Hello! I've been running ProteinProphet as part of the Philosopher pipeline for a while now with no problems. However, one of my datasets seems to be getting stuck in the middle of this function. It doesn't throw an error or anything - just stops advancing (the last line of the output is "Computing degenerate peptides for 69919 proteins: 0%...10%...20%...30%...40%...50%"). Has anyone run into this problem before?
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