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Comment: Migrated to Confluence 5.3

When running the capacitor with BAM input files, I get the following error:

Code Block
[ERROR] Exception creating BAM index for record IPMHD:09324:09018 78b aligned read.
net.sf.samtools.SAMException: Exception creating BAM index for record IPMHD:09324:09018 78b aligned read.
        at net.sf.samtools.BAMIndexer.processAlignment(BAMIndexer.java:94)
        at barna.io.sam.SAMReader.createIndex(SAMReader.java:190)
        at barna.io.sam.SAMReader.isApplicable(SAMReader.java:143)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.fileInit(FluxCapacitor.java:2744)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1795)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
        at barna.commons.launcher.Flux.main(Flux.java:198)
Caused by: net.sf.samtools.SAMException: Unexpected reference 4 when constructing index for 18 for record IPMHD:09324:09018 78b aligned read.
        at net.sf.samtools.BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:198)
        at net.sf.samtools.BAMIndexer.processAlignment(BAMIndexer.java:92)
        ... 6 more

What is going wrong?