REQUIRED for all errors and issues:
a) GATK version used:

gatk-package-4.3.0.0

b) Exact command used:

!/bin/sh

#SBATCH --time=2-10:15 -N 2  --cpus-per-task=24 -p l_long --qos ll

#SBATCH -J Mark_duplicates

#SBATCH --output=Mark_duplicates.o

#SBATCH --error=Mark_duplicates.e

gatk MarkDuplicatesSpark -I ${aligned_reads}/$1 -O ${aligned_reads}/MK264_sorted_dedup_reads.bam

c) Entire program log:

Runtime.totalMemory()=7683964928

org.apache.spark.SparkException: Job aborted due to stage failure: Task 1899 in stage 1.0 failed 1 times, most recent failure: Lost>

        at htsjdk.samtools.SAMRecordSparkCodec.encode(SAMRecordSparkCodec.java:114)

        at org.broadinstitute.hellbender.engine.spark.SAMRecordToGATKReadAdapterSerializer.write(SAMRecordToGATKReadAdapterSerializ>

        at org.broadinstitute.hellbender.engine.spark.SAMRecordToGATKReadAdapterSerializer.write(SAMRecordToGATKReadAdapterSerializ>

        at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)

        at org.apache.spark.serializer.KryoSerializationStream.writeObject(KryoSerializer.scala:245)

        at org.apache.spark.serializer.SerializationStream.writeKey(Serializer.scala:132)

        at org.apache.spark.shuffle.sort.UnsafeShuffleWriter.insertRecordIntoSorter(UnsafeShuffleWriter.java:260)

        at org.apache.spark.shuffle.sort.UnsafeShuffleWriter.write(UnsafeShuffleWriter.java:188)

        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99)

        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:55)

        at org.apache.spark.scheduler.Task.run(Task.scala:123)

        at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)

        at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)

        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

        at java.lang.Thread.run(Thread.java:750)

Driver stacktrace:

        at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGSchedule>

        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1879)

        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1878)

        at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)

        at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)

        at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1878)

        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)

        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)

        at scala.Option.foreach(Option.scala:257)

Driver stacktrace:

        at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGSchedule>

        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1879)

        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1878)

        at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)

        at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)

        at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1878)

        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)

        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)

        at scala.Option.foreach(Option.scala:257)

        at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:927)

        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2112)

        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2061)

        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2050)

        at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)

        at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:738)

        at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)

        at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)

        at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)

        at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)

        at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:990)

        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)

        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)

        at org.apache.spark.rdd.RDD.withScope(RDD.scala:385)

        at org.apache.spark.rdd.RDD.collect(RDD.scala:989)

        at org.apache.spark.api.java.JavaRDDLike$class.collect(JavaRDDLike.scala:361)

        at org.apache.spark.api.java.AbstractJavaRDDLike.collect(JavaRDDLike.scala:45)

        at org.broadinstitute.hellbender.utils.spark.SparkUtils.putReadsWithTheSameNameInTheSamePartition(SparkUtils.java:205)

        at org.broadinstitute.hellbender.utils.spark.SparkUtils.sortReadsAccordingToHeader(SparkUtils.java:144)

        at org.broadinstitute.hellbender.utils.spark.SparkUtils.querynameSortReadsIfNecessary(SparkUtils.java:306)

        at org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark.mark(MarkDuplicatesSpark.java:20>

        at org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark.mark(MarkDuplicatesSpark.java:27>

        at org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark.runTool(MarkDuplicatesSpark.java>

        at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:546)

        at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)

        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)

        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)