Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • BWA sampe fails - invalid BAM binary header (

    Hi,
    I am trying to use BWA for analysing human whole exome PE data (Illumina HiSeq) for the first time.
    I downloaded the hg19 genome as a reference as indexed it with bwa index.
    Then aligned with bwa aln with the following format of command (for eacg fastq file):

    nohup bwa aln ~/work_area/hg19_genome/hg19_chromFa.tar.gz SG1177_2_sequence.txt > SG1177_2_aln_sa.sai &

    from the ~10Gb fastq files I got ~1.3 Gb sai files.

    But when I am trying to use sampe to get the sam files, it doesn't work, and the output file contains the following comments:
    [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 63.
    then the list of chromosomes
    and end.

    Here is the sampe command I used:
    nohup bwa sampe ~/work_area/hg19_genome/hg19_chromFa.tar.gz SG1177_1_aln_sa.sai SG1177_2_aln_sa.sai SG1177_1_sequence.txt SG1177_2_sequence.txt &

    What did I do wrong?

    Many thanks in advance!

  • #2
    Hello,

    According to the bwa documentation, the reference should be a FASTA file.


    http://bio-bwa.sourceforge.net/bwa.shtml


    Your reference is hg19_chromFa.tar.gz -- this is a compressed archive likely containing many files.

    Sébastien Boisvert

    Originally posted by Lilach View Post
    Hi,
    I am trying to use BWA for analysing human whole exome PE data (Illumina HiSeq) for the first time.
    I downloaded the hg19 genome as a reference as indexed it with bwa index.
    Then aligned with bwa aln with the following format of command (for eacg fastq file):

    nohup bwa aln ~/work_area/hg19_genome/hg19_chromFa.tar.gz SG1177_2_sequence.txt > SG1177_2_aln_sa.sai &

    from the ~10Gb fastq files I got ~1.3 Gb sai files.

    But when I am trying to use sampe to get the sam files, it doesn't work, and the output file contains the following comments:
    [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 63.
    then the list of chromosomes
    and end.

    Here is the sampe command I used:
    nohup bwa sampe ~/work_area/hg19_genome/hg19_chromFa.tar.gz SG1177_1_aln_sa.sai SG1177_2_aln_sa.sai SG1177_1_sequence.txt SG1177_2_sequence.txt &

    What did I do wrong?

    Many thanks in advance!

    Comment


    • #3
      solution

      After solving the prolem, I am writing here the solution, in case somebody else will search for a solution for this proble:

      The problem was not in giving hg19_chromFa.tar.gz as a reference file. BWA knows to work with it.

      The reason for the problem was that I tried to run the bwa commands in the background (in nohup...&) or via a Putty SSH terminal (that crashed in the middle).
      This command should NOT be executed in the background, so the only way to run it in a far computer in by VPN. Then, run it without nohup ... &.

      Comment


      • #4
        Yeah, incompatibility with nohup has been reported on other threads on Seqanswers.

        Comment


        • #5
          The program screen is useful for that kind of workflow.

          You can start your things in a screen, close your window. After that, you can re-ssh to
          your box and reconnect to your screen. In one screen, you can have several tabs too.

          Sébastien

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Exploring the Dynamics of the Tumor Microenvironment
            by seqadmin




            The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
            07-08-2024, 03:19 PM
          • seqadmin
            Exploring Human Diversity Through Large-Scale Omics
            by seqadmin


            In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
            06-25-2024, 06:43 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 07-19-2024, 07:20 AM
          0 responses
          37 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-16-2024, 05:49 AM
          0 responses
          47 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-15-2024, 06:53 AM
          0 responses
          57 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-10-2024, 07:30 AM
          0 responses
          43 views
          0 likes
          Last Post seqadmin  
          Working...
          X