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This crops up when running with "-mode INDEL". Not sure why there is no data. (See attached log file with stack trace.)
All input files are non-empty (except the .R file). A similar execution using "-mode SNP" completes with no problems. Since I'm simply looking to get the scripting and flags correct, I've used a public data set. Could it be that I'm unlucky and chose something that has no indels from the reference, which is causing the error? Could there be a more graceful method of termination?