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  • Jurek
    Junior Member
    • May 2010
    • 2
    #1

    BWA installation failure

    Hello World,

    I downloaded the bwa version 5.7 and cannot compile it.

    [Jurek@fg-pc22 bwa-0.5.7]$ make
    make[1]: Entering directory `/home/Jurek/Desktop/bwa2/bwa-0.5.7'
    make[1]: Nothing to be done for `lib'.
    make[1]: Leaving directory `/home/Jurek/Desktop/bwa2/bwa-0.5.7'
    make[1]: Entering directory `/home/Jurek/Desktop/bwa2/bwa-0.5.7/bwt_gen'
    gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
    bwt_gen.c:1: sorry, unimplemented: 64-bit mode not compiled in
    make[1]: *** [bwt_gen.o] Error 1
    make[1]: Leaving directory `/home/Jurek/Desktop/bwa2/bwa-0.5.7/bwt_gen'
    make: *** [lib-recur] Error 1

    What am I doing wrong (I appreciate it may be very simple)?
    Tags: None
  • lh3
    Senior Member
    • Feb 2008
    • 686
    #2
    Remove -m64 from the "CFLAGS" line in Makefile. Nonetheless, bwa works better on 64-bit machines.

    Comment

    • Jurek
      Junior Member
      • May 2010
      • 2
      #3
      It worked. Thank you!

      Comment

      • chrisW
        Junior Member
        • Jun 2010
        • 7
        #4
        similar install problems

        Greetings, I am novice as novice can be. I have a rudimentary knowledge of things UNIX, so understanding the error messages is currently difficult. I had a similar error wrt -m64. I removed that from the CFLAGS line and now have different errors. To whit:

        Error code 127, which follows immediately after 2 lines that start "gcc" and two lines that appear to be instructing some change to

        ar -cru libbwtgen.a bwt_gen.o QSufSort.o

        and then the following Stop messages:

        Stop in .../bwa-0.5.7/bwt_gen (line 18 of Makefile) Error code 1

        Stop in..../bwa-0.5.7 (line 33 of Makefile)

        Any help would be much appreciated!

        Comment

        • chrisW
          Junior Member
          • Jun 2010
          • 7
          #5
          similar install problems

          Greetings, I am novice as novice can be. I have a rudimentary knowledge of things UNIX, so understanding the error messages is currently difficult. I had a similar error wrt -m64. I removed that from the CFLAGS line and now have different errors. To whit:

          Error code 127, which follows immediately after 2 lines that start "gcc" and two lines that appear to be instructing some change to

          ar -cru libbwtgen.a bwt_gen.o QSufSort.o

          and then the following Stop messages:

          Stop in .../bwa-0.5.7/bwt_gen (line 18 of Makefile) Error code 1

          Stop in..../bwa-0.5.7 (line 33 of Makefile)

          Any help would be much appreciated!

          Comment

          • raela
            Member
            • Apr 2010
            • 39
            #6
            It would be more helpful if you could produce the full results of 'make'. You can use code tags to keep the paste to a reasonable size. Try [code]make results here.[/code]

            Comment

            • chrisW
              Junior Member
              • Jun 2010
              • 7
              #7
              I should note that I'm using a Windows 7 machine. I have downloaded the Subsystem for Unix-based apps and have been teaching myself the basic use of Korn Shell. When I type "make" into the ksh prompt the following appears:

              ar -cru libbwtgen.a bwt_gen.o QSufSort.o
              ar: Either the AR_LIBRARIAN environment variable must be set
              ar: or you must include the directory containing 'lib.exe' in PATH
              ***Error code 127

              Stop in /dev/fs/C/Users/my.name/Desktop/Mastigo-genomics/bwa-0.5.7/bwt_gen (line 18 of Makefile).
              ***Error Code 1

              Stop in /dev/fs/C/Users/my.name/Desktop/Mastigo-genomics/bwa-0.5.7 (line 33 of Makefile).

              Comment

              • drio
                Senior Member
                • Oct 2008
                • 323
                #8
                Originally posted by chrisW View Post
                I should note that I'm using a Windows 7 machine. I have downloaded the Subsystem for Unix-based apps and have been teaching myself the basic use of Korn Shell. When I type "make" into the ksh prompt the following appears:

                ar -cru libbwtgen.a bwt_gen.o QSufSort.o
                ar: Either the AR_LIBRARIAN environment variable must be set
                ar: or you must include the directory containing 'lib.exe' in PATH
                ***Error code 127

                Stop in /dev/fs/C/Users/my.name/Desktop/Mastigo-genomics/bwa-0.5.7/bwt_gen (line 18 of Makefile).
                ***Error Code 1

                Stop in /dev/fs/C/Users/my.name/Desktop/Mastigo-genomics/bwa-0.5.7 (line 33 of Makefile).
                Are you using cygwin?

                If not install it: http://www.cygwin.com/

                It will install the POSIX libraries and the environment to compile bwa and other open sources tools.
                -drd

                Comment

                • t59175
                  Junior Member
                  • Sep 2010
                  • 6
                  #9
                  not enough memory allocated

                  Hello,

                  I am using bwa-0.5.8c and I got an installation failure Error 1. After successful compilation without -m4 in the CFLAGS line, I got an error message saying not enough memory allocated when running it. I have 136G memory. I'd like to know how to allocate more memory. Thanks,

                  Comment

                  • t59175
                    Junior Member
                    • Sep 2010
                    • 6
                    #10
                    If the 32bit installation restricted memmory usage to about 3GB. Then Can onyone tell me how to install it on ia64 machine? Thanks.

                    Comment

                    • fenciso
                      Junior Member
                      • Apr 2011
                      • 5
                      #11
                      Hello,

                      I am new using bwa. I am trying to install bwa-0.5.9 but I can not compile it:

                      make[1]: Entering directory `/local/home/felix/cornell/bwa-0.5.9'
                      make[1]: Nothing to be done for `lib'.
                      make[1]: Leaving directory `/local/home/felix/cornell/bwa-0.5.9'
                      make[1]: Entering directory `/local/home/felix/cornell/bwa-0.5.9/bwt_gen'
                      make[1]: Nothing to be done for `lib'.
                      make[1]: Leaving directory `/local/home/felix/cornell/bwa-0.5.9/bwt_gen'
                      gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
                      utils.o: In function `err_xzopen_core':
                      /local/home/felix/cornell/bwa-0.5.9/utils.c:61: undefined reference to `egzopen'
                      /local/home/felix/cornell/bwa-0.5.9/utils.c:60: undefined reference to `egzdopen'
                      bntseq.o: In function `ks_getuntil':
                      /local/home/felix/cornell/bwa-0.5.9/bntseq.c:37: undefined reference to `egzread'
                      bntseq.o: In function `ks_getc':
                      /local/home/felix/cornell/bwa-0.5.9/bntseq.c:191: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bntseq.c:37: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bntseq.c:237: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bntseq.c:237: undefined reference to `egzread'
                      bntseq.o: In function `bwa_fa2pac':
                      /local/home/felix/cornell/bwa-0.5.9/bntseq.c:265: undefined reference to `egzclose'
                      bwtindex.o: In function `bwa_index':
                      /local/home/felix/cornell/bwa-0.5.9/bwtindex.c:84: undefined reference to `egzclose'
                      /local/home/felix/cornell/bwa-0.5.9/bwtindex.c:92: undefined reference to `egzclose'
                      simple_dp.o: In function `ks_getuntil':
                      /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:11: undefined reference to `egzread'
                      simple_dp.o: In function `ks_getc':
                      /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
                      simple_dp.o: In function `load_seqs':
                      /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:83: undefined reference to `egzclose'
                      simple_dp.o: In function `aln_seqs':
                      /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:126: undefined reference to `egzclose'
                      bwaseqio.o: In function `ks_getuntil':
                      /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:8: undefined reference to `egzread'
                      bwaseqio.o: In function `bwa_seq_close':
                      /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:49: undefined reference to `egzclose'
                      /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:47: undefined reference to `egzclose'
                      bwaseqio.o: In function `bwa_bam_open':
                      /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:28: undefined reference to `egzopen'
                      bwaseqio.o: In function `ks_getc':
                      /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:105: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:8: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:177: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:177: undefined reference to `egzread'
                      bwtsw2_aux.o: In function `ks_getuntil':
                      /local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:18: undefined reference to `egzread'
                      bwtsw2_aux.o:/local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:624: more undefined references to `egzread' follow
                      bwtsw2_aux.o: In function `bsw2_aln':
                      /local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:648: undefined reference to `egzclose'
                      bamlite.o: In function `bam_read1':
                      /local/home/felix/cornell/bwa-0.5.9/bamlite.c:131: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bamlite.c:135: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bamlite.c:151: undefined reference to `egzread'
                      bamlite.o: In function `bam_header_read':
                      /local/home/felix/cornell/bwa-0.5.9/bamlite.c:80: undefined reference to `egzread'
                      /local/home/felix/cornell/bwa-0.5.9/bamlite.c:87: undefined reference to `egzread'
                      bamlite.o:/local/home/felix/cornell/bwa-0.5.9/bamlite.c:90: more undefined references to `egzread' follow
                      collect2: ld returned 1 exit status
                      make: *** [bwa] Error 1

                      I do not what is the problem

                      Comment

                      • nilshomer
                        Nils Homer
                        • Nov 2008
                        • 1283
                        #12
                        The answer is found in this forum (try searching first):
                        EMBOSS and BFAST interference? - SEQanswers
                        http://seqanswers.com/forums/showthread.php?t=6155
                        Application of sequencing to RNA analysis (RNA-Seq, whole transcriptome, SAGE, expression analysis, novel organism mining, splice variants)

                        Comment

                        • l.miozzi
                          Junior Member
                          • Feb 2011
                          • 3
                          #13
                          Hi,
                          I have the same problem. When I type "make", I obtained this error:
                          /home/lauram/bin/bwa-0.5.9/bwtsw2_aux.c:635: undefined reference to `egzread'
                          bamlite.o: In function `bam_read1':
                          /home/lauram/bin/bwa-0.5.9/bamlite.c:131: undefined reference to `egzread'
                          bamlite.o:/home/lauram/bin/bwa-0.5.9/bamlite.c:135: more undefined references to `egzread' follow
                          collect2: ld returned 1 exit status
                          make: *** [bwa] Error 1


                          Does anyone can help, please?

                          Thanks!


                          Originally posted by fenciso View Post
                          Hello,

                          I am new using bwa. I am trying to install bwa-0.5.9 but I can not compile it:

                          make[1]: Entering directory `/local/home/felix/cornell/bwa-0.5.9'
                          make[1]: Nothing to be done for `lib'.
                          make[1]: Leaving directory `/local/home/felix/cornell/bwa-0.5.9'
                          make[1]: Entering directory `/local/home/felix/cornell/bwa-0.5.9/bwt_gen'
                          make[1]: Nothing to be done for `lib'.
                          make[1]: Leaving directory `/local/home/felix/cornell/bwa-0.5.9/bwt_gen'
                          gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
                          utils.o: In function `err_xzopen_core':
                          /local/home/felix/cornell/bwa-0.5.9/utils.c:61: undefined reference to `egzopen'
                          /local/home/felix/cornell/bwa-0.5.9/utils.c:60: undefined reference to `egzdopen'
                          bntseq.o: In function `ks_getuntil':
                          /local/home/felix/cornell/bwa-0.5.9/bntseq.c:37: undefined reference to `egzread'
                          bntseq.o: In function `ks_getc':
                          /local/home/felix/cornell/bwa-0.5.9/bntseq.c:191: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bntseq.c:37: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bntseq.c:237: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bntseq.c:237: undefined reference to `egzread'
                          bntseq.o: In function `bwa_fa2pac':
                          /local/home/felix/cornell/bwa-0.5.9/bntseq.c:265: undefined reference to `egzclose'
                          bwtindex.o: In function `bwa_index':
                          /local/home/felix/cornell/bwa-0.5.9/bwtindex.c:84: undefined reference to `egzclose'
                          /local/home/felix/cornell/bwa-0.5.9/bwtindex.c:92: undefined reference to `egzclose'
                          simple_dp.o: In function `ks_getuntil':
                          /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:11: undefined reference to `egzread'
                          simple_dp.o: In function `ks_getc':
                          /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
                          simple_dp.o: In function `load_seqs':
                          /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:83: undefined reference to `egzclose'
                          simple_dp.o: In function `aln_seqs':
                          /local/home/felix/cornell/bwa-0.5.9/simple_dp.c:126: undefined reference to `egzclose'
                          bwaseqio.o: In function `ks_getuntil':
                          /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:8: undefined reference to `egzread'
                          bwaseqio.o: In function `bwa_seq_close':
                          /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:49: undefined reference to `egzclose'
                          /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:47: undefined reference to `egzclose'
                          bwaseqio.o: In function `bwa_bam_open':
                          /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:28: undefined reference to `egzopen'
                          bwaseqio.o: In function `ks_getc':
                          /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:105: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:8: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:177: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:177: undefined reference to `egzread'
                          bwtsw2_aux.o: In function `ks_getuntil':
                          /local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:18: undefined reference to `egzread'
                          bwtsw2_aux.o:/local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:624: more undefined references to `egzread' follow
                          bwtsw2_aux.o: In function `bsw2_aln':
                          /local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:648: undefined reference to `egzclose'
                          bamlite.o: In function `bam_read1':
                          /local/home/felix/cornell/bwa-0.5.9/bamlite.c:131: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bamlite.c:135: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bamlite.c:151: undefined reference to `egzread'
                          bamlite.o: In function `bam_header_read':
                          /local/home/felix/cornell/bwa-0.5.9/bamlite.c:80: undefined reference to `egzread'
                          /local/home/felix/cornell/bwa-0.5.9/bamlite.c:87: undefined reference to `egzread'
                          bamlite.o:/local/home/felix/cornell/bwa-0.5.9/bamlite.c:90: more undefined references to `egzread' follow
                          collect2: ld returned 1 exit status
                          make: *** [bwa] Error 1

                          I do not what is the problem

                          Comment

                          • nilshomer
                            Nils Homer
                            • Nov 2008
                            • 1283
                            #14
                            Did you follow the link or attempt at all to search for it? You can imagine our frustration when the post above gives a link to the answer?

                            Comment

                            • l.miozzi
                              Junior Member
                              • Feb 2011
                              • 3
                              #15
                              I tried to follow the link but it didn't work, so I decided to post my problem.
                              Thanks to one of my colleagues I find out what was the problem...the ubuntu release in the server wasn't updated...so now everything is working.

                              Thanks

                              Laura

                              Comment

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