Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 2
  • Filter
  • Time
  • Show
Clear All
new posts
Previous 1 2 template Next
  • 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

                              Previous 1 2 template Next

                              Latest Articles

                              Collapse
                              • SEQadmin2
                                From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
                                by SEQadmin2


                                Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

                                The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
                                ...
                                06-02-2026, 10:05 AM
                              • SEQadmin2
                                Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends
                                by SEQadmin2


                                With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.

                                Introduction

                                Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
                                05-22-2026, 06:42 AM
                              • SEQadmin2
                                Environmental Genomics in the Age of NGS: From Microbes to Conservation Strategies
                                by SEQadmin2

                                Studying ecosystems means dealing with complex, multi-species communities that are hard to observe at scale. This complexity, however, hides many important questions to be answered, from how biogeochemical cycles work and how climate change can affect species distribution to how conservation strategies can work best.

                                Genomics, particularly since the expansion of NGS, has transformed ecosystem ecology. By sequencing environmental DNA, we can now assess biodiversity without direct...
                                05-06-2026, 09:04 AM
                              View All

                              ad_right_rmr

                              Collapse

                              News

                              Collapse
                              Topics Statistics Last Post
                              Long-Read RNA Sequencing Uncovers a Hidden Layer of Immune Cell Regulation by SEQadmin2
                              Started by SEQadmin2, 06-02-2026, 12:03 PM
                              0 responses
                              19 views
                              0 reactions
                              		 Last Post SEQadmin2
                              by SEQadmin2
                              06-02-2026, 12:03 PM  
                              DNA Methylation Study Reveals How Epigenetic Changes Pass Between Generations by SEQadmin2
                              Started by SEQadmin2, 06-02-2026, 11:40 AM
                              0 responses
                              14 views
                              0 reactions
                              		 Last Post SEQadmin2
                              by SEQadmin2
                              06-02-2026, 11:40 AM  
                              MetaBeeAI Helps Scientists Process Research Literature Faster by SEQadmin2
                              Started by SEQadmin2, 05-28-2026, 11:40 AM
                              0 responses
                              29 views
                              0 reactions
                              		 Last Post SEQadmin2
                              by SEQadmin2
                              05-28-2026, 11:40 AM  
                              Scientists Solve a 25-Year Mystery in RNA Interference by SEQadmin2
                              Started by SEQadmin2, 05-26-2026, 10:12 AM
                              0 responses
                              31 views
                              0 reactions
                              		 Last Post SEQadmin2
                              by SEQadmin2
                              05-26-2026, 10:12 AM  
                              View All
                              Working...