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  • #16
    Okay, so what can I do now? My gcc was already newest version.

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    • #17
      Originally posted by jmwhitha View Post
      Okay, so what can I do now? My gcc was already newest version.
      This kind of debugging may have to be done sitting in front of the computer. Do you have access to a local expert who can help?

      I am surprised that you have run into so many problems with this.

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      • #18
        I suspect the problem is in the read simulator, not bwa

        We have had the same problem, getting the same results with bwa when using simulated reads. I suspect the problem you are having is with your read simulator, not bwa. Something in your simulated fastq files is not in the format that bwa expects.

        Originally posted by jmwhitha View Post
        Good morning,

        I am trying to map simulated reads generated from GemSIM to an index generated from a multi-fasta of the CLJU (bacteria) coding sequence from NCBI. I used these two commands and discovered there were no alignment lines in the SAM file, only header lines. Commands head and tail only returned lines starting with @, and grep -vnm1 '^@' returned nothing.

        bwa-0.7.3a/bwa index -a is -p CLJU ./CLJUcoding.fasta

        bwa-0.7.3a/bwa mem CLJU CLJUsimreadsCodeTrial.single.fastq > CLJUsimreadsCodeTrial.single.sam

        Any suggestions?

        Thanks and God bless,
        Jason

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