev
      - libpng12-dev
      - libreadline-dev
      - libssl-dev
      - uuid
      - uuid-dev
      - libxml2
      - libxml2-dev
      - libxslt1-dev
      - libxslt1.1
      - xz-utils
      - liblzma-dev
      - zlib1g-dev

      Thank you again and God bless,
      Jason

      Comment


      • #4
        Run this:

        cat /proc/cpuinfo | grep flags

        Should get output like this ....
        flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt rdtscp lm 3dnowext 3dnow pni cx16 lahf_lm cmp_legacy svm extapic cr8_legacy
        flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt rdtscp lm 3dnowext 3dnow pni cx16 lahf_lm cmp_legacy svm extapic cr8_legacy
        [ ... more output removed ]

        Look for sse2.

        If you have it , good. Otherwise use an older version of bwa.

        gcc has the -msse2 flag; you might try it.

        Comment


        • #5
          Thank you! Yes, I see the sse2 in my second set of flags. I also apt-get the gcc, but still when I execute make, I get the same error. What do you suggest?

          Comment


          • #6
            This might work.

            Try the -msse2 flag.

            Append to CFLAGS line in "Makefile" ....
            like this ...

            CFLAGS= -g -Wall -O2 -msse2

            Comment


            • #7
              Originally posted by Richard Finney View Post
              This might work.

              Try the -msse2 flag.

              Append to CFLAGS line in "Makefile" ....
              like this ...

              CFLAGS= -g -Wall -O2 -msse2
              I'm in the same boat as OP, but this did not work unfortunately :/

              Comment


              • #8
                Some clown gave you either a bum gcc or butchered your include file system.
                SSE2's been around since 2001 and you DO have it.
                You could try downloading and making your own gcc but this is a hassle.

                If you have a sysadmin, talk with him. Ask them to update gcc. If you are the sysadmin on your own system, re-install an upgraded gcc.

                Comment


                • #9
                  SSE2 is present on all x86_64, but not all i686 has that. Given that you can find the sse2 flag from /proc/cpuinfo, your system must have that. 4.7 is pretty new. I use 4.2.1. I guess this gcc is compiled without the SSE2 support. If so, you should compile gcc from source.

                  Comment


                  • #10
                    A whole new set of warnings came up when I changed the make file.

                    jmwhitha@Linux-OptiPlex-755:~/bwa-0.7.3a$ make
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD ksw.c -o ksw.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwt.c -o bwt.o
                    bwt.c: In function ‘bwt_restore_bwt’:
                    bwt.c:408:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt.c:409:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt.c:410:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt.c: In function ‘bwt_restore_sa’:
                    bwt.c:382:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt.c:384:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt.c:385:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt.c:386:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt.c:393:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
                    bntseq.c: In function ‘bns_restore_core’:
                    bntseq.c:98:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
                    bntseq.c:106:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
                    bntseq.c:114:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
                    bntseq.c:123:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
                    bntseq.c:129:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwa.c -o bwa.o
                    bwa.c: In function ‘bwa_idx_load’:
                    bwa.c:261:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwamem.c -o bwamem.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o
                    bwamem_pair.c: In function ‘mem_pestat’:
                    bwamem_pair.c:59:2: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ [-Wformat]
                    bwamem_pair.c:59:2: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ [-Wformat]
                    bwamem_pair.c:59:2: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ [-Wformat]
                    bwamem_pair.c:59:2: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ [-Wformat]
                    ar -csru libbwa.a utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
                    bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
                    bwt_gen.c:873:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
                    bwt_gen.c: In function ‘BWTIncMergeBwt’:
                    bwt_gen.c:947:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
                    bwt_gen.c: In function ‘BWTIncConstructFromPacked’:
                    bwt_gen.c:1452:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt_gen.c:1468:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwt_gen.c:1483:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwase.c -o bwase.o
                    bwase.c: In function ‘bwa_sai2sam_se_core’:
                    bwase.c:516:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwase.c:530:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwase.c:535:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwase.c: In function ‘bwa_refine_gapped’:
                    bwase.c:309:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD is.c -o is.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
                    bwtindex.c: In function ‘bwt_pac2bwt’:
                    bwtindex.c:73:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwtindex.c: In function ‘bwa_seq_len’:
                    bwtindex.c:52:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwape.c -o bwape.o
                    bwape.c: In function ‘bwa_sai2sam_pe_core’:
                    bwape.c:642:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwape.c:645:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwape.c:653:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwape.c: In function ‘bwa_paired_sw’:
                    bwape.c:497:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwape.c: In function ‘bwa_cal_pac_pos_pe’:
                    bwape.c:278:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    bwape.c:282:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD kopen.c -o kopen.o
                    kopen.c: In function ‘kopen’:
                    kopen.c:265:8: warning: ignoring return value of ‘pipe’, declared with attribute warn_unused_result [-Wunused-result]
                    kopen.c: In function ‘http_open’:
                    kopen.c:93:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
                    kopen.c: In function ‘kftp_send_cmd’:
                    kopen.c:146:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD pemerge.c -o pemerge.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
                    bwtsw2_aux.c: In function ‘bsw2_aln’:
                    bwtsw2_aux.c:738:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD fastmap.c -o fastmap.o
                    fastmap.c: In function ‘main_fastmap’:
                    fastmap.c:164:3: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ [-Wformat]
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD main.c -o main.o
                    gcc -g -Wall -O2 -msse2 -DHAVE_PTHREAD QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread
                    gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD example.c -o example.o
                    gcc -g -Wall -O2 -msse2 -DHAVE_PTHREAD example.o -o bwamem-lite -L. -lbwa -lm -lz -lpthread

                    Comment


                    • #11
                      You're good. I think. Those are just warnings, not errors.

                      Comment


                      • #12
                        I have SSE2 according to cat /proc/cpuinfo | grep flags, but I do not have msse2. I have i686 and when I execute apt-get install gcc, it says I have the newest version of gcc. When you says, "from the source", are you saying that I wget from ubuntu? What is the command?

                        Comment


                        • #13
                          Seriously, you're probably good. Ignore the warnings.
                          What happens when you run bwa ? Just type "./bwa".

                          Making gcc from source is major hassle and you're gcc is up to date.

                          Comment


                          • #14
                            Thank you very much Richard! The compiling seems to have worked.

                            There seems to be a new problem now though with the SAM file only containing header lines and no alignment lines. I am posting a new topic for this.

                            Comment


                            • #15
                              Here it is:
                              Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

                              Comment

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