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  • BWA error

    I am trying to map solexa pair end reads using BWA.
    1. As the first step, I converted solexa fastq format into sanger fastq using maq.
    Code:
    maq-0.7.1/maq sol2sanger s_5_2_sequence.txt s_5_2_fastq.txt
    2. I build the indices for BWA for human genome
    Code:
    BWA/bwa-0.5.6/bwa index -a bwtsw -p hg18 hg18.fa
    3. Next step is to generate suffice array coordiantes for read1 as below:
    Code:
     BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18.fa s_5_1_fastq.txt > s_5_1.sai
    I am getting error as below.
    Code:
    [bwa_aln] 17bp reads: max_diff = 2
    [bwa_aln] 38bp reads: max_diff = 3
    [bwa_aln] 64bp reads: max_diff = 4
    [bwa_aln] 93bp reads: max_diff = 5
    [bwa_aln] 124bp reads: max_diff = 6
    [bwa_aln] 157bp reads: max_diff = 7
    [bwa_aln] 190bp reads: max_diff = 8
    [bwa_aln] 225bp reads: max_diff = 9
    [bwt_restore_bwt] fail to open file '/BWA/Genomes/hg18/hg18.fa.bwt'. Abort!
    Aborted
    I have all the fasta as well as built indices under the same directory as below:
    hg18.fa
    hg18.pac
    hg18.ann
    hg18.amb
    hg18.rpac
    hg18.bwt
    hg18.rbwt
    hg18.sa
    hg18.rsa

    Anything wrong with this or do I have to move hg18.fa out of this directory? Thanks.

  • #2
    If you used "hg18" as your prefix in your "bwa index" step, you should use the same prefix in your "bwa aln" step:
    Code:
     BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_1_fastq.txt > s_5_1.sai
    Ideally, you would not specify "-p" (unless of course you use both Illumina and ABI SOLiD data).

    Comment


    • #3
      Thanks and it works.

      Comment


      • #4
        For a pair end read, I tried as below:
        Code:
        BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_1_fastq.txt > s_5_1.sai
        BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_2_fastq.txt > s_5_2.sai
        
        BWA/bwa-0.5.6/bwa sampe BWA/Genomes/hg18/hg18 s_5_1.sai s_5_2.sai s_5_1_fastq.txt s_5_2_fastq.txt > out.sam
        I get the following error:
        Code:
        [bwa_read_seq] 0.0% bases are trimmed.
        [bwa_read_seq] 0.0% bases are trimmed.
        [bwa_sai2sam_pe_core] convert to sequence coordinate... 
         Segmentation fault
        How to resolve the issue? Thanks.
        Last edited by seq_GA; 05-24-2010, 09:26 PM.

        Comment


        • #5
          Originally posted by seq_GA View Post
          For a pair end read, I tried as below:
          Code:
          BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_1_fastq.txt > s_5_1.sai
          BWA/bwa-0.5.6/bwa aln /BWA/Genomes/hg18/hg18 s_5_2_fastq.txt > s_5_2.sai
          
          BWA/bwa-0.5.6/bwa sampe BWA/Genomes/hg18/hg18 s_5_1.sai s_5_2.sai s_5_1_fastq.txt s_5_2_fastq.txt > out.sam
          I get the following error:
          Code:
          [bwa_read_seq] 0.0% bases are trimmed.
          [bwa_read_seq] 0.0% bases are trimmed.
          [bwa_sai2sam_pe_core] convert to sequence coordinate...
          How to resolve the issue? Thanks.
          What's the error (the above is a status message)? Did it not finish?

          Comment


          • #6
            I was trying to edit my post.. You are too fast.. Anyway I get segmentation fault. Thanks.

            Comment


            • #7
              Originally posted by seq_GA View Post
              I was trying to edit my post.. You are too fast.. Anyway I get segmentation fault. Thanks.
              Sounds like a bug. Did you try sending an email to the BWA mailing list or author (lh3 is his handle on seqanswers)?

              Comment


              • #8
                I am not able to join the mailing list and post because of some error.
                I am trying to contenate all fasta of hg18 as hg18.fa and then build index. Anything wrong in that approach?

                Comment


                • #9
                  Originally posted by seq_GA View Post
                  I am not able to join the mailing list and post because of some error.
                  I am trying to contenate all fasta of hg18 as hg18.fa and then build index. Anything wrong in that approach?
                  You are using an old version of bwa. Please update to -svn or get the latest release.
                  -drd

                  Comment


                  • #10
                    Hi,
                    Thx for the response. I am using bwa-0.5.6 and I am upgrading to latest version available bwa-0.5.7. How to check out the version from svn? Can you please provide me the link? Thanks.

                    Comment


                    • #11
                      Originally posted by seq_GA View Post
                      Hi,
                      Thx for the response. I am using bwa-0.5.6 and I am upgrading to latest version available bwa-0.5.7. How to check out the version from svn? Can you please provide me the link? Thanks.
                      Here's the command. Make sure you have subversion installed:
                      Code:
                      svn co http://bio-bwa.svn.sourceforge.net/svnroot/bio-bwa bio-bwa

                      Comment


                      • #12
                        Thx for the info.

                        Comment


                        • #13
                          Originally posted by seq_GA View Post
                          Hi,
                          Thx for the response. I am using bwa-0.5.6 and I am upgrading to latest version available bwa-0.5.7. How to check out the version from svn? Can you please provide me the link? Thanks.
                          If you want to avoid svn (I'd suggest you don't), from here:



                          click in SF download page. That will take you to the latest release (already binary).

                          ALso, perhaps you can tell Heng how you got to the older version. I think there are some links there that still point to old versions.
                          -drd

                          Comment


                          • #14
                            Hi,
                            i get the same error even if I use the build from svn..

                            Comment


                            • #15
                              Run your binary via gdb:

                              Code:
                              $ gdb your_bwa_binary
                              .... gdb output ... 
                              > run sampe BWA/Genomes/hg18/hg18 s_5_1.sai s_5_2.sai s_5_1_fastq.txt s_5_2_fastq.txt > out.sam
                              .... gdb output ....
                              > bt
                              And show us the output.
                              -drd

                              Comment

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