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bwa - unrecognized command 'aln'



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  • bwa - unrecognized command 'aln'


    I try to run bwa with se reads, but it seems that bew can't find the aln option.
    This is my bwa version:

    USER:~/software/bwa$ which bwa
    Program: bwa (alignment via Burrows-Wheeler transformation)
    Version: 0.7.6a-r433
    Contact: Heng Li <[email protected]sanger.ac.uk>
    Usage:   bwa <command> [options]
    Command: index         index sequences in the FASTA format
             mem           BWA-MEM algorithm
             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
    Note: To use BWA, you need to first index the genome with `bwa index'.
          There are three alignment algorithms in BWA: `mem', `bwasw', and
          `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
          first. Please `man ./bwa.1' for the manual.
    There doesn't seems to be any aln option any more.
    But in compiling bwa there was 'aln'

    USER:~/software/bwa-0.7.6a$ 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  kthread.c -o kthread.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 kthread.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
    The command I try to run is this one:
    bwa aln genome/bwa/Bsub168.fasta NG6444_1_S_1.fastq > bwa_head_aln.sai
    when I change aln to mem it runs perfectly, but as my reads are only 20bp long, I think I need the aln/samse option.

    any ideas?


  • #2
    From Heng Li in the "NEWS" file of the new bwa release:

    There are no changes to BWA-backtrack in this release. However, it has a few
    known issues yet to be fixed. If you prefer BWA-track, It is still advised to
    use bwa-0.6.x.

    While I developed BWA-MEM, I also found a few issues with BWA-SW. It is now
    possible to improve BWA-SW with the lessons learned from BWA-MEM. However, as
    BWA-MEM is usually better, I will not improve BWA-SW until I find applications
    where BWA-SW may excel.
    If you want to stay with the 0.7.x series then 0.7.5 should have "aln" available.
    Last edited by GenoMax; 02-12-2014, 02:19 AM.


    • #3
      It's not just you, it seems that that most recent version is missing aln (as well as samse and sampe). I don't see mention of this in either the NEWS file or the mailing list, but presumably this was done on purpose since the commands were removed from main.c (it looks like the source for them is there, you just can't get to them).

      @GenoMax: I guess I hadn't read that quote to mean that they were actually removed, though I guess that that must be the reason.


      • #4

        I guess I missed it.



        • #5
          The man page bwa.1 has been updated for v 0.7.6 and it still has an 'aln' command. The c-code appears to still be there so this appears to be an oversight. I'm reverting th 0.7.5a rather than rewrite my workflows.


          • #6
            Appears to be fixed now, see
            I'll wait for a new release rather pull this from the development site.


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