REQUIRED for all errors and issues:
a) GATK version used: gatk-4.6.1.0
b) Exact command used: gatk MarkDuplicatesSpark -I SRR062641.paired.sam -O SRR062641_sorted_dedup.bam
c) Entire program log: Using GATK jar /home/meenameena048/softwares/gatk-4.6.1.0/gatk-package-4.6.1.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/meenameena048/softwares/gatk-4.6.1.0/gatk-package-4.6.1.0-local.jar MarkDuplicatesSpark -I SRR062641.paired.sam -O SRR062641_sorted_dedup.bam
14:15:25.730 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/meenameena048/softwares/gatk-4.6.1.0/gatk-package-4.6.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
SLF4J(W): Class path contains multiple SLF4J providers.
SLF4J(W): Found provider [org.apache.logging.slf4j.SLF4JServiceProvider@7faa0680]
SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@4c635edc]
SLF4J(W): See https://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J(I): Actual provider is of type [org.apache.logging.slf4j.SLF4JServiceProvider@7faa0680]
14:15:25.867 INFO  MarkDuplicatesSpark - ------------------------------------------------------------
14:15:25.870 INFO  MarkDuplicatesSpark - The Genome Analysis Toolkit (GATK) v4.6.1.0
14:15:25.870 INFO  MarkDuplicatesSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
14:15:25.870 INFO  MarkDuplicatesSpark - Executing as meenameena048@ubuntu1 on Linux v6.8.0-1017-gcp amd64
14:15:25.870 INFO  MarkDuplicatesSpark - Java runtime: OpenJDK 64-Bit Server VM v23.0.1+11-39
14:15:25.871 INFO  MarkDuplicatesSpark - Start Date/Time: November 3, 2024, 2:15:25 PM UTC
14:15:25.871 INFO  MarkDuplicatesSpark - ------------------------------------------------------------
14:15:25.871 INFO  MarkDuplicatesSpark - ------------------------------------------------------------
14:15:25.872 INFO  MarkDuplicatesSpark - HTSJDK Version: 4.1.3
14:15:25.872 INFO  MarkDuplicatesSpark - Picard Version: 3.3.0
14:15:25.872 INFO  MarkDuplicatesSpark - Built for Spark Version: 3.5.0
14:15:25.874 INFO  MarkDuplicatesSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:15:25.875 INFO  MarkDuplicatesSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:15:25.875 INFO  MarkDuplicatesSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:15:25.875 INFO  MarkDuplicatesSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:15:25.875 INFO  MarkDuplicatesSpark - Deflater: IntelDeflater
14:15:25.875 INFO  MarkDuplicatesSpark - Inflater: IntelInflater
14:15:25.875 INFO  MarkDuplicatesSpark - GCS max retries/reopens: 20
14:15:25.876 INFO  MarkDuplicatesSpark - Requester pays: disabled
14:15:25.876 INFO  MarkDuplicatesSpark - Initializing engine
14:15:25.876 INFO  MarkDuplicatesSpark - Done initializing engine
14:15:26.201 INFO  SparkContext - Running Spark version 3.5.0
14:15:26.201 INFO  SparkContext - OS info Linux, 6.8.0-1017-gcp, amd64
14:15:26.202 INFO  SparkContext - Java version 23.0.1
14:15:26.348 WARN  NativeCodeLoader - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
14:15:26.365 INFO  MarkDuplicatesSpark - Shutting down engine
[November 3, 2024, 2:15:26 PM UTC] org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=96468992
java.lang.UnsupportedOperationException: getSubject is supported only if a security manager is allowed
        at java.base/javax.security.auth.Subject.getSubject(Subject.java:347)
        at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:577)
        at org.apache.spark.util.Utils$.$anonfun$getCurrentUserName$1(Utils.scala:2416)
        at scala.Option.getOrElse(Option.scala:201)
        at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2416)
        at org.apache.spark.SparkContext.<init>(SparkContext.scala:334)
        at org.apache.spark.api.java.JavaSparkContext.<init>(JavaSparkContext.scala:58)
        at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.createSparkContext(SparkContextFactory.java:185)
        at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.getSparkContext(SparkContextFactory.java:117)
        at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:28)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
        at org.broadinstitute.hellbender.Main.main(Main.java:306)