Error processing chr 'chr7': Failed to process variants for MN01972:49:000H5KYMY:1:11102:26356:2968

Question

[ManuelDB]

I got this error from time to time when running PISCES (Variante calling). Do you have any idea about the reason may be producing this?

 System.Exception: RACP2-6poolv4_P5-A_FINAL_SORTED.bam: Error processing chr 'chr7': Failed to process variants for MN01972:49:000H5KYMY:1:11102:26356:2968 ... 150S ---> System.Exception: Failed to process variants for MN01972:49:000H5KYMY:1:11102:26356:2968 ... 150S
   at Pisces.Domain.Logic.CandidateVariantFinder.ProcessCigarOps(Read alignment, String refChromosome, Int32 readStartPosition, String chromosomeName)
   at Pisces.Logic.SomaticVariantCaller.Execute()
   at Pisces.Processing.Logic.BaseGenomeProcessor.ProcessByBam(BamWorkRequest workRequest, String chrName)
   --- End of inner exception stack trace ---.
8/19/23 7:21 PM 1  Exception reported:
System.Exception: RACP2-6poolv4_P5-A_FINAL_SORTED.bam: Error processing chr 'chrX': Failed to process variants for MN01972:49:000H5KYMY:1:22101:7666:3361 ... 151S ---> System.Exception: Failed to process variants for MN01972:49:000H5KYMY:1:22101:7666:3361 ... 151S
   at Pisces.Domain.Logic.CandidateVariantFinder.ProcessCigarOps(Read alignment, String refChromosome, Int32 readStartPosition, String chromosomeName)
   at Pisces.Logic.SomaticVariantCaller.Execute()
   at Pisces.Processing.Logic.BaseGenomeProcessor.ProcessByBam(BamWorkRequest workRequest, String chrName)
   --- End of inner exception stack trace ---.
8/19/23 7:21 PM 1  Exception reported:
System.Exception: Failed to process variants for MN01972:49:000H5KYMY:1:11102:26356:2968 ... 150S
   at Pisces.Processing.Logic.BaseProcessor.Execute(Int32 maxThreads)
   at Pisces.Program.ProgramExecution()
   at CommandLine.Application.BaseApplication`1.Execute().

EDIT:

I have investigated this and the problem is this 151S. There are reads that are completely soft-clip.