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  • difficult executing bwa-mem

    Hello all,
    I am trying to run bwa mem. I have downloaded the program and exectued the 'make' command. However, when I try to run the bwa mem command, I get the message: [main] unrecognized command 'mem'

    Any help you can provide on what further steps I need to take in order to be able to execute this command would be greatly appreciated.

    Thanks!

  • #2
    please show us what you got after running 'make'

    Comment


    • #3
      Also post an example of the command line you are using to run bwa.

      Comment


      • #4
        Please use the latest version.

        Comment


        • #5
          Originally posted by harryzs View Post
          please show us what you got after running 'make'
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
          ar -csru libbwa.a utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o malloc_wrap.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o
          bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
          bwt_gen.c:878:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
          bwt_gen.c: In function ‘BWTIncMergeBwt’:
          bwt_gen.c:952:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o
          gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o
          gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS 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

          Comment


          • #6
            Example of command line

            Originally posted by GenoMax View Post
            Also post an example of the command line you are using to run bwa.
            bwa mem Erysipelothrix_genome.fasta MX1-H_uniq1.fastq MX1-H_uniq2.fastq > MX1-H.sam

            Comment


            • #7
              BWA version

              Originally posted by lh3 View Post
              Please use the latest version.
              I'm using version 0.7.5a
              Thanks for your help!

              Comment


              • #8
                If I Just run
                ${path_to_bwa}/bwa

                I get following message :
                ----------------------------------
                Program: bwa (alignment via Burrows-Wheeler transformation)
                Version: 0.7.5a-r405
                Contact: Heng Li <[email protected]>

                Usage: bwa <command> [options]

                Command:
                index index sequences in the FASTA format
                mem BWA-MEM algorithm
                fastmap identify super-maximal exact matches
                pemerge merge overlapping paired ends (EXPERIMENTAL)
                aln gapped/ungapped alignment
                samse generate alignment (single ended)
                sampe generate alignment (paired ended)
                bwasw BWA-SW for long queries

                fa2pac convert FASTA to PAC format
                pac2bwt generate BWT from PAC
                pac2bwtgen alternative algorithm for generating BWT
                bwtupdate update .bwt to the new format
                bwt2sa generate SA from BWT and Occ
                .....
                ----------------------------------

                How about you??

                Comment


                • #9
                  Originally posted by harryzs View Post
                  If I Just run
                  ${path_to_bwa}/bwa

                  I get following message :
                  ----------------------------------
                  Program: bwa (alignment via Burrows-Wheeler transformation)
                  Version: 0.7.5a-r405
                  Contact: Heng Li <[email protected]>

                  Usage: bwa <command> [options]

                  Command:
                  index index sequences in the FASTA format
                  mem BWA-MEM algorithm
                  fastmap identify super-maximal exact matches
                  pemerge merge overlapping paired ends (EXPERIMENTAL)
                  aln gapped/ungapped alignment
                  samse generate alignment (single ended)
                  sampe generate alignment (paired ended)
                  bwasw BWA-SW for long queries

                  fa2pac convert FASTA to PAC format
                  pac2bwt generate BWT from PAC
                  pac2bwtgen alternative algorithm for generating BWT
                  bwtupdate update .bwt to the new format
                  bwt2sa generate SA from BWT and Occ
                  .....
                  ----------------------------------

                  How about you??
                  This is what I am seeing:
                  Program: bwa (alignment via Burrows-Wheeler transformation)
                  Version: 0.6.1-r104
                  Contact: Heng Li <[email protected]>

                  Usage: bwa <command> [options]

                  Command: index index sequences in the FASTA format
                  aln gapped/ungapped alignment
                  samse generate alignment (single ended)
                  sampe generate alignment (paired ended)
                  bwasw BWA-SW for long queries
                  fastmap identify super-maximal exact matches

                  fa2pac convert FASTA to PAC format
                  pac2bwt generate BWT from PAC
                  pac2bwtgen alternative algorithm for generating BWT
                  bwtupdate update .bwt to the new format
                  bwt2sa generate SA from BWT and Occ
                  pac2cspac convert PAC to color-space PAC
                  stdsw standard SW/NW alignment

                  As you can see, mem does not appear to be in the list. I have already made all of the files in this directory executable. There are 5 bwamem files in this directory, which seems to be what other people have there as well.

                  Comment


                  • #10
                    Your version is
                    Version: 0.6.1-r104
                    May want to redownload the latest from sourceforge?

                    BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read…


                    If you are feeling trusty, you can quickly pop this into your linux terminal

                    Code:
                    wget http://sourceforge.net/projects/bio-bwa/files/latest/download?source=files
                    And if multiple versions of bwa could be at play, type

                    Code:
                    which bwa
                    And see which version is being invoked when you type

                    Code:
                    bwa
                    Last edited by winsettz; 10-04-2013, 05:54 AM.

                    Comment


                    • #11
                      Originally posted by tforde View Post
                      I'm using version 0.7.5a
                      Thanks for your help!
                      It is possible that you have multiple versions of bwa installed on your machine (unless you are the "administrator" and know that there is only one version). In that case you are not using the newest version based on your other posts.

                      Comment


                      • #12
                        Just do what I did

                        run: ${path_to_bwa}/bwa

                        path_to_bwa = where you exectued the 'make' command

                        Comment


                        • #13
                          Originally posted by winsettz View Post
                          Your version is

                          May want to redownload the latest from sourceforge?

                          BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read…


                          If you are feeling trusty, you can quickly pop this into your linux terminal

                          Code:
                          wget http://sourceforge.net/projects/bio-bwa/files/latest/download?source=files
                          And if multiple versions of bwa could be at play, type

                          Code:
                          which bwa
                          And see which version is being invoked when you type

                          Code:
                          bwa
                          It was indeed an issue with multiple versions downloaded; had to get some help here to redirect the path, but now appears to be working. Thanks very much for your help!

                          Comment

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