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Align Error - no bwa in path

maramara Member Posts: 10
edited August 2012 in Ask the GATK team

I am trying to realign a .bam file to a new reference (ex: new.fasta), however when I run the task "Align", I am given the following error message:

no bwa in java.library.path

This same error message occurs with I try and use the task "AlignmentValidation". Do you know how I might fix this problem or another method to realign a bam file to a new reference?

Thank you.

Answers

  • CarneiroCarneiro Charlestown, MAMember Posts: 274 admin

    Do you have BWA installed? Install it if you don't, and point the java library path to it, so the program can find it.

    We recommend you use BWA on it's own if you're simply aligning a bam file. There is no need to use the GATK for that.

    If you're going to reprocess the BAM file from scratch, take a look at our Best Practices and the Data Processing Pipeline script.

  • yyshi1yyshi1 Posts: 1

    I have the same problem with using cluster. Although I loaded both modules as following:
    module load gatk-2.2-4
    module load bwa-0.6.2

    Any suggestion on running "-T AlignmentValidation" in cluster?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    Sorry, we don't provide support for problems with setting up cluster operations; you'll need to get it to work on your own. Good luck!

    Geraldine Van der Auwera, PhD

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