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20 hours ago •
broadinstitute
broadinstitute
GermlineCNVCaller - python exited with 2
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
