Dear GATK team,

hi.  now I am discovering for pathogenic CNV via GATK germline CNV pipelin.

Previously, I analyzed the other cohort and pipeline worked well.

However, I faced with the following error, even though it was at the same environment and setting.

Is it problem with size of memory in my machine?

If you have any advices to solved this, can you tell it to me?

Additionally, is there any options for GermlineCNVcaller to specify the number of cores or threads to use?

Best,

Shun

a) GATK version used:

4.2.5.0
b) Exact command used:

/home/inos0304/modules/gatk-4.2.5.0/gatk GermlineCNVCaller --run-mode COHORT -L /home/inos0304/human_genome_analysis/cnv/analysis_female/scatter/temp_0001_of_41/scattered.interval_list -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_04.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_13.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_17.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_20.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_23.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_24.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_25.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_27.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_29.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_30.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_31.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_32.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_36.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_41.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_47.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_49.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_56.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_59.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_60.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_64.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_67.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_68.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_85.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_86.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_05.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_07.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_09.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_18.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_20.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_28.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_32.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_34.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_35.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_39.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_41.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_44.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_50.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_56.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_57.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_59.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_63.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_73.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_78.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_92.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_95.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_07.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_15.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_16.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_23.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_25.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_31.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_37.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_43.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_45.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_46.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_48.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_50.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_56.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_58.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_60.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_03.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_11.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_16.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_17.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_21.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_23.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_29.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_30.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_33.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_34.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_41.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_43.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_52.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_55.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_58.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_61.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_73.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_77.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_90.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_96.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_02.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_07.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_09.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_10.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_11.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_12.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_19.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_21.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_23.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_26.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_28.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_29.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_30.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_32.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_35.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_39.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_40.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_42.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_45.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_46.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_62.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_65.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_80.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_91.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_93.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_06.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_20.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_28.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_29.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_37.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_39.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_46.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_50.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_53.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_58.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_60.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_61.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_65.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_71.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_81.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_82.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_83.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_87.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_90.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_91.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_01.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_08.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_11.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_13.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_18.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_20.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_23.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_24.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_25.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_27.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_28.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_29.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_31.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_34.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_35.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_46.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_48.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_51.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_52.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_55.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_58.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_63.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_65.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_66.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_67.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_69.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_70.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_74.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_75.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_76.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_77.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_78.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_82.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_85.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_86.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_91.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_92.tsv -I /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_93.tsv --contig-ploidy-calls /home/inos0304/human_genome_analysis/cnv/analysis_female/ploidy-calls --annotated-intervals /home/inos0304/human_genome_analysis/cnv/exome.annotated.tsv --interval-merging-rule OVERLAPPING_ONLY --output /home/inos0304/human_genome_analysis/cnv/analysis_female/cohort_female --output-prefix cohort_female_01 --verbosity DEBUG

c) Entire program log:Picked up JAVA_TOOL_OPTIONS: -XX:+UseSerialGC -Xmx6g -Xms6g
12:52:02.720 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/modules/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:52:02.754 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression6881354295017338112.so
Apr 22, 2022 12:52:02 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:52:02.938 INFO  GermlineCNVCaller - ------------------------------------------------------------
12:52:02.938 INFO  GermlineCNVCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0
12:52:02.938 INFO  GermlineCNVCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
12:52:02.939 INFO  GermlineCNVCaller - Executing as inos0304@rc018i on Linux v4.18.0-348.12.2.el8_5.x86_64 amd64
12:52:02.939 INFO  GermlineCNVCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_181-b13
12:52:02.939 INFO  GermlineCNVCaller - Start Date/Time: 2022/04/22 12:52:02 JST
12:52:02.939 INFO  GermlineCNVCaller - ------------------------------------------------------------
12:52:02.939 INFO  GermlineCNVCaller - ------------------------------------------------------------
12:52:02.940 INFO  GermlineCNVCaller - HTSJDK Version: 2.24.1
12:52:02.940 INFO  GermlineCNVCaller - Picard Version: 2.25.4
12:52:02.940 INFO  GermlineCNVCaller - Built for Spark Version: 2.4.5
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.BUFFER_SIZE : 131072
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.CREATE_INDEX : false
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.CREATE_MD5 : false
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.CUSTOM_READER_FACTORY : 
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.REFERENCE_FASTA : null
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:52:02.941 INFO  GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:52:02.942 INFO  GermlineCNVCaller - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
12:52:02.942 DEBUG ConfigFactory - Configuration file values: 
12:52:02.944 DEBUG ConfigFactory -     gcsMaxRetries = 20
12:52:02.944 DEBUG ConfigFactory -     gcsProjectForRequesterPays = 
12:52:02.944 DEBUG ConfigFactory -     gatk_stacktrace_on_user_exception = false
12:52:02.944 DEBUG ConfigFactory -     samjdk.use_async_io_read_samtools = false
12:52:02.944 DEBUG ConfigFactory -     samjdk.use_async_io_write_samtools = true
12:52:02.944 DEBUG ConfigFactory -     samjdk.use_async_io_write_tribble = false
12:52:02.944 DEBUG ConfigFactory -     samjdk.compression_level = 2
12:52:02.945 DEBUG ConfigFactory -     spark.kryoserializer.buffer.max = 512m
12:52:02.945 DEBUG ConfigFactory -     spark.driver.maxResultSize = 0
12:52:02.945 DEBUG ConfigFactory -     spark.driver.userClassPathFirst = true
12:52:02.945 DEBUG ConfigFactory -     spark.io.compression.codec = lzf
12:52:02.945 DEBUG ConfigFactory -     spark.executor.memoryOverhead = 600
12:52:02.945 DEBUG ConfigFactory -     spark.driver.extraJavaOptions = 
12:52:02.945 DEBUG ConfigFactory -     spark.executor.extraJavaOptions = 
12:52:02.945 DEBUG ConfigFactory -     codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
12:52:02.945 DEBUG ConfigFactory -     read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
12:52:02.945 DEBUG ConfigFactory -     annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
12:52:02.945 DEBUG ConfigFactory -     cloudPrefetchBuffer = 40
12:52:02.945 DEBUG ConfigFactory -     cloudIndexPrefetchBuffer = -1
12:52:02.945 DEBUG ConfigFactory -     createOutputBamIndex = true
12:52:02.945 INFO  GermlineCNVCaller - Deflater: IntelDeflater
12:52:02.945 INFO  GermlineCNVCaller - Inflater: IntelInflater
12:52:02.945 INFO  GermlineCNVCaller - GCS max retries/reopens: 20
12:52:02.945 INFO  GermlineCNVCaller - Requester pays: disabled
12:52:02.946 INFO  GermlineCNVCaller - Initializing engine
12:52:02.948 DEBUG ScriptExecutor - Executing:
12:52:02.948 DEBUG ScriptExecutor -   python
12:52:02.948 DEBUG ScriptExecutor -   -c
12:52:02.948 DEBUG ScriptExecutor -   import gcnvkernel

12:53:49.009 DEBUG ScriptExecutor - Result: 0
12:53:49.010 INFO  GermlineCNVCaller - Done initializing engine
12:53:53.493 INFO  GermlineCNVCaller - Intervals specified...
12:53:53.858 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
12:53:53.858 DEBUG GenomeLocParser -  chr1 (248956422 bp)
12:53:53.858 DEBUG GenomeLocParser -  chr2 (242193529 bp)
12:53:53.858 DEBUG GenomeLocParser -  chr3 (198295559 bp)
12:53:53.858 DEBUG GenomeLocParser -  chr4 (190214555 bp)
12:53:53.858 DEBUG GenomeLocParser -  chr5 (181538259 bp)
12:53:53.858 DEBUG GenomeLocParser -  chr6 (170805979 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr7 (159345973 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr8 (145138636 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr9 (138394717 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr10 (133797422 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr11 (135086622 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr12 (133275309 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr13 (114364328 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr14 (107043718 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr15 (101991189 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr16 (90338345 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr17 (83257441 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr18 (80373285 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr19 (58617616 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr20 (64444167 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr21 (46709983 bp)
12:53:53.859 DEBUG GenomeLocParser -  chr22 (50818468 bp)
12:53:53.859 DEBUG GenomeLocParser -  chrX (156040895 bp)
12:53:53.860 DEBUG GenomeLocParser -  chrY (57227415 bp)
12:53:53.860 DEBUG GenomeLocParser -  chrM (16569 bp)
12:53:53.860 DEBUG GenomeLocParser -  chrEBV (171823 bp)
12:53:53.860 DEBUG GenomeLocParser -  decoy (6391639 bp)
12:53:54.283 INFO  FeatureManager - Using codec IntervalListCodec to read file file:///home/inos0304/human_genome_analysis/cnv/analysis_female/scatter/temp_0001_of_41/scattered.interval_list
12:53:54.425 DEBUG FeatureDataSource - Cache statistics for FeatureInput /home/inos0304/human_genome_analysis/cnv/analysis_female/scatter/temp_0001_of_41/scattered.interval_list:/home/inos0304/human_genome_analysis/cnv/analysis_female/scatter/temp_0001_of_41/scattered.interval_list:
12:53:54.425 DEBUG FeatureCache - Cache hit rate  was 0.00% (0 out of 0 total queries)
12:53:54.430 INFO  IntervalArgumentCollection - Processing 2938994 bp from intervals
12:53:54.446 INFO  GermlineCNVCaller - Reading and validating annotated intervals...
12:53:54.878 WARN  GermlineCNVCaller - Sequence dictionary in annotated-intervals file does not match the master sequence dictionary.
12:53:54.894 INFO  GermlineCNVCaller - GC-content annotations for intervals found; explicit GC-bias correction will be performed...
12:53:54.930 INFO  GermlineCNVCaller - Running the tool in COHORT mode...
12:53:54.930 INFO  GermlineCNVCaller - Validating and aggregating data from input read-count files...
12:53:54.930 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
12:53:54.930 DEBUG GenomeLocParser -  chr1 (248956422 bp)
12:53:54.930 DEBUG GenomeLocParser -  chr2 (242193529 bp)
12:53:54.930 DEBUG GenomeLocParser -  chr3 (198295559 bp)
12:53:54.930 DEBUG GenomeLocParser -  chr4 (190214555 bp)
12:53:54.930 DEBUG GenomeLocParser -  chr5 (181538259 bp)
12:53:54.930 DEBUG GenomeLocParser -  chr6 (170805979 bp)
12:53:54.930 DEBUG GenomeLocParser -  chr7 (159345973 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr8 (145138636 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr9 (138394717 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr10 (133797422 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr11 (135086622 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr12 (133275309 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr13 (114364328 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr14 (107043718 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr15 (101991189 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr16 (90338345 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr17 (83257441 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr18 (80373285 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr19 (58617616 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr20 (64444167 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr21 (46709983 bp)
12:53:54.931 DEBUG GenomeLocParser -  chr22 (50818468 bp)
12:53:54.931 DEBUG GenomeLocParser -  chrX (156040895 bp)
12:53:54.931 DEBUG GenomeLocParser -  chrY (57227415 bp)
12:53:54.931 DEBUG GenomeLocParser -  chrM (16569 bp)
12:53:54.931 DEBUG GenomeLocParser -  chrEBV (171823 bp)
12:53:54.932 DEBUG GenomeLocParser -  decoy (6391639 bp)
12:53:54.940 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_04.tsv (1 / 163)
12:53:55.166 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_13.tsv (2 / 163)
12:53:55.440 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_17.tsv (3 / 163)
12:53:55.723 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_20.tsv (4 / 163)
12:53:55.968 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_23.tsv (5 / 163)
12:53:56.197 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_24.tsv (6 / 163)
12:53:56.405 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_25.tsv (7 / 163)
12:53:56.617 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_27.tsv (8 / 163)
12:53:57.033 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_29.tsv (9 / 163)
12:53:57.228 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_30.tsv (10 / 163)
12:53:57.434 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_31.tsv (11 / 163)
12:53:57.654 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_32.tsv (12 / 163)
12:53:57.845 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_36.tsv (13 / 163)
12:53:58.061 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_41.tsv (14 / 163)
12:53:58.292 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_47.tsv (15 / 163)
12:53:58.499 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_49.tsv (16 / 163)
12:53:58.693 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_56.tsv (17 / 163)
12:53:58.904 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_59.tsv (18 / 163)
12:53:59.115 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_60.tsv (19 / 163)
12:53:59.321 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_64.tsv (20 / 163)
12:53:59.521 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_67.tsv (21 / 163)
12:53:59.712 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_68.tsv (22 / 163)
12:53:59.913 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_85.tsv (23 / 163)
12:54:00.128 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/HN7448_86.tsv (24 / 163)
12:54:00.387 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_05.tsv (25 / 163)
12:54:00.614 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_07.tsv (26 / 163)
12:54:00.831 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_09.tsv (27 / 163)
12:54:01.056 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_18.tsv (28 / 163)
12:54:01.251 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_20.tsv (29 / 163)
12:54:01.468 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_28.tsv (30 / 163)
12:54:01.719 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_32.tsv (31 / 163)
12:54:02.025 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_34.tsv (32 / 163)
12:54:02.320 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_35.tsv (33 / 163)
12:54:02.517 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_39.tsv (34 / 163)
12:54:02.750 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_41.tsv (35 / 163)
12:54:02.948 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_44.tsv (36 / 163)
12:54:03.156 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_50.tsv (37 / 163)
12:54:03.356 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_56.tsv (38 / 163)
12:54:03.546 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_57.tsv (39 / 163)
12:54:03.743 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_59.tsv (40 / 163)
12:54:03.978 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_63.tsv (41 / 163)
12:54:04.182 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_73.tsv (42 / 163)
12:54:04.384 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_78.tsv (43 / 163)
12:54:04.590 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_92.tsv (44 / 163)
12:54:04.784 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/JN6556_95.tsv (45 / 163)
12:54:04.982 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_07.tsv (46 / 163)
12:54:05.168 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_15.tsv (47 / 163)
12:54:05.346 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_16.tsv (48 / 163)
12:54:05.546 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_23.tsv (49 / 163)
12:54:05.750 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_25.tsv (50 / 163)
12:54:05.938 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_31.tsv (51 / 163)
12:54:06.379 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_37.tsv (52 / 163)
12:54:06.589 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_43.tsv (53 / 163)
12:54:06.785 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_45.tsv (54 / 163)
12:54:06.981 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_46.tsv (55 / 163)
12:54:07.173 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_48.tsv (56 / 163)
12:54:07.382 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_50.tsv (57 / 163)
12:54:07.560 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_56.tsv (58 / 163)
12:54:07.757 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_58.tsv (59 / 163)
12:54:07.939 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4100_60.tsv (60 / 163)
12:54:08.115 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_03.tsv (61 / 163)
12:54:08.333 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_11.tsv (62 / 163)
12:54:08.515 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_16.tsv (63 / 163)
12:54:08.699 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_17.tsv (64 / 163)
12:54:08.892 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_21.tsv (65 / 163)
12:54:09.112 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_23.tsv (66 / 163)
12:54:09.309 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_29.tsv (67 / 163)
12:54:09.492 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_30.tsv (68 / 163)
12:54:09.679 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_33.tsv (69 / 163)
12:54:09.881 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_34.tsv (70 / 163)
12:54:10.075 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_41.tsv (71 / 163)
12:54:10.274 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_43.tsv (72 / 163)
12:54:10.467 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_52.tsv (73 / 163)
12:54:10.869 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_55.tsv (74 / 163)
12:54:11.060 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_58.tsv (75 / 163)
12:54:11.254 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_61.tsv (76 / 163)
12:54:11.587 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_73.tsv (77 / 163)
12:54:11.766 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_77.tsv (78 / 163)
12:54:11.972 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_90.tsv (79 / 163)
12:54:12.171 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4213_96.tsv (80 / 163)
12:54:12.380 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_02.tsv (81 / 163)
12:54:12.590 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_07.tsv (82 / 163)
12:54:12.783 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_09.tsv (83 / 163)
12:54:12.987 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_10.tsv (84 / 163)
12:54:13.191 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_11.tsv (85 / 163)
12:54:13.384 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_12.tsv (86 / 163)
12:54:13.957 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_19.tsv (87 / 163)
12:54:14.166 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_21.tsv (88 / 163)
12:54:14.357 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_23.tsv (89 / 163)
12:54:14.552 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_26.tsv (90 / 163)
12:54:14.750 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_28.tsv (91 / 163)
12:54:14.943 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_29.tsv (92 / 163)
12:54:15.148 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_30.tsv (93 / 163)
12:54:15.352 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_32.tsv (94 / 163)
12:54:15.573 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_35.tsv (95 / 163)
12:54:15.756 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_39.tsv (96 / 163)
12:54:15.968 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_40.tsv (97 / 163)
12:54:16.549 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_42.tsv (98 / 163)
12:54:16.740 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_45.tsv (99 / 163)
12:54:16.928 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_46.tsv (100 / 163)
12:54:17.139 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_62.tsv (101 / 163)
12:54:17.333 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_65.tsv (102 / 163)
12:54:17.531 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_80.tsv (103 / 163)
12:54:17.735 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_91.tsv (104 / 163)
12:54:17.978 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4344_93.tsv (105 / 163)
12:54:18.171 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_06.tsv (106 / 163)
12:54:18.356 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_20.tsv (107 / 163)
12:54:18.728 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_28.tsv (108 / 163)
12:54:18.924 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_29.tsv (109 / 163)
12:54:19.114 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_37.tsv (110 / 163)
12:54:19.313 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_39.tsv (111 / 163)
12:54:19.512 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_46.tsv (112 / 163)
12:54:19.695 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_50.tsv (113 / 163)
12:54:19.889 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_53.tsv (114 / 163)
12:54:20.140 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_58.tsv (115 / 163)
12:54:20.348 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_60.tsv (116 / 163)
12:54:20.545 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_61.tsv (117 / 163)
12:54:20.752 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_65.tsv (118 / 163)
12:54:20.943 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_71.tsv (119 / 163)
12:54:21.136 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_81.tsv (120 / 163)
12:54:21.356 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_82.tsv (121 / 163)
12:54:21.558 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_83.tsv (122 / 163)
12:54:21.772 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_87.tsv (123 / 163)
12:54:21.962 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_90.tsv (124 / 163)
12:54:22.157 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4446_91.tsv (125 / 163)
12:54:22.383 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_01.tsv (126 / 163)
12:54:22.586 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_08.tsv (127 / 163)
12:54:22.811 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_11.tsv (128 / 163)
12:54:23.022 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_13.tsv (129 / 163)
12:54:23.243 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_18.tsv (130 / 163)
12:54:23.462 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_20.tsv (131 / 163)
12:54:23.664 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_23.tsv (132 / 163)
12:54:23.848 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_24.tsv (133 / 163)
12:54:24.046 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_25.tsv (134 / 163)
12:54:24.236 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_27.tsv (135 / 163)
12:54:24.424 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_28.tsv (136 / 163)
12:54:24.609 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_29.tsv (137 / 163)
12:54:24.825 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_31.tsv (138 / 163)
12:54:25.045 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_34.tsv (139 / 163)
12:54:25.241 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_35.tsv (140 / 163)
12:54:25.424 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_46.tsv (141 / 163)
12:54:25.627 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_48.tsv (142 / 163)
12:54:25.802 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_51.tsv (143 / 163)
12:54:25.986 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_52.tsv (144 / 163)
12:54:26.180 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_55.tsv (145 / 163)
12:54:26.374 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_58.tsv (146 / 163)
12:54:26.563 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_63.tsv (147 / 163)
12:54:26.770 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_65.tsv (148 / 163)
12:54:26.990 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_66.tsv (149 / 163)
12:54:27.218 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_67.tsv (150 / 163)
12:54:27.421 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_69.tsv (151 / 163)
12:54:27.599 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_70.tsv (152 / 163)
12:54:27.809 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_74.tsv (153 / 163)
12:54:27.991 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_75.tsv (154 / 163)
12:54:28.197 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_76.tsv (155 / 163)
12:54:28.388 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_77.tsv (156 / 163)
12:54:28.588 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_78.tsv (157 / 163)
12:54:28.796 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_82.tsv (158 / 163)
12:54:28.995 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_85.tsv (159 / 163)
12:54:29.197 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_86.tsv (160 / 163)
12:54:29.388 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_91.tsv (161 / 163)
12:54:29.570 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_92.tsv (162 / 163)
12:54:29.769 INFO  GermlineCNVCaller - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_female/tsv/PG4482_93.tsv (163 / 163)
12:54:29.984 DEBUG ScriptExecutor - Executing:
12:54:29.984 DEBUG ScriptExecutor -   python
12:54:29.984 DEBUG ScriptExecutor -   /tmp/cohort_denoising_calling.7897284268644721648.py
12:54:29.984 DEBUG ScriptExecutor -   --ploidy_calls_path=/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/human_genome_analysis/cnv/analysis_female/ploidy-calls
12:54:29.984 DEBUG ScriptExecutor -   --output_calls_path=/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/human_genome_analysis/cnv/analysis_female/cohort_female/cohort_female_01-calls
12:54:29.985 DEBUG ScriptExecutor -   --output_tracking_path=/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/human_genome_analysis/cnv/analysis_female/cohort_female/cohort_female_01-tracking
12:54:29.985 DEBUG ScriptExecutor -   --random_seed=1984
12:54:29.985 DEBUG ScriptExecutor -   --modeling_interval_list=/tmp/intervals6686287929758062705.tsv
12:54:29.985 DEBUG ScriptExecutor -   --output_model_path=/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/human_genome_analysis/cnv/analysis_female/cohort_female/cohort_female_01-model
12:54:29.985 DEBUG ScriptExecutor -   --enable_explicit_gc_bias_modeling=True
12:54:29.985 DEBUG ScriptExecutor -   --read_count_tsv_files
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_04_L000.rc3951587632584113947.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_13_L000.rc2817140940332361158.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_17_L000.rc1353160991793239294.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_20_L000.rc5443290680079975178.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_23_L000.rc4202726641846501882.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_24_L000.rc3844372011522155562.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_25_L000.rc4211871239448496430.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_27_L000.rc2078571147927776793.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_29_L000.rc2312984411399163832.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_30_L000.rc2671859470812939841.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_31_L000.rc8131997912022436685.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_32_L000.rc5425924761380826027.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_36_L000.rc6077081999421275427.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_41_L000.rc4638880017656916034.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_47_L000.rc2179592229410555594.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_49_L000.rc4821910718672553988.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_56_L000.rc3585817649894912371.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_59_L000.rc4331814691458776405.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_60_L000.rc8417982606093213458.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_64_L000.rc6668246980776702645.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_67_L000.rc2676667985183619979.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_68_L000.rc1794788848788372038.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_85_L000.rc9042912601102939235.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_HN7448_01_a_86_L000.rc2652207305853661414.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_05_L000.rc1111206176752049324.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_07_L000.rc7105431395795554091.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_09_L000.rc5428672356749640673.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_18_L000.rc8229478461003434380.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_20_L000.rc4810986761376980399.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_28_L000.rc2384284316666061771.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_32_L000.rc7861634724068653184.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_34_L000.rc4204853300704529512.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_35_L000.rc6844750191396362839.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_39_L000.rc8002672096565237796.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_41_L000.rc1137860610266666648.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_44_L000.rc3171143126262253794.tsv
12:54:29.985 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_50_L000.rc7011748867762950617.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_56_L000.rc2753646992781650104.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_57_L000.rc606489262117838130.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_59_L000.rc851684893997579592.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_63_L000.rc7169492100184240653.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_73_L000.rc2787351745864609149.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_78_L000.rc5716756861494644029.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_92_L000.rc2137441952589913936.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/MACROGENS_JN6556_01_a_95_L000.rc8696648545731031379.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_07_L001.rc8092308563994820453.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_15_L001.rc613253478399407214.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_16_L001.rc9118660059916664518.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_23_L001.rc6773583503002125141.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_25_L001.rc2029164227123734817.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_31_L001.rc1672437625058768986.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_37_L001.rc5011170813985009137.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_43_L001.rc214536849684356150.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_45_L001.rc2088461843657343218.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_46_L001.rc6608157904977623379.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_48_L001.rc8397835078346418111.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_50_L001.rc7088661352140005377.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_56_L001.rc7516295595985160954.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_58_L001.rc1633620828004506686.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNWKVDSXY_PG4100_01_a_60_L001.rc3459926246738767901.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_03_L004.rc1544699126476654640.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_11_L004.rc8701139391591637730.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_16_L004.rc7265091205097035653.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_17_L004.rc7078160573973872162.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_21_L004.rc3384115793271128925.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_23_L004.rc4272558804190696863.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_29_L004.rc3406270535943325188.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_30_L004.rc8880942446235540722.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_33_L004.rc5787789947556885395.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_34_L004.rc8254006981823894376.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_41_L004.rc777724503250344569.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_43_L004.rc810086566455872122.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_52_L004.rc5294500601568685380.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_55_L004.rc594815798861214391.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_58_L004.rc6870952332611476492.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_61_L004.rc7305346801297675488.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_73_L004.rc7618359998248316828.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_77_L004.rc8801102784041877120.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_90_L004.rc8543182381532340835.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HNCCFDSXY_PG4213_01_a_96_L004.rc5613757984559731531.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_02_L003.rc9060982360343357017.tsv
12:54:29.986 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_07_L003.rc5679251610922898999.tsv
12:54:29.987 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_09_L003.rc5275868109922003313.tsv
12:54:29.987 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_10_L003.rc1366773845716946573.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_11_L003.rc8232290981762080452.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_12_L003.rc8339345692048573300.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_19_L003.rc5900047828306812145.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_21_L003.rc8156377833835540728.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_23_L003.rc42959568866036864.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_26_L003.rc8434713712820844094.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_28_L003.rc7203215237348512062.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_29_L003.rc4674770261106361504.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_30_L003.rc5322389575874734115.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_32_L003.rc8927967894789378203.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_35_L003.rc4860503731074248210.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_39_L003.rc7508312406042017413.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_40_L003.rc5262387860669136438.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_42_L003.rc949798095708877936.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_45_L003.rc974578986510147550.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_46_L003.rc2731204219838229404.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_62_L003.rc6031131594467053610.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_65_L003.rc5686231609551740393.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_80_L003.rc3797688145367021518.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_91_L003.rc6633033096651079038.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HYNWKDSXY_PG4344_01_a_93_L003.rc4068784655326701496.tsv
12:54:29.988 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_06_L003.rc75171311512305807.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_20_L003.rc8428199540919941009.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_28_L003.rc2454938050462352339.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_29_L003.rc6715947823202456266.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_37_L003.rc9177288614149244615.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_39_L003.rc8536316557077026286.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_46_L003.rc4038707486176834177.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_50_L003.rc1108725580972503433.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_53_L003.rc7966930746639168897.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_58_L003.rc7787918230122445158.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_60_L003.rc1745017445525676236.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_61_L003.rc1203992529574252929.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_65_L003.rc5355240559784398903.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_71_L003.rc6019297211299163794.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_81_L003.rc7438880056592234431.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_82_L003.rc8395282881772400033.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_83_L003.rc725100834105174829.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_87_L003.rc2310637225307992510.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_90_L003.rc8185573960692241242.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HL2WFDSX2_PG4446_01_a_91_L003.rc8721216208246830813.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_01_L002.rc4096525963468523075.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_08_L002.rc3877077002371659090.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_11_L002.rc2864445185458197198.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_13_L002.rc6766590653864943389.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_18_L002.rc6783546502924137756.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_20_L002.rc2668835601045195742.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_23_L002.rc27479877263449498.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_24_L002.rc8623004488533807753.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_25_L002.rc8928435576344215912.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_27_L002.rc821493315693280621.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_28_L002.rc315728919931511944.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_29_L002.rc2245488671200137356.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_31_L002.rc7536102176033986039.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_34_L002.rc7204601429431029134.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_35_L002.rc8163812312182142292.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_46_L002.rc3896110869651005079.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_48_L002.rc3846189428458233717.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_51_L002.rc3976483851212626670.tsv
12:54:29.989 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_52_L002.rc4555755135723076219.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_55_L002.rc5517749886337105144.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_58_L002.rc4550622138560177470.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_63_L002.rc4752717824772712822.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_65_L002.rc139534854162955232.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_66_L002.rc842027218534683306.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_67_L002.rc4597135044764632167.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_69_L002.rc6048306688849017341.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_70_L002.rc6517226226529420061.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_74_L002.rc196572769228029819.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_75_L002.rc490116393549817957.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_76_L002.rc4277028080765178474.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_77_L002.rc7367174451648432877.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_78_L002.rc916503889335873182.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_82_L002.rc8944143391850314976.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_85_L002.rc667154302528512491.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_86_L002.rc5008187721685497393.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_91_L002.rc7011770976962256032.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_92_L002.rc5255433541987261995.tsv
12:54:29.990 DEBUG ScriptExecutor -   /tmp/HMCJWDSX2_PG4482_01_a_93_L002.rc6396810383002884095.tsv
12:54:29.990 DEBUG ScriptExecutor -   --psi_s_scale=1.000000e-04
12:54:29.990 DEBUG ScriptExecutor -   --mapping_error_rate=1.000000e-02
12:54:29.990 DEBUG ScriptExecutor -   --depth_correction_tau=1.000000e+04
12:54:29.990 DEBUG ScriptExecutor -   --q_c_expectation_mode=hybrid
12:54:29.990 DEBUG ScriptExecutor -   --num_samples_copy_ratio_approx=200
12:54:29.990 DEBUG ScriptExecutor -   --max_bias_factors=5
12:54:29.990 DEBUG ScriptExecutor -   --psi_t_scale=1.000000e-03
12:54:29.990 DEBUG ScriptExecutor -   --log_mean_bias_std=1.000000e-01
12:54:29.990 DEBUG ScriptExecutor -   --init_ard_rel_unexplained_variance=1.000000e-01
12:54:29.990 DEBUG ScriptExecutor -   --num_gc_bins=20
12:54:29.990 DEBUG ScriptExecutor -   --gc_curve_sd=1.000000e+00
12:54:29.990 DEBUG ScriptExecutor -   --active_class_padding_hybrid_mode=50000
12:54:29.990 DEBUG ScriptExecutor -   --enable_bias_factors=True
12:54:29.990 DEBUG ScriptExecutor -   --disable_bias_factors_in_active_class=False
12:54:29.990 DEBUG ScriptExecutor -   --p_alt=1.000000e-06
12:54:29.990 DEBUG ScriptExecutor -   --cnv_coherence_length=1.000000e+04
12:54:29.990 DEBUG ScriptExecutor -   --max_copy_number=5
12:54:29.990 DEBUG ScriptExecutor -   --p_active=0.010000
12:54:29.990 DEBUG ScriptExecutor -   --class_coherence_length=10000.000000
12:54:29.990 DEBUG ScriptExecutor -   --learning_rate=1.000000e-02
12:54:29.990 DEBUG ScriptExecutor -   --adamax_beta1=9.000000e-01
12:54:29.990 DEBUG ScriptExecutor -   --adamax_beta2=9.900000e-01
12:54:29.990 DEBUG ScriptExecutor -   --log_emission_samples_per_round=50
12:54:29.990 DEBUG ScriptExecutor -   --log_emission_sampling_rounds=10
12:54:29.990 DEBUG ScriptExecutor -   --log_emission_sampling_median_rel_error=5.000000e-03
12:54:29.990 DEBUG ScriptExecutor -   --max_advi_iter_first_epoch=5000
12:54:29.990 DEBUG ScriptExecutor -   --max_advi_iter_subsequent_epochs=200
12:54:29.990 DEBUG ScriptExecutor -   --min_training_epochs=10
12:54:29.990 DEBUG ScriptExecutor -   --max_training_epochs=50
12:54:29.990 DEBUG ScriptExecutor -   --initial_temperature=1.500000e+00
12:54:29.990 DEBUG ScriptExecutor -   --num_thermal_advi_iters=2500
12:54:29.990 DEBUG ScriptExecutor -   --convergence_snr_averaging_window=500
12:54:29.990 DEBUG ScriptExecutor -   --convergence_snr_trigger_threshold=1.000000e-01
12:54:29.990 DEBUG ScriptExecutor -   --convergence_snr_countdown_window=10
12:54:29.990 DEBUG ScriptExecutor -   --max_calling_iters=10
12:54:29.990 DEBUG ScriptExecutor -   --caller_update_convergence_threshold=1.000000e-03
12:54:29.991 DEBUG ScriptExecutor -   --caller_internal_admixing_rate=7.500000e-01
12:54:29.991 DEBUG ScriptExecutor -   --caller_external_admixing_rate=1.000000e+00
12:54:29.991 DEBUG ScriptExecutor -   --disable_caller=false
12:54:29.991 DEBUG ScriptExecutor -   --disable_sampler=false
12:54:29.991 DEBUG ScriptExecutor -   --disable_annealing=false
13:23:10.459 INFO  GermlineCNVCaller - Shutting down engine
[2022/04/22 13:23:10 JST] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 31.13 minutes.
Runtime.totalMemory()=6227755008
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
python exited with 135
Command Line: python /tmp/cohort_denoising_calling.7897284268644721648.py --ploidy_calls_path=/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/human_genome_analysis/cnv/analysis_female/ploidy-calls --output_calls_path=/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/human_genome_analysis/cnv/analysis_female/cohort_female/cohort_female_01-calls --output_tracking_path=/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/human_genome_analysis/cnv/analysis_female/cohort_female/cohort_female_01-tracking --random_seed=1984 --modeling_interval_list=/tmp/intervals6686287929758062705.tsv --output_model_path=/rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/human_genome_analysis/cnv/analysis_female/cohort_female/cohort_female_01-model --enable_explicit_gc_bias_modeling=True --read_count_tsv_files /tmp/MACROGENS_HN7448_01_a_04_L000.rc3951587632584113947.tsv /tmp/MACROGENS_HN7448_01_a_13_L000.rc2817140940332361158.tsv /tmp/MACROGENS_HN7448_01_a_17_L000.rc1353160991793239294.tsv /tmp/MACROGENS_HN7448_01_a_20_L000.rc5443290680079975178.tsv /tmp/MACROGENS_HN7448_01_a_23_L000.rc4202726641846501882.tsv /tmp/MACROGENS_HN7448_01_a_24_L000.rc3844372011522155562.tsv /tmp/MACROGENS_HN7448_01_a_25_L000.rc4211871239448496430.tsv /tmp/MACROGENS_HN7448_01_a_27_L000.rc2078571147927776793.tsv /tmp/MACROGENS_HN7448_01_a_29_L000.rc2312984411399163832.tsv /tmp/MACROGENS_HN7448_01_a_30_L000.rc2671859470812939841.tsv /tmp/MACROGENS_HN7448_01_a_31_L000.rc8131997912022436685.tsv /tmp/MACROGENS_HN7448_01_a_32_L000.rc5425924761380826027.tsv /tmp/MACROGENS_HN7448_01_a_36_L000.rc6077081999421275427.tsv /tmp/MACROGENS_HN7448_01_a_41_L000.rc4638880017656916034.tsv /tmp/MACROGENS_HN7448_01_a_47_L000.rc2179592229410555594.tsv /tmp/MACROGENS_HN7448_01_a_49_L000.rc4821910718672553988.tsv /tmp/MACROGENS_HN7448_01_a_56_L000.rc3585817649894912371.tsv /tmp/MACROGENS_HN7448_01_a_59_L000.rc4331814691458776405.tsv /tmp/MACROGENS_HN7448_01_a_60_L000.rc8417982606093213458.tsv /tmp/MACROGENS_HN7448_01_a_64_L000.rc6668246980776702645.tsv /tmp/MACROGENS_HN7448_01_a_67_L000.rc2676667985183619979.tsv /tmp/MACROGENS_HN7448_01_a_68_L000.rc1794788848788372038.tsv /tmp/MACROGENS_HN7448_01_a_85_L000.rc9042912601102939235.tsv /tmp/MACROGENS_HN7448_01_a_86_L000.rc2652207305853661414.tsv /tmp/MACROGENS_JN6556_01_a_05_L000.rc1111206176752049324.tsv /tmp/MACROGENS_JN6556_01_a_07_L000.rc7105431395795554091.tsv /tmp/MACROGENS_JN6556_01_a_09_L000.rc5428672356749640673.tsv /tmp/MACROGENS_JN6556_01_a_18_L000.rc8229478461003434380.tsv /tmp/MACROGENS_JN6556_01_a_20_L000.rc4810986761376980399.tsv /tmp/MACROGENS_JN6556_01_a_28_L000.rc2384284316666061771.tsv /tmp/MACROGENS_JN6556_01_a_32_L000.rc7861634724068653184.tsv /tmp/MACROGENS_JN6556_01_a_34_L000.rc4204853300704529512.tsv /tmp/MACROGENS_JN6556_01_a_35_L000.rc6844750191396362839.tsv /tmp/MACROGENS_JN6556_01_a_39_L000.rc8002672096565237796.tsv /tmp/MACROGENS_JN6556_01_a_41_L000.rc1137860610266666648.tsv /tmp/MACROGENS_JN6556_01_a_44_L000.rc3171143126262253794.tsv /tmp/MACROGENS_JN6556_01_a_50_L000.rc7011748867762950617.tsv /tmp/MACROGENS_JN6556_01_a_56_L000.rc2753646992781650104.tsv /tmp/MACROGENS_JN6556_01_a_57_L000.rc606489262117838130.tsv /tmp/MACROGENS_JN6556_01_a_59_L000.rc851684893997579592.tsv /tmp/MACROGENS_JN6556_01_a_63_L000.rc7169492100184240653.tsv /tmp/MACROGENS_JN6556_01_a_73_L000.rc2787351745864609149.tsv /tmp/MACROGENS_JN6556_01_a_78_L000.rc5716756861494644029.tsv /tmp/MACROGENS_JN6556_01_a_92_L000.rc2137441952589913936.tsv /tmp/MACROGENS_JN6556_01_a_95_L000.rc8696648545731031379.tsv /tmp/HNWKVDSXY_PG4100_01_a_07_L001.rc8092308563994820453.tsv /tmp/HNWKVDSXY_PG4100_01_a_15_L001.rc613253478399407214.tsv /tmp/HNWKVDSXY_PG4100_01_a_16_L001.rc9118660059916664518.tsv /tmp/HNWKVDSXY_PG4100_01_a_23_L001.rc6773583503002125141.tsv /tmp/HNWKVDSXY_PG4100_01_a_25_L001.rc2029164227123734817.tsv /tmp/HNWKVDSXY_PG4100_01_a_31_L001.rc1672437625058768986.tsv /tmp/HNWKVDSXY_PG4100_01_a_37_L001.rc5011170813985009137.tsv /tmp/HNWKVDSXY_PG4100_01_a_43_L001.rc214536849684356150.tsv /tmp/HNWKVDSXY_PG4100_01_a_45_L001.rc2088461843657343218.tsv /tmp/HNWKVDSXY_PG4100_01_a_46_L001.rc6608157904977623379.tsv /tmp/HNWKVDSXY_PG4100_01_a_48_L001.rc8397835078346418111.tsv /tmp/HNWKVDSXY_PG4100_01_a_50_L001.rc7088661352140005377.tsv /tmp/HNWKVDSXY_PG4100_01_a_56_L001.rc7516295595985160954.tsv /tmp/HNWKVDSXY_PG4100_01_a_58_L001.rc1633620828004506686.tsv /tmp/HNWKVDSXY_PG4100_01_a_60_L001.rc3459926246738767901.tsv /tmp/HNCCFDSXY_PG4213_01_a_03_L004.rc1544699126476654640.tsv /tmp/HNCCFDSXY_PG4213_01_a_11_L004.rc8701139391591637730.tsv /tmp/HNCCFDSXY_PG4213_01_a_16_L004.rc7265091205097035653.tsv /tmp/HNCCFDSXY_PG4213_01_a_17_L004.rc7078160573973872162.tsv /tmp/HNCCFDSXY_PG4213_01_a_21_L004.rc3384115793271128925.tsv /tmp/HNCCFDSXY_PG4213_01_a_23_L004.rc4272558804190696863.tsv /tmp/HNCCFDSXY_PG4213_01_a_29_L004.rc3406270535943325188.tsv /tmp/HNCCFDSXY_PG4213_01_a_30_L004.rc8880942446235540722.tsv /tmp/HNCCFDSXY_PG4213_01_a_33_L004.rc5787789947556885395.tsv /tmp/HNCCFDSXY_PG4213_01_a_34_L004.rc8254006981823894376.tsv /tmp/HNCCFDSXY_PG4213_01_a_41_L004.rc777724503250344569.tsv /tmp/HNCCFDSXY_PG4213_01_a_43_L004.rc810086566455872122.tsv /tmp/HNCCFDSXY_PG4213_01_a_52_L004.rc5294500601568685380.tsv /tmp/HNCCFDSXY_PG4213_01_a_55_L004.rc594815798861214391.tsv /tmp/HNCCFDSXY_PG4213_01_a_58_L004.rc6870952332611476492.tsv /tmp/HNCCFDSXY_PG4213_01_a_61_L004.rc7305346801297675488.tsv /tmp/HNCCFDSXY_PG4213_01_a_73_L004.rc7618359998248316828.tsv /tmp/HNCCFDSXY_PG4213_01_a_77_L004.rc8801102784041877120.tsv /tmp/HNCCFDSXY_PG4213_01_a_90_L004.rc8543182381532340835.tsv /tmp/HNCCFDSXY_PG4213_01_a_96_L004.rc5613757984559731531.tsv /tmp/HYNWKDSXY_PG4344_01_a_02_L003.rc9060982360343357017.tsv /tmp/HYNWKDSXY_PG4344_01_a_07_L003.rc5679251610922898999.tsv /tmp/HYNWKDSXY_PG4344_01_a_09_L003.rc5275868109922003313.tsv /tmp/HYNWKDSXY_PG4344_01_a_10_L003.rc1366773845716946573.tsv /tmp/HYNWKDSXY_PG4344_01_a_11_L003.rc8232290981762080452.tsv /tmp/HYNWKDSXY_PG4344_01_a_12_L003.rc8339345692048573300.tsv /tmp/HYNWKDSXY_PG4344_01_a_19_L003.rc5900047828306812145.tsv /tmp/HYNWKDSXY_PG4344_01_a_21_L003.rc8156377833835540728.tsv /tmp/HYNWKDSXY_PG4344_01_a_23_L003.rc42959568866036864.tsv /tmp/HYNWKDSXY_PG4344_01_a_26_L003.rc8434713712820844094.tsv /tmp/HYNWKDSXY_PG4344_01_a_28_L003.rc7203215237348512062.tsv /tmp/HYNWKDSXY_PG4344_01_a_29_L003.rc4674770261106361504.tsv /tmp/HYNWKDSXY_PG4344_01_a_30_L003.rc5322389575874734115.tsv /tmp/HYNWKDSXY_PG4344_01_a_32_L003.rc8927967894789378203.tsv /tmp/HYNWKDSXY_PG4344_01_a_35_L003.rc4860503731074248210.tsv /tmp/HYNWKDSXY_PG4344_01_a_39_L003.rc7508312406042017413.tsv /tmp/HYNWKDSXY_PG4344_01_a_40_L003.rc5262387860669136438.tsv /tmp/HYNWKDSXY_PG4344_01_a_42_L003.rc949798095708877936.tsv /tmp/HYNWKDSXY_PG4344_01_a_45_L003.rc974578986510147550.tsv /tmp/HYNWKDSXY_PG4344_01_a_46_L003.rc2731204219838229404.tsv /tmp/HYNWKDSXY_PG4344_01_a_62_L003.rc6031131594467053610.tsv /tmp/HYNWKDSXY_PG4344_01_a_65_L003.rc5686231609551740393.tsv /tmp/HYNWKDSXY_PG4344_01_a_80_L003.rc3797688145367021518.tsv /tmp/HYNWKDSXY_PG4344_01_a_91_L003.rc6633033096651079038.tsv /tmp/HYNWKDSXY_PG4344_01_a_93_L003.rc4068784655326701496.tsv /tmp/HL2WFDSX2_PG4446_01_a_06_L003.rc75171311512305807.tsv /tmp/HL2WFDSX2_PG4446_01_a_20_L003.rc8428199540919941009.tsv /tmp/HL2WFDSX2_PG4446_01_a_28_L003.rc2454938050462352339.tsv /tmp/HL2WFDSX2_PG4446_01_a_29_L003.rc6715947823202456266.tsv /tmp/HL2WFDSX2_PG4446_01_a_37_L003.rc9177288614149244615.tsv /tmp/HL2WFDSX2_PG4446_01_a_39_L003.rc8536316557077026286.tsv /tmp/HL2WFDSX2_PG4446_01_a_46_L003.rc4038707486176834177.tsv /tmp/HL2WFDSX2_PG4446_01_a_50_L003.rc1108725580972503433.tsv /tmp/HL2WFDSX2_PG4446_01_a_53_L003.rc7966930746639168897.tsv /tmp/HL2WFDSX2_PG4446_01_a_58_L003.rc7787918230122445158.tsv /tmp/HL2WFDSX2_PG4446_01_a_60_L003.rc1745017445525676236.tsv /tmp/HL2WFDSX2_PG4446_01_a_61_L003.rc1203992529574252929.tsv /tmp/HL2WFDSX2_PG4446_01_a_65_L003.rc5355240559784398903.tsv /tmp/HL2WFDSX2_PG4446_01_a_71_L003.rc6019297211299163794.tsv /tmp/HL2WFDSX2_PG4446_01_a_81_L003.rc7438880056592234431.tsv /tmp/HL2WFDSX2_PG4446_01_a_82_L003.rc8395282881772400033.tsv /tmp/HL2WFDSX2_PG4446_01_a_83_L003.rc725100834105174829.tsv /tmp/HL2WFDSX2_PG4446_01_a_87_L003.rc2310637225307992510.tsv /tmp/HL2WFDSX2_PG4446_01_a_90_L003.rc8185573960692241242.tsv /tmp/HL2WFDSX2_PG4446_01_a_91_L003.rc8721216208246830813.tsv /tmp/HMCJWDSX2_PG4482_01_a_01_L002.rc4096525963468523075.tsv /tmp/HMCJWDSX2_PG4482_01_a_08_L002.rc3877077002371659090.tsv /tmp/HMCJWDSX2_PG4482_01_a_11_L002.rc2864445185458197198.tsv /tmp/HMCJWDSX2_PG4482_01_a_13_L002.rc6766590653864943389.tsv /tmp/HMCJWDSX2_PG4482_01_a_18_L002.rc6783546502924137756.tsv /tmp/HMCJWDSX2_PG4482_01_a_20_L002.rc2668835601045195742.tsv /tmp/HMCJWDSX2_PG4482_01_a_23_L002.rc27479877263449498.tsv /tmp/HMCJWDSX2_PG4482_01_a_24_L002.rc8623004488533807753.tsv /tmp/HMCJWDSX2_PG4482_01_a_25_L002.rc8928435576344215912.tsv /tmp/HMCJWDSX2_PG4482_01_a_27_L002.rc821493315693280621.tsv /tmp/HMCJWDSX2_PG4482_01_a_28_L002.rc315728919931511944.tsv /tmp/HMCJWDSX2_PG4482_01_a_29_L002.rc2245488671200137356.tsv /tmp/HMCJWDSX2_PG4482_01_a_31_L002.rc7536102176033986039.tsv /tmp/HMCJWDSX2_PG4482_01_a_34_L002.rc7204601429431029134.tsv /tmp/HMCJWDSX2_PG4482_01_a_35_L002.rc8163812312182142292.tsv /tmp/HMCJWDSX2_PG4482_01_a_46_L002.rc3896110869651005079.tsv /tmp/HMCJWDSX2_PG4482_01_a_48_L002.rc3846189428458233717.tsv /tmp/HMCJWDSX2_PG4482_01_a_51_L002.rc3976483851212626670.tsv /tmp/HMCJWDSX2_PG4482_01_a_52_L002.rc4555755135723076219.tsv /tmp/HMCJWDSX2_PG4482_01_a_55_L002.rc5517749886337105144.tsv /tmp/HMCJWDSX2_PG4482_01_a_58_L002.rc4550622138560177470.tsv /tmp/HMCJWDSX2_PG4482_01_a_63_L002.rc4752717824772712822.tsv /tmp/HMCJWDSX2_PG4482_01_a_65_L002.rc139534854162955232.tsv /tmp/HMCJWDSX2_PG4482_01_a_66_L002.rc842027218534683306.tsv /tmp/HMCJWDSX2_PG4482_01_a_67_L002.rc4597135044764632167.tsv /tmp/HMCJWDSX2_PG4482_01_a_69_L002.rc6048306688849017341.tsv /tmp/HMCJWDSX2_PG4482_01_a_70_L002.rc6517226226529420061.tsv /tmp/HMCJWDSX2_PG4482_01_a_74_L002.rc196572769228029819.tsv /tmp/HMCJWDSX2_PG4482_01_a_75_L002.rc490116393549817957.tsv /tmp/HMCJWDSX2_PG4482_01_a_76_L002.rc4277028080765178474.tsv /tmp/HMCJWDSX2_PG4482_01_a_77_L002.rc7367174451648432877.tsv /tmp/HMCJWDSX2_PG4482_01_a_78_L002.rc916503889335873182.tsv /tmp/HMCJWDSX2_PG4482_01_a_82_L002.rc8944143391850314976.tsv /tmp/HMCJWDSX2_PG4482_01_a_85_L002.rc667154302528512491.tsv /tmp/HMCJWDSX2_PG4482_01_a_86_L002.rc5008187721685497393.tsv /tmp/HMCJWDSX2_PG4482_01_a_91_L002.rc7011770976962256032.tsv /tmp/HMCJWDSX2_PG4482_01_a_92_L002.rc5255433541987261995.tsv /tmp/HMCJWDSX2_PG4482_01_a_93_L002.rc6396810383002884095.tsv --psi_s_scale=1.000000e-04 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --num_samples_copy_ratio_approx=200 --max_bias_factors=5 --psi_t_scale=1.000000e-03 --log_mean_bias_std=1.000000e-01 --init_ard_rel_unexplained_variance=1.000000e-01 --num_gc_bins=20 --gc_curve_sd=1.000000e+00 --active_class_padding_hybrid_mode=50000 --enable_bias_factors=True --disable_bias_factors_in_active_class=False --p_alt=1.000000e-06 --cnv_coherence_length=1.000000e+04 --max_copy_number=5 --p_active=0.010000 --class_coherence_length=10000.000000 --learning_rate=1.000000e-02 --adamax_beta1=9.000000e-01 --adamax_beta2=9.900000e-01 --log_emission_samples_per_round=50 --log_emission_sampling_rounds=10 --log_emission_sampling_median_rel_error=5.000000e-03 --max_advi_iter_first_epoch=5000 --max_advi_iter_subsequent_epochs=200 --min_training_epochs=10 --max_training_epochs=50 --initial_temperature=1.500000e+00 --num_thermal_advi_iters=2500 --convergence_snr_averaging_window=500 --convergence_snr_trigger_threshold=1.000000e-01 --convergence_snr_countdown_window=10 --max_calling_iters=10 --caller_update_convergence_threshold=1.000000e-03 --caller_internal_admixing_rate=7.500000e-01 --caller_external_admixing_rate=1.000000e+00 --disable_caller=false --disable_sampler=false --disable_annealing=false
    at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
    at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:351)
    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)
Using GATK jar /rshare1/ZETTAI_path_WA_slash_home_KARA/home/inos0304/modules/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar

 

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