Dear All,

I am trying to run MarkDuplicatesSpark on a server using putty but I am getting errors with the logs below:

a) GATK version is gatk4.1.9.0

b) command used

./gatk MarkDuplicatesSpark -I Kaito.fixrg.bam -M Kaitodedupmetrics.txt -O Kaito_sorted_dedup_reads.bam

c) Error log:

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/naika/gatk4/gatk-package-4.1.9.0-local.jar MarkDuplicatesSpark -I Kaito.fixrg.bam -M Kaitodedupmetrics.txt -O Kaito_sorted_dedup_reads.bam
12:30:53.128 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/naika/gatk4/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 15, 2020 12:30:53 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:30:53.772 INFO MarkDuplicatesSpark - ------------------------------------------------------------
12:30:53.773 INFO MarkDuplicatesSpark - The Genome Analysis Toolkit (GATK) v4.1.9.0
12:30:53.773 INFO MarkDuplicatesSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
12:30:53.775 INFO MarkDuplicatesSpark - Initializing engine
12:30:53.775 INFO MarkDuplicatesSpark - Done initializing engine
12:30:54.796 INFO MarkDuplicatesSpark - Shutting down engine
[2020/12/15 12:30:54 JST] org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=2361917440
Exception in thread "main" java.lang.ExceptionInInitializerError
at org.apache.spark.SparkConf$.<init>(SparkConf.scala:716)
at org.apache.spark.SparkConf$.<clinit>(SparkConf.scala)
at org.apache.spark.SparkConf.set(SparkConf.scala:95)
at org.apache.spark.SparkConf$$anonfun$loadFromSystemProperties$3.apply(SparkConf.scala:77)
at org.apache.spark.SparkConf$$anonfun$loadFromSystemProperties$3.apply(SparkConf.scala:76)
at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733)
at scala.collection.immutable.HashMap$HashMap1.foreach(HashMap.scala:221)
at scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:428)
at scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:428)
at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732)
at org.apache.spark.SparkConf.loadFromSystemProperties(SparkConf.scala:76)
at org.apache.spark.SparkConf.<init>(SparkConf.scala:71)
at org.apache.spark.SparkConf.<init>(SparkConf.scala:58)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.setupSparkConf(SparkContextFactory.java:173)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.createSparkContext(SparkContextFactory.java:183)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.getSparkContext(SparkContextFactory.java:117)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:28)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.net.UnknownHostException: ororon: ororon: 名前またはサービスが不明です
at java.net.InetAddress.getLocalHost(InetAddress.java:1505)
at org.apache.spark.util.Utils$.findLocalInetAddress(Utils.scala:946)
at org.apache.spark.util.Utils$.org$apache$spark$util$Utils$$localIpAddress$lzycompute(Utils.scala:939)
at org.apache.spark.util.Utils$.org$apache$spark$util$Utils$$localIpAddress(Utils.scala:939)
at org.apache.spark.util.Utils$$anonfun$localCanonicalHostName$1.apply(Utils.scala:996)
at org.apache.spark.util.Utils$$anonfun$localCanonicalHostName$1.apply(Utils.scala:996)
at scala.Option.getOrElse(Option.scala:121)
at org.apache.spark.util.Utils$.localCanonicalHostName(Utils.scala:996)
at org.apache.spark.internal.config.package$.<init>(package.scala:302)
at org.apache.spark.internal.config.package$.<clinit>(package.scala)
... 23 more
Caused by: java.net.UnknownHostException: ororon: 名前またはサービスが不明です
at java.net.Inet6AddressImpl.lookupAllHostAddr(Native Method)
at java.net.InetAddress$2.lookupAllHostAddr(InetAddress.java:928)
at java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1323)
at java.net.InetAddress.getLocalHost(InetAddress.java:1500)
... 32 more

名前またはサービスが不明です this Japanese sentence translates into Name or Service Unknown.

I have tried changing host name etc but I do not own the server and I have no government over the host names, is there anything I can do about this?

I have no problem running MarkDuplicatesSpark with bam files under 50GB in my own desktop though.

Thank you!