While running 'CreatePanelOfNormals' , some errors occured. Here is the code i ran 'java -Xmx16g -Djava.library.path=/Workspace/Software/HDFView/HDFView-2.13.0-Linux/HDFView/2.13.0/lib/ -jar /Workspace/Software/gatk4-latest/gatk-protected.jar reatePanelOfNormals -I merge.txt -O PoN.tsv '. And the log file as following :
[January 9, 2017 6:11:58 PM CST] org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals --input merge.txt --output PoN.tsv --minimumTargetFactorPercentileThreshold 25.0 --maximumColumnZerosPercentage 2.0 --maximumTargetZerosPercentage 5.0 --extremeColumnMedianCountPercentileThreshold 2.5 --truncatePercentileThreshold 0.1 --numberOfEigenSamples auto --noQC false --dryRun false --disableSpark false --sparkMaster local[*] --help false --version false --verbosity INFO --QUIET false
[January 9, 2017 6:11:58 PM CST] Executing as yangjiatao@R930 on Linux 3.10.0-514.2.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_111-b15; Version: Version:version-unknown-SNAPSHOT
18:11:58.749 INFO CreatePanelOfNormals - Defaults.BUFFER_SIZE : 131072
18:11:58.750 INFO CreatePanelOfNormals - Defaults.COMPRESSION_LEVEL : 5
18:11:58.750 INFO CreatePanelOfNormals - Defaults.CREATE_INDEX : false
18:11:58.750 INFO CreatePanelOfNormals - Defaults.CREATE_MD5 : false
18:11:58.750 INFO CreatePanelOfNormals - Defaults.CUSTOM_READER_FACTORY :
18:11:58.750 INFO CreatePanelOfNormals - Defaults.EBI_REFERENCE_SEVICE_URL_MASK : http://www.ebi.ac.uk/ena/cram/md5/%s
18:11:58.750 INFO CreatePanelOfNormals - Defaults.INTEL_DEFLATER_SHARED_LIBRARY_PATH : null
18:11:58.750 INFO CreatePanelOfNormals - Defaults.NON_ZERO_BUFFER_SIZE : 131072
18:11:58.751 INFO CreatePanelOfNormals - Defaults.REFERENCE_FASTA : null
18:11:58.751 INFO CreatePanelOfNormals - Defaults.TRY_USE_INTEL_DEFLATER : true
18:11:58.751 INFO CreatePanelOfNormals - Defaults.USE_ASYNC_IO : false
18:11:58.751 INFO CreatePanelOfNormals - Defaults.USE_ASYNC_IO_FOR_SAMTOOLS : false
18:11:58.751 INFO CreatePanelOfNormals - Defaults.USE_ASYNC_IO_FOR_TRIBBLE : false
18:11:58.751 INFO CreatePanelOfNormals - Defaults.USE_CRAM_REF_DOWNLOAD : false
18:11:58.752 INFO CreatePanelOfNormals - Deflater JdkDeflater
18:11:58.752 INFO CreatePanelOfNormals - Initializing engine
18:11:58.753 INFO CreatePanelOfNormals - Done initializing engine
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
17/01/09 18:11:59 INFO SparkContext: Running Spark version 1.5.0
17/01/09 18:11:59 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
17/01/09 18:11:59 INFO SecurityManager: Changing view acls to: yangjiatao
17/01/09 18:11:59 INFO SecurityManager: Changing modify acls to: yangjiatao
17/01/09 18:11:59 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(yangjiatao); users with modify permissions: Set(yangjiatao)
17/01/09 18:11:59 INFO Slf4jLogger: Slf4jLogger started
17/01/09 18:11:59 INFO Remoting: Starting remoting
17/01/09 18:11:59 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkDriver@192.168.0.131:46229]
17/01/09 18:11:59 INFO Utils: Successfully started service 'sparkDriver' on port 46229.
17/01/09 18:11:59 INFO SparkEnv: Registering MapOutputTracker
17/01/09 18:11:59 INFO SparkEnv: Registering BlockManagerMaster
17/01/09 18:12:00 INFO DiskBlockManager: Created local directory at /tmp/yangjiatao/blockmgr-60a33e19-35f0-4969-8ba4-eb844485d298
17/01/09 18:12:00 INFO MemoryStore: MemoryStore started with capacity 7.7 GB
17/01/09 18:12:00 INFO HttpFileServer: HTTP File server directory is /tmp/yangjiatao/spark-9dd82bfd-6256-43a9-a5c0-b8b831b0bc21/httpd-927e1211-e7c3-42e8-b528-786f806ed19b
17/01/09 18:12:00 INFO HttpServer: Starting HTTP Server
17/01/09 18:12:00 INFO Utils: Successfully started service 'HTTP file server' on port 35578.
17/01/09 18:12:00 INFO SparkEnv: Registering OutputCommitCoordinator
17/01/09 18:12:00 INFO Utils: Successfully started service 'SparkUI' on port 4040.
17/01/09 18:12:00 INFO SparkUI: Started SparkUI at http://192.168.0.131:4040
17/01/09 18:12:00 WARN MetricsSystem: Using default name DAGScheduler for source because spark.app.id is not set.
17/01/09 18:12:00 INFO Executor: Starting executor ID driver on host localhost
17/01/09 18:12:00 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 37751.
17/01/09 18:12:00 INFO NettyBlockTransferService: Server created on 37751
17/01/09 18:12:00 INFO BlockManagerMaster: Trying to register BlockManager
17/01/09 18:12:00 INFO BlockManagerMasterEndpoint: Registering block manager localhost:37751 with 7.7 GB RAM, BlockManagerId(driver, localhost, 37751)
17/01/09 18:12:00 INFO BlockManagerMaster: Registered BlockManager
18:12:01.177 INFO CreatePanelOfNormals - QC: Beginning creation of QC PoN...
18:12:01.235 INFO HDF5PoNCreator - All 283 targets are kept
17/01/09 18:12:01 INFO SparkUI: Stopped Spark web UI at http://192.168.0.131:4040
17/01/09 18:12:01 INFO DAGScheduler: Stopping DAGScheduler
17/01/09 18:12:01 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
17/01/09 18:12:01 INFO MemoryStore: MemoryStore cleared
17/01/09 18:12:01 INFO BlockManager: BlockManager stopped
17/01/09 18:12:01 INFO BlockManagerMaster: BlockManagerMaster stopped
17/01/09 18:12:01 INFO SparkContext: Successfully stopped SparkContext
18:12:01.673 INFO CreatePanelOfNormals - Shutting down engine
17/01/09 18:12:01 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
[January 9, 2017 6:12:01 PM CST] org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2264399872
Exception in thread "main" java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5dont_atexit()I
at ncsa.hdf.hdf5lib.H5.H5dont_atexit(Native Method)
at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:365)
at ncsa.hdf.hdf5lib.H5.(H5.java:274)
at ncsa.hdf.hdf5lib.HDF5Constants.(HDF5Constants.java:28)
at org.broadinstitute.hellbender.utils.hdf5.HDF5File$OpenMode.(HDF5File.java:505)
at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.writeTargetFactorNormalizeReadCountsAndTargetFactors(HDF5PoNCreator.java:185)
at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.createPoNGivenReadCountCollection(HDF5PoNCreator.java:118)
at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.createPoN(HDF5PoNCreator.java:88)
at org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals.runPipeline(CreatePanelOfNormals.java:244)
at org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram.doWork(SparkToggleCommandLineProgram.java:39)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:102)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:155)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:174)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:69)
at org.broadinstitute.hellbender.Main.main(Main.java:84)
17/01/09 18:12:01 INFO ShutdownHookManager: Shutdown hook called
17/01/09 18:12:01 INFO ShutdownHookManager: Deleting directory /tmp/yangjiatao/spark-9dd82bfd-6256-43a9-a5c0-b8b831b0bc21