StructuralVariationDiscoveryPipeline IllegalArgumentException

[dsilencio]

Have been having the following issue running StructuralVariationDiscoveryPipeline on previous and the newest release of GATK(4.1.0.0). Currently attempting to use on a computing cluster without spark enabled.

Command line used:
gatk/gatk-4.1.0.0/gatk StructuralVariationDiscoveryPipelineSpark
-I $CRAM
-R $Hg38
--aligner-index-image reference.fasta.Hg38.img
--kmers-to-ignore kmers_to_ignore_hg38.txt
--contig-sam-file aligned_contigs.sam
-O ${base}_GATK_SV_output.vcf

Error Log:
19/02/01 21:28:27 INFO TaskSetManager: Starting task 700.0 in stage 5.0 (TID 4405, localhost, executor driver, partition 700, PROCESS_LOCAL, 4940 bytes)
19/02/01 21:28:27 INFO Executor: Running task 700.0 in stage 5.0 (TID 4405)
19/02/01 21:28:27 INFO TaskSetManager: Finished task 668.0 in stage 5.0 (TID 4373) in 37331 ms on localhost (executor driver) (669/741)
19/02/01 21:28:27 INFO BlockManagerInfo: Removed taskresult_4373 on 10.120.16.54:34926 in memory (size: 1645.1 KB, free: 15.8 GB)
19/02/01 21:28:27 INFO NewHadoopRDD: Input split: file: /cram8/1-00004__CG0000-1789.GMKF2.cram:23488102400+33554432
19/02/01 21:28:28 ERROR Executor: Exception in task 698.0 in stage 5.0 (TID 4403)
java.lang.IllegalArgumentException: provided start is negative: -24
at org.broadinstitute.hellbender.tools.spark.sv.utils.SVInterval$SVIntervalConstructorArgsValidator.lambda$static$3(SVInterval.java:76)
at org.broadinstitute.hellbender.tools.spark.sv.utils.SVInterval$SVIntervalConstructorArgsValidator.lambda$andThen$0(SVInterval.java:61)
at org.broadinstitute.hellbender.tools.spark.sv.utils.SVInterval.(SVInterval.java:86)
at org.broadinstitute.hellbender.tools.spark.sv.utils.SVInterval.(SVInterval.java:51)
at org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameFinder.apply(QNameFinder.java:48)
at org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameFinder.apply(QNameFinder.java:16)
at org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer.hasNext(FlatMapGluer.java:44)
at scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42)
at scala.collection.Iterator$class.foreach(Iterator.scala:893)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
at scala.collection.AbstractIterator.to(Iterator.scala:1336)
at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:936)
at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:936)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2062)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2062)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
19/02/01 21:28:28 INFO TaskSetManager: Starting task 701.0 in stage 5.0 (TID 4406, localhost, executor driver, partition 701, PROCESS_LOCAL, 4940 bytes)
19/02/01 21:28:28 INFO Executor: Running task 701.0 in stage 5.0 (TID 4406)

[cwhelan]

Hoping this is also closed via #5864