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Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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GermlineCNVCaller - python exited with 2 #8938

Open lovelycatZ opened 3 months ago

lovelycatZ commented 3 months ago

Hello,

I'm testing gatk4.3 against 3 WES samples. For less time comsuption, I scattered the bed file into 45 small interval list. But an error prompted out in the GermlineCNVCaller step with the err below:

23:43:52.386 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/hpc/home/lijc/xiangxud/software/miniconda3/envs/gatk4/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:43:52.401 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression16416313594950485777.so
23:43:52.469 INFO  GermlineCNVCaller - ------------------------------------------------------------
23:43:52.469 INFO  GermlineCNVCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0
23:43:52.469 INFO  GermlineCNVCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
23:43:52.470 INFO  GermlineCNVCaller - Executing as xiangxud@cu22 on Linux v3.10.0-1160.el7.x86_64 amd64
23:43:52.470 INFO  GermlineCNVCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.8-internal+0-adhoc..src
23:43:52.470 INFO  GermlineCNVCaller - Start Date/Time: August 3, 2024 at 11:43:52 PM CST
23:43:52.470 INFO  GermlineCNVCaller - ------------------------------------------------------------
23:43:52.470 INFO  GermlineCNVCaller - ------------------------------------------------------------
23:43:52.470 INFO  GermlineCNVCaller - HTSJDK Version: 3.0.1
23:43:52.470 INFO  GermlineCNVCaller - Picard Version: 2.27.5
23:43:52.470 INFO  GermlineCNVCaller - Built for Spark Version: 2.4.5
23:43:52.471 INFO  GermlineCNVCaller - HTSJDK Defaults.BUFFER_SIZE : 131072
23:43:52.471 INFO  GermlineCNVCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:43:52.471 INFO  GermlineCNVCaller - HTSJDK Defaults.CREATE_INDEX : false
23:43:52.471 INFO  GermlineCNVCaller - HTSJDK Defaults.CREATE_MD5 : false
23:43:52.471 INFO  GermlineCNVCaller - HTSJDK Defaults.CUSTOM_READER_FACTORY : 
23:43:52.471 INFO  GermlineCNVCaller - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
23:43:52.471 INFO  GermlineCNVCaller - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
23:43:52.471 INFO  GermlineCNVCaller - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
23:43:52.472 INFO  GermlineCNVCaller - HTSJDK Defaults.REFERENCE_FASTA : null
23:43:52.472 INFO  GermlineCNVCaller - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
23:43:52.472 INFO  GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:43:52.472 INFO  GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:43:52.472 INFO  GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:43:52.472 INFO  GermlineCNVCaller - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
23:43:52.472 DEBUG ConfigFactory - Configuration file values: 
23:43:52.474 DEBUG ConfigFactory -  gcsMaxRetries = 20
23:43:52.474 DEBUG ConfigFactory -  gcsProjectForRequesterPays = 
23:43:52.474 DEBUG ConfigFactory -  gatk_stacktrace_on_user_exception = false
23:43:52.474 DEBUG ConfigFactory -  samjdk.use_async_io_read_samtools = false
23:43:52.474 DEBUG ConfigFactory -  samjdk.use_async_io_write_samtools = true
23:43:52.474 DEBUG ConfigFactory -  samjdk.use_async_io_write_tribble = false
23:43:52.474 DEBUG ConfigFactory -  samjdk.compression_level = 2
23:43:52.474 DEBUG ConfigFactory -  spark.kryoserializer.buffer.max = 512m
23:43:52.474 DEBUG ConfigFactory -  spark.driver.maxResultSize = 0
23:43:52.474 DEBUG ConfigFactory -  spark.driver.userClassPathFirst = true
23:43:52.474 DEBUG ConfigFactory -  spark.io.compression.codec = lzf
23:43:52.474 DEBUG ConfigFactory -  spark.executor.memoryOverhead = 600
23:43:52.475 DEBUG ConfigFactory -  spark.driver.extraJavaOptions = 
23:43:52.475 DEBUG ConfigFactory -  spark.executor.extraJavaOptions = 
23:43:52.475 DEBUG ConfigFactory -  codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
23:43:52.475 DEBUG ConfigFactory -  read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
23:43:52.475 DEBUG ConfigFactory -  annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
23:43:52.477 DEBUG ConfigFactory -  cloudPrefetchBuffer = 40
23:43:52.477 DEBUG ConfigFactory -  cloudIndexPrefetchBuffer = -1
23:43:52.477 DEBUG ConfigFactory -  createOutputBamIndex = true
23:43:52.477 INFO  GermlineCNVCaller - Deflater: IntelDeflater
23:43:52.477 INFO  GermlineCNVCaller - Inflater: IntelInflater
23:43:52.477 INFO  GermlineCNVCaller - GCS max retries/reopens: 20
23:43:52.477 INFO  GermlineCNVCaller - Requester pays: disabled
23:43:52.477 INFO  GermlineCNVCaller - Initializing engine
23:43:52.479 DEBUG ScriptExecutor - Executing:
23:43:52.479 DEBUG ScriptExecutor -   python
23:43:52.479 DEBUG ScriptExecutor -   -c
23:43:52.480 DEBUG ScriptExecutor -   import gcnvkernel

INFO (theano.gof.compilelock): Waiting for existing lock by process '11848' (I am process '19216')
INFO (theano.gof.compilelock): To manually release the lock, delete /gpfs/hpc/home/lijc/xiangxud/.theano/compiledir_Linux-3.10-el7.x86_64-x86_64-with-centos-7.9.2009-Core-x86_64-3.6.10-64/lock_dir
INFO (theano.gof.compilelock): Waiting for existing lock by process '11848' (I am process '19216')
INFO (theano.gof.compilelock): To manually release the lock, delete /gpfs/hpc/home/lijc/xiangxud/.theano/compiledir_Linux-3.10-el7.x86_64-x86_64-with-centos-7.9.2009-Core-x86_64-3.6.10-64/lock_dir
INFO (theano.gof.compilelock): Waiting for existing lock by process '11848' (I am process '19216')
INFO (theano.gof.compilelock): To manually release the lock, delete /gpfs/hpc/home/lijc/xiangxud/.theano/compiledir_Linux-3.10-el7.x86_64-x86_64-with-centos-7.9.2009-Core-x86_64-3.6.10-64/lock_dir
INFO (theano.gof.compilelock): Waiting for existing lock by process '18570' (I am process '19216')
INFO (theano.gof.compilelock): To manually release the lock, delete /gpfs/hpc/home/lijc/xiangxud/.theano/compiledir_Linux-3.10-el7.x86_64-x86_64-with-centos-7.9.2009-Core-x86_64-3.6.10-64/lock_dir
23:44:42.124 DEBUG ScriptExecutor - Result: 0
23:44:42.124 INFO  GermlineCNVCaller - Done initializing engine
23:44:42.126 INFO  GermlineCNVCaller - Intervals specified...
23:44:42.534 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
23:44:42.534 DEBUG GenomeLocParser -  chr1 (248956422 bp)
23:44:42.534 DEBUG GenomeLocParser -  chr2 (242193529 bp)
23:44:42.534 DEBUG GenomeLocParser -  chr3 (198295559 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr4 (190214555 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr5 (181538259 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr6 (170805979 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr7 (159345973 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr8 (145138636 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr9 (138394717 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr10 (133797422 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr11 (135086622 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr12 (133275309 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr13 (114364328 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr14 (107043718 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr15 (101991189 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr16 (90338345 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr17 (83257441 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr18 (80373285 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr19 (58617616 bp)
23:44:42.535 DEBUG GenomeLocParser -  chr20 (64444167 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr21 (46709983 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr22 (50818468 bp)
23:44:42.536 DEBUG GenomeLocParser -  chrX (156040895 bp)
23:44:42.536 DEBUG GenomeLocParser -  chrY (57227415 bp)
23:44:42.536 DEBUG GenomeLocParser -  chrM (16569 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270706v1_random (175055 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270707v1_random (32032 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270708v1_random (127682 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270709v1_random (66860 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270710v1_random (40176 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270711v1_random (42210 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270712v1_random (176043 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270713v1_random (40745 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr1_KI270714v1_random (41717 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr2_KI270715v1_random (161471 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr2_KI270716v1_random (153799 bp)
23:44:42.536 DEBUG GenomeLocParser -  chr3_GL000221v1_random (155397 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr4_GL000008v2_random (209709 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr5_GL000208v1_random (92689 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr9_KI270717v1_random (40062 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr9_KI270718v1_random (38054 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr9_KI270719v1_random (176845 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr9_KI270720v1_random (39050 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr11_KI270721v1_random (100316 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr14_GL000009v2_random (201709 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr14_GL000225v1_random (211173 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr14_KI270722v1_random (194050 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr14_GL000194v1_random (191469 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr14_KI270723v1_random (38115 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr14_KI270724v1_random (39555 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr14_KI270725v1_random (172810 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr14_KI270726v1_random (43739 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr15_KI270727v1_random (448248 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr16_KI270728v1_random (1872759 bp)
23:44:42.537 DEBUG GenomeLocParser -  chr17_GL000205v2_random (185591 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr17_KI270729v1_random (280839 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr17_KI270730v1_random (112551 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270731v1_random (150754 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270732v1_random (41543 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270733v1_random (179772 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270734v1_random (165050 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270735v1_random (42811 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270736v1_random (181920 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270737v1_random (103838 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270738v1_random (99375 bp)
23:44:42.538 DEBUG GenomeLocParser -  chr22_KI270739v1_random (73985 bp)
23:44:42.538 DEBUG GenomeLocParser -  chrY_KI270740v1_random (37240 bp)
23:44:42.538 DEBUG GenomeLocParser -  chrUn_KI270302v1 (2274 bp)
23:44:42.538 DEBUG GenomeLocParser -  chrUn_KI270304v1 (2165 bp)
23:44:42.538 DEBUG GenomeLocParser -  chrUn_KI270303v1 (1942 bp)
23:44:42.538 DEBUG GenomeLocParser -  chrUn_KI270305v1 (1472 bp)
23:44:42.538 DEBUG GenomeLocParser -  chrUn_KI270322v1 (21476 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270320v1 (4416 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270310v1 (1201 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270316v1 (1444 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270315v1 (2276 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270312v1 (998 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270311v1 (12399 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270317v1 (37690 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270412v1 (1179 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270411v1 (2646 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270414v1 (2489 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270419v1 (1029 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270418v1 (2145 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270420v1 (2321 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270424v1 (2140 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270417v1 (2043 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270422v1 (1445 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270423v1 (981 bp)
23:44:42.539 DEBUG GenomeLocParser -  chrUn_KI270425v1 (1884 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270429v1 (1361 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270442v1 (392061 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270466v1 (1233 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270465v1 (1774 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270467v1 (3920 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270435v1 (92983 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270438v1 (112505 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270468v1 (4055 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270510v1 (2415 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270509v1 (2318 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270518v1 (2186 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270508v1 (1951 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270516v1 (1300 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270512v1 (22689 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270519v1 (138126 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270522v1 (5674 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270511v1 (8127 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270515v1 (6361 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270507v1 (5353 bp)
23:44:42.540 DEBUG GenomeLocParser -  chrUn_KI270517v1 (3253 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270529v1 (1899 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270528v1 (2983 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270530v1 (2168 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270539v1 (993 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270538v1 (91309 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270544v1 (1202 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270548v1 (1599 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270583v1 (1400 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270587v1 (2969 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270580v1 (1553 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270581v1 (7046 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270579v1 (31033 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270589v1 (44474 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270590v1 (4685 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270584v1 (4513 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270582v1 (6504 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270588v1 (6158 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270593v1 (3041 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270591v1 (5796 bp)
23:44:42.541 DEBUG GenomeLocParser -  chrUn_KI270330v1 (1652 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270329v1 (1040 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270334v1 (1368 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270333v1 (2699 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270335v1 (1048 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270338v1 (1428 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270340v1 (1428 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270336v1 (1026 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270337v1 (1121 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270363v1 (1803 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270364v1 (2855 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270362v1 (3530 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270366v1 (8320 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270378v1 (1048 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270379v1 (1045 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270389v1 (1298 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270390v1 (2387 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270387v1 (1537 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270395v1 (1143 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270396v1 (1880 bp)
23:44:42.542 DEBUG GenomeLocParser -  chrUn_KI270388v1 (1216 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270394v1 (970 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270386v1 (1788 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270391v1 (1484 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270383v1 (1750 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270393v1 (1308 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270384v1 (1658 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270392v1 (971 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270381v1 (1930 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270385v1 (990 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270382v1 (4215 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270376v1 (1136 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270374v1 (2656 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270372v1 (1650 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270373v1 (1451 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270375v1 (2378 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270371v1 (2805 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270448v1 (7992 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_KI270521v1 (7642 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_GL000195v1 (182896 bp)
23:44:42.543 DEBUG GenomeLocParser -  chrUn_GL000219v1 (179198 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_GL000220v1 (161802 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_GL000224v1 (179693 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270741v1 (157432 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_GL000226v1 (15008 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_GL000213v1 (164239 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270743v1 (210658 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270744v1 (168472 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270745v1 (41891 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270746v1 (66486 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270747v1 (198735 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270748v1 (93321 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270749v1 (158759 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270750v1 (148850 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270751v1 (150742 bp)
23:44:42.544 DEBUG GenomeLocParser -  chrUn_KI270752v1 (27745 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_KI270753v1 (62944 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_KI270754v1 (40191 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_KI270755v1 (36723 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_KI270756v1 (79590 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_KI270757v1 (71251 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_GL000214v1 (137718 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_KI270742v1 (186739 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_GL000216v2 (176608 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrUn_GL000218v1 (161147 bp)
23:44:42.545 DEBUG GenomeLocParser -  chrEBV (171823 bp)
23:44:42.632 INFO  FeatureManager - Using codec IntervalListCodec to read file file:///gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/scatter/scatter_30.interval_list
23:44:42.739 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/scatter/scatter_30.interval_list:/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/scatter/scatter_30.interval_list:
23:44:42.740 DEBUG FeatureCache - Cache hit rate  was 0.00% (0 out of 0 total queries)
23:44:42.743 INFO  IntervalArgumentCollection - Processing 1022379 bp from intervals
23:44:42.756 INFO  GermlineCNVCaller - Reading and validating annotated intervals...
23:44:43.119 INFO  GermlineCNVCaller - GC-content annotations for intervals found; explicit GC-bias correction will be performed...
23:44:43.160 INFO  GermlineCNVCaller - Running the tool in COHORT mode...
23:44:43.160 INFO  GermlineCNVCaller - Validating and aggregating data from input read-count files...
23:44:43.160 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
23:44:43.160 DEBUG GenomeLocParser -  chr1 (248956422 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr2 (242193529 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr3 (198295559 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr4 (190214555 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr5 (181538259 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr6 (170805979 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr7 (159345973 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr8 (145138636 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr9 (138394717 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr10 (133797422 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr11 (135086622 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr12 (133275309 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr13 (114364328 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr14 (107043718 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr15 (101991189 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr16 (90338345 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr17 (83257441 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr18 (80373285 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr19 (58617616 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr20 (64444167 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr21 (46709983 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr22 (50818468 bp)
23:44:43.161 DEBUG GenomeLocParser -  chrX (156040895 bp)
23:44:43.161 DEBUG GenomeLocParser -  chrY (57227415 bp)
23:44:43.161 DEBUG GenomeLocParser -  chrM (16569 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr1_KI270706v1_random (175055 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr1_KI270707v1_random (32032 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr1_KI270708v1_random (127682 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr1_KI270709v1_random (66860 bp)
23:44:43.161 DEBUG GenomeLocParser -  chr1_KI270710v1_random (40176 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr1_KI270711v1_random (42210 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr1_KI270712v1_random (176043 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr1_KI270713v1_random (40745 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr1_KI270714v1_random (41717 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr2_KI270715v1_random (161471 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr2_KI270716v1_random (153799 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr3_GL000221v1_random (155397 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr4_GL000008v2_random (209709 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr5_GL000208v1_random (92689 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr9_KI270717v1_random (40062 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr9_KI270718v1_random (38054 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr9_KI270719v1_random (176845 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr9_KI270720v1_random (39050 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr11_KI270721v1_random (100316 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr14_GL000009v2_random (201709 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr14_GL000225v1_random (211173 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr14_KI270722v1_random (194050 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr14_GL000194v1_random (191469 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr14_KI270723v1_random (38115 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr14_KI270724v1_random (39555 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr14_KI270725v1_random (172810 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr14_KI270726v1_random (43739 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr15_KI270727v1_random (448248 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr16_KI270728v1_random (1872759 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr17_GL000205v2_random (185591 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr17_KI270729v1_random (280839 bp)
23:44:43.162 DEBUG GenomeLocParser -  chr17_KI270730v1_random (112551 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270731v1_random (150754 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270732v1_random (41543 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270733v1_random (179772 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270734v1_random (165050 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270735v1_random (42811 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270736v1_random (181920 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270737v1_random (103838 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270738v1_random (99375 bp)
23:44:43.163 DEBUG GenomeLocParser -  chr22_KI270739v1_random (73985 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrY_KI270740v1_random (37240 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270302v1 (2274 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270304v1 (2165 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270303v1 (1942 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270305v1 (1472 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270322v1 (21476 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270320v1 (4416 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270310v1 (1201 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270316v1 (1444 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270315v1 (2276 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270312v1 (998 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270311v1 (12399 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270317v1 (37690 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270412v1 (1179 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270411v1 (2646 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270414v1 (2489 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270419v1 (1029 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270418v1 (2145 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270420v1 (2321 bp)
23:44:43.163 DEBUG GenomeLocParser -  chrUn_KI270424v1 (2140 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270417v1 (2043 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270422v1 (1445 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270423v1 (981 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270425v1 (1884 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270429v1 (1361 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270442v1 (392061 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270466v1 (1233 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270465v1 (1774 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270467v1 (3920 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270435v1 (92983 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270438v1 (112505 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270468v1 (4055 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270510v1 (2415 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270509v1 (2318 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270518v1 (2186 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270508v1 (1951 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270516v1 (1300 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270512v1 (22689 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270519v1 (138126 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270522v1 (5674 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270511v1 (8127 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270515v1 (6361 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270507v1 (5353 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270517v1 (3253 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270529v1 (1899 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270528v1 (2983 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270530v1 (2168 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270539v1 (993 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270538v1 (91309 bp)
23:44:43.164 DEBUG GenomeLocParser -  chrUn_KI270544v1 (1202 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270548v1 (1599 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270583v1 (1400 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270587v1 (2969 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270580v1 (1553 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270581v1 (7046 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270579v1 (31033 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270589v1 (44474 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270590v1 (4685 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270584v1 (4513 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270582v1 (6504 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270588v1 (6158 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270593v1 (3041 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270591v1 (5796 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270330v1 (1652 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270329v1 (1040 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270334v1 (1368 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270333v1 (2699 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270335v1 (1048 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270338v1 (1428 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270340v1 (1428 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270336v1 (1026 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270337v1 (1121 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270363v1 (1803 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270364v1 (2855 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270362v1 (3530 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270366v1 (8320 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270378v1 (1048 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270379v1 (1045 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270389v1 (1298 bp)
23:44:43.165 DEBUG GenomeLocParser -  chrUn_KI270390v1 (2387 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270387v1 (1537 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270395v1 (1143 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270396v1 (1880 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270388v1 (1216 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270394v1 (970 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270386v1 (1788 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270391v1 (1484 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270383v1 (1750 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270393v1 (1308 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270384v1 (1658 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270392v1 (971 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270381v1 (1930 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270385v1 (990 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270382v1 (4215 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270376v1 (1136 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270374v1 (2656 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270372v1 (1650 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270373v1 (1451 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270375v1 (2378 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270371v1 (2805 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270448v1 (7992 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270521v1 (7642 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_GL000195v1 (182896 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_GL000219v1 (179198 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_GL000220v1 (161802 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_GL000224v1 (179693 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270741v1 (157432 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_GL000226v1 (15008 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_GL000213v1 (164239 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270743v1 (210658 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270744v1 (168472 bp)
23:44:43.166 DEBUG GenomeLocParser -  chrUn_KI270745v1 (41891 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270746v1 (66486 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270747v1 (198735 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270748v1 (93321 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270749v1 (158759 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270750v1 (148850 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270751v1 (150742 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270752v1 (27745 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270753v1 (62944 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270754v1 (40191 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270755v1 (36723 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270756v1 (79590 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270757v1 (71251 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_GL000214v1 (137718 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_KI270742v1 (186739 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_GL000216v2 (176608 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrUn_GL000218v1 (161147 bp)
23:44:43.167 DEBUG GenomeLocParser -  chrEBV (171823 bp)
23:44:43.173 INFO  GermlineCNVCaller - Aggregating read-count file /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/counts/V300033254_96.tsv (1 / 3)
23:44:43.345 INFO  GermlineCNVCaller - Aggregating read-count file /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/counts/V300033256_95.tsv (2 / 3)
23:44:43.521 INFO  GermlineCNVCaller - Aggregating read-count file /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/counts/V300033254_97.tsv (3 / 3)
23:44:43.683 DEBUG ScriptExecutor - Executing:
23:44:43.683 DEBUG ScriptExecutor -   python
23:44:43.683 DEBUG ScriptExecutor -   /tmp/cohort_denoising_calling.6786136740079319091.py
23:44:43.683 DEBUG ScriptExecutor -   --ploidy_calls_path=/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/ploidy/ploidy-calls
23:44:43.683 DEBUG ScriptExecutor -   --output_calls_path=/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/cohort_all/cohort_30-calls
23:44:43.683 DEBUG ScriptExecutor -   --output_tracking_path=/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/cohort_all/cohort_30-tracking
23:44:43.683 DEBUG ScriptExecutor -   --random_seed=1984
23:44:43.683 DEBUG ScriptExecutor -   --modeling_interval_list=/tmp/intervals15539986661449841065.tsv
23:44:43.684 DEBUG ScriptExecutor -   --output_model_path=/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/cohort_all/cohort_30-model
23:44:43.684 DEBUG ScriptExecutor -   --enable_explicit_gc_bias_modeling=True
23:44:43.684 DEBUG ScriptExecutor -   --read_count_tsv_files
23:44:43.684 DEBUG ScriptExecutor -   /tmp/V300033254_96.rc5147399438960401577.tsv
23:44:43.684 DEBUG ScriptExecutor -   /tmp/V300033256_95.rc16057077786486760637.tsv
23:44:43.684 DEBUG ScriptExecutor -   /tmp/V300033254_97.rc18322117796550461836.tsv
23:44:43.684 DEBUG ScriptExecutor -   --psi_s_scale=1.000000e-04
23:44:43.684 DEBUG ScriptExecutor -   --mapping_error_rate=1.000000e-02
23:44:43.684 DEBUG ScriptExecutor -   --depth_correction_tau=1.000000e+04
23:44:43.684 DEBUG ScriptExecutor -   --q_c_expectation_mode=hybrid
23:44:43.684 DEBUG ScriptExecutor -   --num_samples_copy_ratio_approx=200
23:44:43.684 DEBUG ScriptExecutor -   --max_bias_factors=5
23:44:43.684 DEBUG ScriptExecutor -   --psi_t_scale=1.000000e-03
23:44:43.684 DEBUG ScriptExecutor -   --log_mean_bias_std=1.000000e-01
23:44:43.684 DEBUG ScriptExecutor -   --init_ard_rel_unexplained_variance=1.000000e-01
23:44:43.684 DEBUG ScriptExecutor -   --num_gc_bins=20
23:44:43.684 DEBUG ScriptExecutor -   --gc_curve_sd=1.000000e+00
23:44:43.684 DEBUG ScriptExecutor -   --active_class_padding_hybrid_mode=50000
23:44:43.684 DEBUG ScriptExecutor -   --enable_bias_factors=True
23:44:43.684 DEBUG ScriptExecutor -   --disable_bias_factors_in_active_class=False
23:44:43.684 DEBUG ScriptExecutor -   --p_alt=1.000000e-06
23:44:43.684 DEBUG ScriptExecutor -   --cnv_coherence_length=1.000000e+04
23:44:43.684 DEBUG ScriptExecutor -   --max_copy_number=5
23:44:43.684 DEBUG ScriptExecutor -   --p_active=0.010000
23:44:43.684 DEBUG ScriptExecutor -   --class_coherence_length=10000.000000
23:44:43.684 DEBUG ScriptExecutor -   --learning_rate=1.000000e-02
23:44:43.684 DEBUG ScriptExecutor -   --adamax_beta1=9.000000e-01
23:44:43.684 DEBUG ScriptExecutor -   --adamax_beta2=9.900000e-01
23:44:43.684 DEBUG ScriptExecutor -   --log_emission_samples_per_round=50
23:44:43.684 DEBUG ScriptExecutor -   --log_emission_sampling_rounds=10
23:44:43.684 DEBUG ScriptExecutor -   --log_emission_sampling_median_rel_error=5.000000e-03
23:44:43.684 DEBUG ScriptExecutor -   --max_advi_iter_first_epoch=5000
23:44:43.684 DEBUG ScriptExecutor -   --max_advi_iter_subsequent_epochs=200
23:44:43.684 DEBUG ScriptExecutor -   --min_training_epochs=10
23:44:43.684 DEBUG ScriptExecutor -   --max_training_epochs=50
23:44:43.684 DEBUG ScriptExecutor -   --initial_temperature=1.500000e+00
23:44:43.684 DEBUG ScriptExecutor -   --num_thermal_advi_iters=2500
23:44:43.684 DEBUG ScriptExecutor -   --convergence_snr_averaging_window=500
23:44:43.684 DEBUG ScriptExecutor -   --convergence_snr_trigger_threshold=1.000000e-01
23:44:43.684 DEBUG ScriptExecutor -   --convergence_snr_countdown_window=10
23:44:43.685 DEBUG ScriptExecutor -   --max_calling_iters=10
23:44:43.685 DEBUG ScriptExecutor -   --caller_update_convergence_threshold=1.000000e-03
23:44:43.685 DEBUG ScriptExecutor -   --caller_internal_admixing_rate=7.500000e-01
23:44:43.685 DEBUG ScriptExecutor -   --caller_external_admixing_rate=1.000000e+00
23:44:43.685 DEBUG ScriptExecutor -   --disable_caller=false
23:44:43.685 DEBUG ScriptExecutor -   --disable_sampler=false
23:44:43.685 DEBUG ScriptExecutor -   --disable_annealing=false
usage: cohort_denoising_calling.6786136740079319091.py [-h]
                                                       [--console_log_level {INFO,WARNING,DEBUG}]
                                                       [--logfile_log_level {INFO,WARNING,DEBUG}]
                                                       [--logfile str]
                                                       --modeling_interval_list
                                                       str
                                                       --read_count_tsv_files
                                                       str [str ...]
                                                       --ploidy_calls_path str
                                                       --output_model_path str
                                                       --output_calls_path str
                                                       --output_tracking_path
                                                       str
                                                       [--output_opt_path str]
                                                       [--input_model_path str]
                                                       [--input_calls_path str]
                                                       [--input_opt_path str]
                                                       [--max_bias_factors int]
                                                       [--mapping_error_rate float]
                                                       [--psi_t_scale float]
                                                       [--psi_s_scale float]
                                                       [--depth_correction_tau float]
                                                       [--log_mean_bias_std float]
                                                       [--init_ard_rel_unexplained_variance float]
                                                       [--num_gc_bins int]
                                                       [--gc_curve_sd float]
                                                       [--q_c_expectation_mode {map,exact,hybrid}]
                                                       [--active_class_padding_hybrid_mode int]
                                                       [--enable_bias_factors str_to_bool]
                                                       [--enable_explicit_gc_bias_modeling str_to_bool]
                                                       [--disable_bias_factors_in_active_class str_to_bool]
                                                       [--p_alt float]
                                                       [--p_active float]
                                                       [--cnv_coherence_length float]
                                                       [--class_coherence_length float]
                                                       [--max_copy_number int]
                                                       [--num_calling_processes int]
                                                       [--learning_rate float]
                                                       [--adamax_beta1 float]
                                                       [--adamax_beta2 float]
                                                       [--log_emission_samples_per_round int]
                                                       [--log_emission_sampling_median_rel_error float]
                                                       [--log_emission_sampling_rounds int]
                                                       [--max_advi_iter_first_epoch int]
                                                       [--max_advi_iter_subsequent_epochs int]
                                                       [--min_training_epochs int]
                                                       [--max_training_epochs int]
                                                       [--initial_temperature float]
                                                       [--num_thermal_advi_iters int]
                                                       [--convergence_snr_averaging_window int]
                                                       [--convergence_snr_trigger_threshold float]
                                                       [--convergence_snr_countdown_window int]
                                                       [--max_calling_iters int]
                                                       [--caller_update_convergence_threshold float]
                                                       [--caller_internal_admixing_rate float]
                                                       [--caller_external_admixing_rate float]
                                                       [--disable_sampler str_to_bool]
                                                       [--disable_caller str_to_bool]
                                                       [--disable_annealing str_to_bool]
cohort_denoising_calling.6786136740079319091.py: error: unrecognized arguments: --random_seed=1984 --num_samples_copy_ratio_approx=200
23:44:54.590 INFO  GermlineCNVCaller - Shutting down engine
[August 3, 2024 at 11:44:54 PM CST] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 1.04 minutes.
Runtime.totalMemory()=2147483648
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
python exited with 2
Command Line: python /tmp/cohort_denoising_calling.6786136740079319091.py --ploidy_calls_path=/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/ploidy/ploidy-calls --output_calls_path=/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/cohort_all/cohort_30-calls --output_tracking_path=/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/cohort_all/cohort_30-tracking --random_seed=1984 --modeling_interval_list=/tmp/intervals15539986661449841065.tsv --output_model_path=/gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/cohort_all/cohort_30-model --enable_explicit_gc_bias_modeling=True --read_count_tsv_files /tmp/V300033254_96.rc5147399438960401577.tsv /tmp/V300033256_95.rc16057077786486760637.tsv /tmp/V300033254_97.rc18322117796550461836.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 /gpfs/hpc/home/lijc/xiangxud/software/miniconda3/envs/gatk4/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gpfs/hpc/home/lijc/xiangxud/software/miniconda3/envs/gatk4/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar GermlineCNVCaller --run-mode COHORT -L /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/scatter/scatter_30.interval_list -I /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/counts/V300033254_96.tsv -I /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/counts/V300033256_95.tsv -I /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/counts/V300033254_97.tsv --contig-ploidy-calls /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/ploidy/ploidy-calls --annotated-intervals /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/preprocessed.annotated.tsv --interval-merging-rule OVERLAPPING_ONLY --output /gpfs/hpc/home/lijc/xiangxud/project/test/NGS_WES_test/4_tools_vcf/gatk4/info/cohort_all --verbosity DEBUG --output-prefix cohort_30
droazen commented 3 months ago

@lovelycatZ The problem is most likely a mismatch between the version of GATK you're running, and the version of the GCNV kernel installed in your Python environment. Please try running either within the official GATK conda environment distributed with your version of GATK in the gatkcondaenv.yml file, or within the corresponding docker image at https://hub.docker.com/r/broadinstitute/gatk/.