GATK-4.1.0 GermlineCNVCaller error messages

Hello GATK team,

I have followed the instructions to use conda and created the python environment (gatk conda).
DetermineGermlineContigPloidy went through without error messages but GermlineCNVCaller failed with the following error messages (Several uninformative lines were removed due to a character limit in the body). I would be grateful if you can look into this and help me troubleshoot.

Thank you for your time!
Jungmin

===================
Using GATK jar /ycga-ba/ba_sequencers5/scratch/sz97/Mathieu/jc2545/programs/gatk-4.1.0.0/gatk-package-4.1.0.0-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 -Xmx128g -jar /ycga-ba/ba_sequencers5/scratch/sz97/Mathieu/jc2545/programs/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar GermlineCNVCaller --run-mode COHORT -L /home/wd256/references/capture_coverage/xGen_preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY --contig-ploidy-calls output_dir/normal_cohort-calls --input M_18_SRNS246/M_18_SRNS246.counts.hdf5 --input M_18_SRNS249/M_18_SRNS249.counts.hdf5 --input M_18_SRNS254/M_18_SRNS254.counts.hdf5 --input M_18_SRNS255/M_18_SRNS255.counts.hdf5 ...... --output cohort --output-prefix normal_cohort_run --verbosity DEBUG
17:07:20.126 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/ycga-ba/ba_sequencers5/scratch/sz97/Mathieu/jc2545/programs/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
17:07:20.141 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression8865175445466958388.so
17:07:21.809 INFO GermlineCNVCaller - ------------------------------------------------------------
17:07:21.810 INFO GermlineCNVCaller - The Genome Analysis Toolkit (GATK) v4.1.0.0
17:07:21.811 INFO GermlineCNVCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
17:07:21.811 INFO GermlineCNVCaller - Executing as [email protected] on Linux v3.10.0-693.39.1.el7.x86_64 amd64
17:07:21.811 INFO GermlineCNVCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13
17:07:21.811 INFO GermlineCNVCaller - Start Date/Time: February 15, 2019 5:07:20 PM EST
17:07:21.811 INFO GermlineCNVCaller - ------------------------------------------------------------
17:07:21.811 INFO GermlineCNVCaller - ------------------------------------------------------------
17:07:21.812 INFO GermlineCNVCaller - HTSJDK Version: 2.18.2
17:07:21.812 INFO GermlineCNVCaller - Picard Version: 2.18.25
17:07:21.813 INFO GermlineCNVCaller - HTSJDK Defaults.BUFFER_SIZE : 131072
17:07:21.813 INFO GermlineCNVCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:07:21.813 INFO GermlineCNVCaller - HTSJDK Defaults.CREATE_INDEX : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.CREATE_MD5 : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.CUSTOM_READER_FACTORY :
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.REFERENCE_FASTA : null
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
17:07:21.814 DEBUG ConfigFactory - Configuration file values:
17:07:21.818 DEBUG ConfigFactory - gcsMaxRetries = 20
17:07:21.818 DEBUG ConfigFactory - gcsProjectForRequesterPays =
17:07:21.818 DEBUG ConfigFactory - gatk_stacktrace_on_user_exception = false
17:07:21.818 DEBUG ConfigFactory - samjdk.use_async_io_read_samtools = false
17:07:21.819 DEBUG ConfigFactory - samjdk.use_async_io_write_samtools = true
17:07:21.819 DEBUG ConfigFactory - samjdk.use_async_io_write_tribble = false
17:07:21.819 DEBUG ConfigFactory - samjdk.compression_level = 2
17:07:21.819 DEBUG ConfigFactory - spark.kryoserializer.buffer.max = 512m
17:07:21.819 DEBUG ConfigFactory - spark.driver.maxResultSize = 0
17:07:21.819 DEBUG ConfigFactory - spark.driver.userClassPathFirst = true
17:07:21.819 DEBUG ConfigFactory - spark.io.compression.codec = lzf
17:07:21.819 DEBUG ConfigFactory - spark.yarn.executor.memoryOverhead = 600
17:07:21.819 DEBUG ConfigFactory - spark.driver.extraJavaOptions =
17:07:21.819 DEBUG ConfigFactory - spark.executor.extraJavaOptions =
17:07:21.819 DEBUG ConfigFactory - codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
17:07:21.819 DEBUG ConfigFactory - read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
17:07:21.819 DEBUG ConfigFactory - annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
17:07:21.819 DEBUG ConfigFactory - cloudPrefetchBuffer = 40
17:07:21.819 DEBUG ConfigFactory - cloudIndexPrefetchBuffer = -1
17:07:21.819 DEBUG ConfigFactory - createOutputBamIndex = true
17:07:21.819 INFO GermlineCNVCaller - Deflater: IntelDeflater
17:07:21.819 INFO GermlineCNVCaller - Inflater: IntelInflater
17:07:21.820 INFO GermlineCNVCaller - GCS max retries/reopens: 20
17:07:21.820 INFO GermlineCNVCaller - Requester pays: disabled
17:07:21.820 INFO GermlineCNVCaller - Initializing engine
17:07:21.824 DEBUG ScriptExecutor - Executing:
17:07:21.824 DEBUG ScriptExecutor - python
17:07:21.824 DEBUG ScriptExecutor - -c
17:07:21.824 DEBUG ScriptExecutor - import gcnvkernel

17:07:27.074 DEBUG ScriptExecutor - Result: 0
17:07:27.074 INFO GermlineCNVCaller - Done initializing engine
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
17:07:27.511 INFO GermlineCNVCaller - Intervals specified...
17:07:27.512 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
17:07:27.513 DEBUG GenomeLocParser - 1 (249250621 bp)
17:07:27.513 DEBUG GenomeLocParser - 2 (243199373 bp)
.
.
.
17:07:27.521 DEBUG GenomeLocParser - NC_007605 (171823 bp)
17:07:27.521 DEBUG GenomeLocParser - hs37d5 (35477943 bp)
17:07:28.168 INFO IntervalArgumentCollection - Processing 127088123 bp from intervals
17:07:28.260 INFO GermlineCNVCaller - No annotated intervals were provided...
17:07:28.260 INFO GermlineCNVCaller - No GC-content annotations for intervals found; explicit GC-bias correction will not be performed...
17:07:28.440 INFO GermlineCNVCaller - Running the tool in the COHORT mode...
17:07:28.443 INFO GermlineCNVCaller - Validating and aggregating data from input read-count files...
17:07:28.465 INFO GermlineCNVCaller - Aggregating read-count file M_18_SRNS246/M_18_SRNS246.counts.hdf5 (1 / 162)
.
.
.
17:08:07.074 INFO GermlineCNVCaller - Aggregating read-count file M_18_SRNS528/M_18_SRNS528.counts.hdf5 (161 / 162)
17:08:07.334 INFO GermlineCNVCaller - Aggregating read-count file M_18_SRNS531/M_18_SRNS531.counts.hdf5 (162 / 162)
17:08:07.645 DEBUG ScriptExecutor - Executing:
17:08:07.645 DEBUG ScriptExecutor - python
17:08:07.645 DEBUG ScriptExecutor - /tmp/cohort_denoising_calling.9140535429895089708.py
17:08:07.645 DEBUG ScriptExecutor - --ploidy_calls_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/output_dir/normal_cohort-calls
17:08:07.645 DEBUG ScriptExecutor - --output_calls_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-calls
17:08:07.645 DEBUG ScriptExecutor - --output_tracking_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-tracking
17:08:07.645 DEBUG ScriptExecutor - --modeling_interval_list=/tmp/intervals1873462746347841141.tsv
17:08:07.645 DEBUG ScriptExecutor - --output_model_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-model
17:08:07.645 DEBUG ScriptExecutor - --enable_explicit_gc_bias_modeling=False
17:08:07.645 DEBUG ScriptExecutor - --read_count_tsv_files
17:08:07.645 DEBUG ScriptExecutor - /tmp/sample-08612173870077300650.tsv
.
.
.
17:08:07.649 DEBUG ScriptExecutor - /tmp/sample-1605044828027709654690.tsv
17:08:07.649 DEBUG ScriptExecutor - /tmp/sample-1618759982698618716730.tsv
17:08:07.649 DEBUG ScriptExecutor - --psi_s_scale=1.000000e-04
17:08:07.649 DEBUG ScriptExecutor - --mapping_error_rate=1.000000e-02
17:08:07.649 DEBUG ScriptExecutor - --depth_correction_tau=1.000000e+04
17:08:07.649 DEBUG ScriptExecutor - --q_c_expectation_mode=hybrid
17:08:07.649 DEBUG ScriptExecutor - --max_bias_factors=5
17:08:07.649 DEBUG ScriptExecutor - --psi_t_scale=1.000000e-03
17:08:07.649 DEBUG ScriptExecutor - --log_mean_bias_std=1.000000e-01
17:08:07.649 DEBUG ScriptExecutor - --init_ard_rel_unexplained_variance=1.000000e-01
17:08:07.649 DEBUG ScriptExecutor - --num_gc_bins=20
17:08:07.649 DEBUG ScriptExecutor - --gc_curve_sd=1.000000e+00
17:08:07.649 DEBUG ScriptExecutor - --active_class_padding_hybrid_mode=50000
17:08:07.649 DEBUG ScriptExecutor - --enable_bias_factors=True
17:08:07.649 DEBUG ScriptExecutor - --disable_bias_factors_in_active_class=False
17:08:07.649 DEBUG ScriptExecutor - --p_alt=1.000000e-06
17:08:07.649 DEBUG ScriptExecutor - --cnv_coherence_length=1.000000e+04
17:08:07.649 DEBUG ScriptExecutor - --max_copy_number=5
17:08:07.649 DEBUG ScriptExecutor - --p_active=0.010000
17:08:07.649 DEBUG ScriptExecutor - --class_coherence_length=10000.000000
17:08:07.649 DEBUG ScriptExecutor - --learning_rate=1.000000e-02
17:08:07.649 DEBUG ScriptExecutor - --adamax_beta1=9.000000e-01
17:08:07.649 DEBUG ScriptExecutor - --adamax_beta2=9.900000e-01
17:08:07.649 DEBUG ScriptExecutor - --log_emission_samples_per_round=50
17:08:07.649 DEBUG ScriptExecutor - --log_emission_sampling_rounds=10
17:08:07.649 DEBUG ScriptExecutor - --log_emission_sampling_median_rel_error=5.000000e-03
17:08:07.649 DEBUG ScriptExecutor - --max_advi_iter_first_epoch=5000
17:08:07.649 DEBUG ScriptExecutor - --max_advi_iter_subsequent_epochs=200
17:08:07.649 DEBUG ScriptExecutor - --min_training_epochs=10
17:08:07.649 DEBUG ScriptExecutor - --max_training_epochs=50
17:08:07.649 DEBUG ScriptExecutor - --initial_temperature=1.500000e+00
17:08:07.649 DEBUG ScriptExecutor - --num_thermal_advi_iters=2500
17:08:07.649 DEBUG ScriptExecutor - --convergence_snr_averaging_window=500
17:08:07.649 DEBUG ScriptExecutor - --convergence_snr_trigger_threshold=1.000000e-01
17:08:07.649 DEBUG ScriptExecutor - --convergence_snr_countdown_window=10
17:08:07.649 DEBUG ScriptExecutor - --max_calling_iters=10
17:08:07.649 DEBUG ScriptExecutor - --caller_update_convergence_threshold=1.000000e-03
17:08:07.649 DEBUG ScriptExecutor - --caller_internal_admixing_rate=7.500000e-01
17:08:07.649 DEBUG ScriptExecutor - --caller_external_admixing_rate=1.000000e+00
17:08:07.649 DEBUG ScriptExecutor - --disable_caller=false
17:08:07.649 DEBUG ScriptExecutor - --disable_sampler=false
17:08:07.649 DEBUG ScriptExecutor - --disable_annealing=false
17:08:12.398 INFO cohort_denoising_calling - Loading 162 read counts file(s)...
17:09:17.875 INFO gcnvkernel.io.io_metadata - Loading germline contig ploidy and global read depth metadata...
17:09:55.138 INFO gcnvkernel.tasks.task_cohort_denoising_calling - Instantiating the denoising model (warm-up)...
17:11:20.180 DEBUG ScriptExecutor - Result: 137
17:11:20.181 INFO GermlineCNVCaller - Shutting down engine
[February 15, 2019 5:11:20 PM EST] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 4.00 minutes.
Runtime.totalMemory()=6215958528
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 137
Command Line: python /tmp/cohort_denoising_calling.9140535429895089708.py --ploidy_calls_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/output_dir/normal_cohort-calls --output_calls_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-calls --output_tracking_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-tracking --modeling_interval_list=/tmp/intervals1873462746347841141.tsv --output_model_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-model --enable_explicit_gc_bias_modeling=False --read_count_tsv_files /tmp/sample-08612173870077300650.tsv /tmp/sample-1735339145960625744.tsv /tmp/sample-26703446513270382293.tsv /tmp/sample-35095654387556573137.tsv /tmp/sample-4508962434357349017.tsv /tmp/sample-58460077076107805745.tsv /tmp/sample-6346822365711760370.tsv /tmp/sample-779931899134353312.tsv /tmp/sample-85729935362226663368.tsv /tmp/sample-93257389871598688195.tsv /tmp/sample-1072218606651772505.tsv /tmp/sample-115903914088361457664.tsv /tmp/sample-128235238211199814079.tsv /tmp/sample-137679065752903696578.tsv /tmp/sample-141412526288839282934.tsv /tmp/sample-15519292804984449661.tsv /tmp/sample-161709925844501965417.tsv /tmp/sample-178022787663362200778.tsv /tmp/sample-181125070878149098262.tsv /tmp/sample-194410475879134975275.tsv /tmp/sample-202975550643747300134.tsv /tmp/sample-213009004444143467292.tsv /tmp/sample-221306507585077810612.tsv /tmp/sample-23104024448454209175.tsv /tmp/sample-245133022599306993556.tsv /tmp/sample-25703760885613813312.tsv /tmp/sample-2690774459760965725.tsv /tmp/sample-272313888089716707826.tsv /tmp/sample-288176307810148633677.tsv /tmp/sample-298583951421199428278.tsv /tmp/sample-301692991399952820072.tsv /tmp/sample-317809871850313243733.tsv /tmp/sample-322055164835392021676.tsv /tmp/sample-333188910366149161610.tsv /tmp/sample-341776914456585504962.tsv /tmp/sample-351634383534181696381.tsv /tmp/sample-367781395796149922798.tsv /tmp/sample-3786730386469085354.tsv /tmp/sample-38541771839429688936.tsv /tmp/sample-396058667613341997490.tsv /tmp/sample-402602372245250147133.tsv /tmp/sample-415892540111653423405.tsv /tmp/sample-425671650162117618258.tsv /tmp/sample-437903006633261170767.tsv /tmp/sample-446769403661740456540.tsv /tmp/sample-452807940055394133177.tsv /tmp/sample-468546499565823287044.tsv /tmp/sample-476182160432111186420.tsv /tmp/sample-482196176246104993068.tsv /tmp/sample-497349198039999756481.tsv /tmp/sample-504586740136696693330.tsv /tmp/sample-514629760575640679484.tsv /tmp/sample-521518665764093531540.tsv /tmp/sample-536756030759819452871.tsv /tmp/sample-541814208065030512399.tsv /tmp/sample-557100162055020311558.tsv /tmp/sample-565079065285043205969.tsv /tmp/sample-577473774494155677328.tsv /tmp/sample-585211874134149883927.tsv /tmp/sample-597899152893974380925.tsv /tmp/sample-601774703583028171465.tsv /tmp/sample-615352536760798251526.tsv /tmp/sample-621792155083348440834.tsv /tmp/sample-631065348947130549641.tsv /tmp/sample-641985405380622064199.tsv /tmp/sample-656094636503911408494.tsv /tmp/sample-668415912440582797737.tsv /tmp/sample-676403765944041136118.tsv /tmp/sample-682114045166636957457.tsv /tmp/sample-691095858748617845455.tsv /tmp/sample-701898313659570600550.tsv /tmp/sample-711130096990849289842.tsv /tmp/sample-724909857738488305869.tsv /tmp/sample-733566863875273019740.tsv /tmp/sample-742661156055391989719.tsv /tmp/sample-752900828628492970083.tsv /tmp/sample-767092916011092266094.tsv /tmp/sample-772455948557542008819.tsv /tmp/sample-782509489027797761010.tsv /tmp/sample-796805609730974108586.tsv /tmp/sample-80720962641595403888.tsv /tmp/sample-817173783221065650666.tsv /tmp/sample-822940909550498965708.tsv /tmp/sample-837562722826437020179.tsv /tmp/sample-846265161938613290733.tsv /tmp/sample-853171171276815010438.tsv /tmp/sample-864724444930214959966.tsv /tmp/sample-876678275730001959431.tsv /tmp/sample-887626160582818681387.tsv /tmp/sample-898955761009702615630.tsv /tmp/sample-905439922593393958017.tsv /tmp/sample-912745236161870043640.tsv /tmp/sample-926231084901650523858.tsv /tmp/sample-93935170810944919855.tsv /tmp/sample-9431746064262952062.tsv /tmp/sample-958737018321160287907.tsv /tmp/sample-961802987260101727402.tsv /tmp/sample-977416547149949828041.tsv /tmp/sample-983982274875124448216.tsv /tmp/sample-996198735099776825982.tsv /tmp/sample-1009146208583490663068.tsv /tmp/sample-1018845180303163951595.tsv /tmp/sample-1027135342741286447343.tsv /tmp/sample-1035368514901860687723.tsv /tmp/sample-1042754024539983558009.tsv /tmp/sample-105227740940224097784.tsv /tmp/sample-1067796439126398033702.tsv /tmp/sample-1075076104300625983530.tsv /tmp/sample-1088947366823218733850.tsv /tmp/sample-1096165949344136625979.tsv /tmp/sample-110426075258992495633.tsv /tmp/sample-1116508848571389727702.tsv /tmp/sample-112283331488958653414.tsv /tmp/sample-1132751105099775154028.tsv /tmp/sample-1146473447638075601261.tsv /tmp/sample-1157358912004261216235.tsv /tmp/sample-1163478798295512815260.tsv /tmp/sample-1172106693768918595659.tsv /tmp/sample-1188590848153482833118.tsv /tmp/sample-1193162205698457964430.tsv /tmp/sample-1204202944415748120845.tsv /tmp/sample-121773818989999810769.tsv /tmp/sample-1223745408005714103834.tsv /tmp/sample-1236610659701327035424.tsv /tmp/sample-1245760080493734034654.tsv /tmp/sample-1253807306870096529273.tsv /tmp/sample-1264151487267688408608.tsv /tmp/sample-1277214977153055471289.tsv /tmp/sample-1285224338316659715614.tsv /tmp/sample-1292062026162943299330.tsv /tmp/sample-1301363016348073583379.tsv /tmp/sample-131558554732818920155.tsv /tmp/sample-1325754066569823165479.tsv /tmp/sample-1336042767672212270992.tsv /tmp/sample-1343968514112614746127.tsv /tmp/sample-1355546751716954575927.tsv /tmp/sample-136236845290987331012.tsv /tmp/sample-1374816528101346997220.tsv /tmp/sample-1385317851245406091520.tsv /tmp/sample-1391042137054808258316.tsv /tmp/sample-1403742557849491744561.tsv /tmp/sample-1411502587679797062853.tsv /tmp/sample-1424733541746568284028.tsv /tmp/sample-143238400405838309221.tsv /tmp/sample-1441096103849753405535.tsv /tmp/sample-1452666884939739940900.tsv /tmp/sample-1464156055658986985443.tsv /tmp/sample-1472026389278997599086.tsv /tmp/sample-148589445790255766165.tsv /tmp/sample-1497827386382328631572.tsv /tmp/sample-1504915479842211825427.tsv /tmp/sample-1515203597135250209395.tsv /tmp/sample-1528978682591511597058.tsv /tmp/sample-1535467962477746299596.tsv /tmp/sample-1548510164331176337876.tsv /tmp/sample-1552624811099715500627.tsv /tmp/sample-1562605141662085486436.tsv /tmp/sample-1575754839084389129440.tsv /tmp/sample-1583068624308611691335.tsv /tmp/sample-159139367590923153119.tsv /tmp/sample-1605044828027709654690.tsv /tmp/sample-1618759982698618716730.tsv --psi_s_scale=1.000000e-04 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --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.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:126)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:170)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:151)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:121)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.executeGermlineCNVCallerPythonScript(GermlineCNVCaller.java:441)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:288)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)

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