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  • bwa sampe error

    Hi
    I'm trying to generate SAM alignment file using BWA version 0.5.9-r16.
    I first aligned successfully paired-end reads to the reference using aln:
    bwa aln ref.fasta s_1.fq > s1.aln
    bwa aln ref.fasta s_2.fq > s2.aln

    Then I wanted to use sampe to generate sam file
    bws sampe ref.fasta s1.aln s2.aln s_1.fq s_2.fq > s.sam

    And i got the following
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    [bwa_read_seq] the maximum barcode length is 15.

    Any idea what I did wrong?
    Thanks
    Mali

  • #2
    Could it be running it in BAM mode (the "-b" option in "bwa aln").

    Comment


    • #3
      Thanks nil for your reply, but I haven't used the -b option, my input read files are fastq
      Any other idea?
      Mali

      Comment


      • #4
        Try emailing the bwa help mailling list or sending a PM to lh3 (the author of BWA).

        Nils (not a zero )

        Comment


        • #5
          I have the same problem. I would also like to know the solution. Thanks.

          Comment


          • #6
            I have the same problem too.

            Comment


            • #7
              My problem is caused by backstage running.
              It works by replacing '>' with '-f'.

              bwa aln ref.fasta s_1.fq -f s1.aln

              Comment


              • #8
                I think one easy way to come across this error is by using nohup that can inadvertently result in the console status messages being mixed into the sai output eg

                bwa aln ...parameters ... > output.sai

                works fine, but

                nohup bwa aln ...parameters ... > output.sai &

                can generate a completely messed up mix of index and status updates which will cause bwa sampe or samse etc to generate the corrupt header and barcode errors.

                Comment


                • #9
                  Plattsa described the source of my error exactly. I found this thread helpful to correct the problem.

                  Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


                  Lesson learned: always check for expected output before letting junk alignments run an entire day.

                  Comment


                  • #10
                    how to overcome nohup mess??

                    Originally posted by plattsa View Post
                    I think one easy way to come across this error is by using nohup that can inadvertently result in the console status messages being mixed into the sai output eg

                    bwa aln ...parameters ... > output.sai

                    works fine, but

                    nohup bwa aln ...parameters ... > output.sai &

                    can generate a completely messed up mix of index and status updates which will cause bwa sampe or samse etc to generate the corrupt header and barcode errors.

                    Hi plattsa,
                    If i cant stay next to the computer , how can i let the computer run as nohup do, but without its mess??
                    i found nohup problem only when using BWA aln algorithm...

                    thanks , papori.

                    Comment


                    • #11
                      Two ways around it

                      1. Check out Screen. I recommend this because it is easier to keep your jobs organized if you lots of jobs from different programs. I like to open separate 'screens' for each program, and name the screen accordingly. It is essentially like opening a new terminal that you can interactively open close.

                      Here's a short tutorial


                      (Take a look around the rest of this site too, some great beginner NGS tutorials!)

                      2. Put your bwa commands in a shell script. Then run
                      nohup <script.sh> &

                      This way, the output generated from nohup goes to nohup.out, and the command output is run from inside the script and does not get mixed in.

                      Comment


                      • #12
                        although this forum seems out-dated this info may help a poor newbie as it took me a day to solve the problem: as mentioned above if you run bwa aln in the bg you'll receive an error in the next step (bwa sampe) but the second thing you don't wanna forget is when running bwa sampe is the correct order of input files otherwise it won't work: bwa samp ref.fa in1.sai in2.sai in1.fq in2.fa > out.sam

                        Comment


                        • #13
                          Mali,

                          Using .sai instead of .aln may solve your problem.

                          Best regards,
                          Douglas

                          Comment


                          • #14
                            It does work!
                            Thx!

                            Originally posted by didlefu View Post
                            My problem is caused by backstage running.
                            It works by replacing '>' with '-f'.

                            bwa aln ref.fasta s_1.fq -f s1.aln

                            Comment


                            • #15
                              We are getting a similar error when using bams as input with the -b option during bwa aln step. bwa aln completes ok but bwa sampe fails with the error below. Is there a way around it?

                              [bam_header_read] invalid BAM binary header (this is not a BAM file).

                              Comment

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