Hello all, I am a new GATK user. I'm having problems getting the PathSeq pipeline to run, either by using PathSeqPipelineSpark or by running each of the individual steps. There are no error messages generated, it just freezes mid run. I am using an HPC blade w/ plenty of memory, added a java options flag to up the max memory, I've tried running w/ smaller portions of my dataset and databases, and I've validated my .BAM files w/ picard ValidateSamFile. Running through each step, it seems to be getting stuck on PathSeqBwaSpark (step 2). I should also note that I did get PathSeqPipelineSpark to work with the tutorial data, and it seemed to function without issue. For reference, my GATK version is 18.104.22.168.
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