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DetermineGermlineContigPloidy generating error

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Qianru Lenus SUN

REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

gatk DetermineGermlineContigPloidy \
--contig-ploidy-priors /path/contig_ploidy_priors_clean.tsv \
-I /path/A1.hdf5 -I /path/A2.hdf5 \
-O /output/path/folder \
--output-prefix ploidy-case \
--verbosity DEBUG \
1>/output.log 2>&1 && echo "DetermineGermlineContigPloidy done!"

c) Entire program log:

16:05:49.999 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/qianrusun/.conda/envs/gatk_20241213/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
16:05:50.112 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression2170316634369124856.so
16:05:50.534 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
16:05:50.534 INFO  DetermineGermlineContigPloidy - The Genome Analysis Toolkit (GATK) v4.3.0.0
16:05:50.534 INFO  DetermineGermlineContigPloidy - For support and documentation go to https://software.broadinstitute.org/gatk/
16:05:50.534 INFO  DetermineGermlineContigPloidy - Executing as qianrusun@rsee on Linux v5.4.0-198-generic amd64
16:05:50.534 INFO  DetermineGermlineContigPloidy - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_412-b08
16:05:50.535 INFO  DetermineGermlineContigPloidy - Start Date/Time: December 16, 2024 4:05:49 PM HKT
16:05:50.535 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
16:05:50.535 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
16:05:50.535 INFO  DetermineGermlineContigPloidy - HTSJDK Version: 3.0.1
16:05:50.535 INFO  DetermineGermlineContigPloidy - Picard Version: 2.27.5
16:05:50.535 INFO  DetermineGermlineContigPloidy - Built for Spark Version: 2.4.5
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.BUFFER_SIZE : 131072
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_INDEX : false
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_MD5 : false
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CUSTOM_READER_FACTORY : 
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.REFERENCE_FASTA : null
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
16:05:50.538 DEBUG ConfigFactory - Configuration file values: 
16:05:50.542 DEBUG ConfigFactory - gcsMaxRetries = 20
16:05:50.542 DEBUG ConfigFactory - gcsProjectForRequesterPays = 
16:05:50.542 DEBUG ConfigFactory - gatk_stacktrace_on_user_exception = false
16:05:50.542 DEBUG ConfigFactory - samjdk.use_async_io_read_samtools = false
16:05:50.542 DEBUG ConfigFactory - samjdk.use_async_io_write_samtools = true
16:05:50.542 DEBUG ConfigFactory - samjdk.use_async_io_write_tribble = false
16:05:50.542 DEBUG ConfigFactory - samjdk.compression_level = 2
16:05:50.542 DEBUG ConfigFactory - spark.kryoserializer.buffer.max = 512m
16:05:50.542 DEBUG ConfigFactory - spark.driver.maxResultSize = 0
16:05:50.543 DEBUG ConfigFactory - spark.driver.userClassPathFirst = true
16:05:50.543 DEBUG ConfigFactory - spark.io.compression.codec = lzf
16:05:50.543 DEBUG ConfigFactory - spark.executor.memoryOverhead = 600
16:05:50.543 DEBUG ConfigFactory - spark.driver.extraJavaOptions = 
16:05:50.543 DEBUG ConfigFactory - spark.executor.extraJavaOptions = 
16:05:50.543 DEBUG ConfigFactory - codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
16:05:50.543 DEBUG ConfigFactory - read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
16:05:50.543 DEBUG ConfigFactory - annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
16:05:50.543 DEBUG ConfigFactory - cloudPrefetchBuffer = 40
16:05:50.543 DEBUG ConfigFactory - cloudIndexPrefetchBuffer = -1
16:05:50.543 DEBUG ConfigFactory - createOutputBamIndex = true
16:05:50.543 INFO  DetermineGermlineContigPloidy - Deflater: IntelDeflater
16:05:50.543 INFO  DetermineGermlineContigPloidy - Inflater: IntelInflater
16:05:50.543 INFO  DetermineGermlineContigPloidy - GCS max retries/reopens: 20
16:05:50.544 INFO  DetermineGermlineContigPloidy - Requester pays: disabled
16:05:50.544 INFO  DetermineGermlineContigPloidy - Initializing engine
16:05:50.555 DEBUG ScriptExecutor - Executing:
16:05:50.555 DEBUG ScriptExecutor -   python
16:05:50.555 DEBUG ScriptExecutor -   -c
16:05:50.555 DEBUG ScriptExecutor -   import gcnvkernel
 
16:06:06.795 DEBUG ScriptExecutor - Result: 0
16:06:06.795 INFO  DetermineGermlineContigPloidy - Done initializing engine
16:06:06.813 INFO  DetermineGermlineContigPloidy - No contig-ploidy model was provided, running in cohort mode...
16:06:06.813 INFO  DetermineGermlineContigPloidy - Retrieving intervals from read-count file (/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A1.hdf5)...
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
16:06:10.260 INFO  DetermineGermlineContigPloidy - Validating and aggregating coverage per contig from input read-count files...
16:06:10.848 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
16:06:10.849 DEBUG GenomeLocParser -  chr1 (248956422 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr2 (242193529 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr3 (198295559 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr4 (190214555 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr5 (181538259 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr6 (170805979 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr7 (159345973 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr8 (145138636 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr9 (138394717 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr10 (133797422 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr11 (135086622 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr12 (133275309 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr13 (114364328 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr14 (107043718 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr15 (101991189 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr16 (90338345 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr17 (83257441 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr18 (80373285 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr19 (58617616 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr20 (64444167 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr21 (46709983 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr22 (50818468 bp)
16:06:10.850 DEBUG GenomeLocParser -  chrX (156040895 bp)
16:06:10.850 DEBUG GenomeLocParser -  chrY (57227415 bp)
16:06:10.850 DEBUG GenomeLocParser -  chrM (16569 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr1_KI270706v1_random (175055 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr1_KI270707v1_random (32032 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr1_KI270708v1_random (127682 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr1_KI270709v1_random (66860 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr1_KI270710v1_random (40176 bp)
 
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*06:02:01:02 (3349 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*06:02:01:03 (3349 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*06:23 (3349 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*06:24 (3349 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*06:46N (2987 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:01:01:01 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:01:01:02 (3093 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:01:02 (3352 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:01:19 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:01:27 (3195 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:01:45 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:02:01:01 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:02:01:02 (3074 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:02:01:03 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:02:01:04 (3353 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:02:01:05 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:02:05 (2903 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:02:06 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:02:64 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:04:01 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:04:02 (3343 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:06 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:149 (3098 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:18 (3353 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:19 (3222 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:26 (3069 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:30 (2903 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:32N (3334 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:384 (3349 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:385 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:386 (3183 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:391 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:392 (3354 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:49 (2935 bp)
16:06:10.900 DEBUG GenomeLocParser -  HLA-C*07:56:02 (3354 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-C*07:66 (3354 bp)
 
16:06:10.901 DEBUG GenomeLocParser -  HLA-DQB1*05:01:01:01 (7090 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DQB1*05:01:01:02 (7090 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DQB1*05:03:01:01 (7089 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DQB1*05:03:01:02 (7089 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DQB1*06:01:01 (7111 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DQB1*06:02:01 (7102 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DQB1*06:03:01 (7103 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DQB1*06:09:01 (7102 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*01:01:01 (10741 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*01:02:01 (11229 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*03:01:01:01 (13908 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*03:01:01:02 (13426 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*04:03:01 (15246 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*07:01:01:01 (16110 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*07:01:01:02 (16120 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*08:03:02 (13562 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*09:21 (16039 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*10:01:01 (13501 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*11:01:01 (13921 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*11:01:02 (13931 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*11:04:01 (13919 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*12:01:01 (13404 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*12:17 (11260 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*13:01:01 (13935 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*13:02:01 (13941 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*14:05:01 (13933 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*14:54:01 (13936 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*15:01:01:01 (11080 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*15:01:01:02 (11571 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*15:01:01:03 (11056 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*15:01:01:04 (11056 bp)
16:06:10.901 DEBUG GenomeLocParser -  HLA-DRB1*15:02:01 (10313 bp)
16:06:10.902 DEBUG GenomeLocParser -  HLA-DRB1*15:03:01:01 (11567 bp)
16:06:10.902 DEBUG GenomeLocParser -  HLA-DRB1*15:03:01:02 (11569 bp)
16:06:10.902 DEBUG GenomeLocParser -  HLA-DRB1*16:02:01 (11005 bp)
16:06:11.394 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A1.hdf5 (1 / 2)
16:06:13.320 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A2.hdf5 (2 / 2)
16:06:15.943 DEBUG ScriptExecutor - Executing:
16:06:15.943 DEBUG ScriptExecutor -   python
16:06:15.943 DEBUG ScriptExecutor -   /tmp/cohort_determine_ploidy_and_depth.4042300543819468421.py
16:06:15.943 DEBUG ScriptExecutor -   --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig4109579850664503560.tsv
16:06:15.943 DEBUG ScriptExecutor -   --output_calls_path=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ploidy-case-calls
16:06:15.943 DEBUG ScriptExecutor -   --mapping_error_rate=1.000000e-02
16:06:15.943 DEBUG ScriptExecutor -   --psi_s_scale=1.000000e-04
16:06:15.943 DEBUG ScriptExecutor -   --mean_bias_sd=1.000000e-02
16:06:15.943 DEBUG ScriptExecutor -   --psi_j_scale=1.000000e-03
16:06:15.943 DEBUG ScriptExecutor -   --learning_rate=5.000000e-02
16:06:15.943 DEBUG ScriptExecutor -   --adamax_beta1=9.000000e-01
16:06:15.943 DEBUG ScriptExecutor -   --adamax_beta2=9.990000e-01
16:06:15.943 DEBUG ScriptExecutor -   --log_emission_samples_per_round=2000
16:06:15.943 DEBUG ScriptExecutor -   --log_emission_sampling_rounds=100
16:06:15.943 DEBUG ScriptExecutor -   --log_emission_sampling_median_rel_error=5.000000e-04
16:06:15.943 DEBUG ScriptExecutor -   --max_advi_iter_first_epoch=1000
16:06:15.943 DEBUG ScriptExecutor -   --max_advi_iter_subsequent_epochs=1000
16:06:15.943 DEBUG ScriptExecutor -   --min_training_epochs=20
16:06:15.943 DEBUG ScriptExecutor -   --max_training_epochs=100
16:06:15.943 DEBUG ScriptExecutor -   --initial_temperature=2.000000e+00
16:06:15.943 DEBUG ScriptExecutor -   --num_thermal_advi_iters=5000
16:06:15.943 DEBUG ScriptExecutor -   --convergence_snr_averaging_window=5000
16:06:15.943 DEBUG ScriptExecutor -   --convergence_snr_trigger_threshold=1.000000e-01
16:06:15.943 DEBUG ScriptExecutor -   --convergence_snr_countdown_window=10
16:06:15.943 DEBUG ScriptExecutor -   --max_calling_iters=1
16:06:15.943 DEBUG ScriptExecutor -   --caller_update_convergence_threshold=1.000000e-03
16:06:15.943 DEBUG ScriptExecutor -   --caller_internal_admixing_rate=7.500000e-01
16:06:15.943 DEBUG ScriptExecutor -   --caller_external_admixing_rate=7.500000e-01
16:06:15.943 DEBUG ScriptExecutor -   --disable_caller=false
16:06:15.943 DEBUG ScriptExecutor -   --disable_sampler=false
16:06:15.943 DEBUG ScriptExecutor -   --disable_annealing=false
16:06:15.943 DEBUG ScriptExecutor -   --interval_list=/tmp/intervals6497179731716617468.tsv
16:06:15.943 DEBUG ScriptExecutor -   --contig_ploidy_prior_table=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/contig_ploidy_priors_clean.tsv
16:06:15.943 DEBUG ScriptExecutor -   --output_model_path=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ploidy-case-model
16:06:20.708 INFO cohort_determine_ploidy_and_depth - THEANO_FLAGS environment variable has been set to: device=cpu,floatX=float64,optimizer=fast_run,compute_test_value=ignore,openmp=true,blas.ldflags=-lmkl_rt,openmp_elemwise_minsize=10
16:06:35.368 INFO gcnvkernel.structs.metadata - Generating intervals metadata...
Traceback (most recent call last):
  File "/tmp/cohort_determine_ploidy_and_depth.4042300543819468421.py", line 121, in <module>
    sample_metadata_collection)
  File "/home/qianrusun/.conda/envs/gatk_20241213/lib/python3.6/site-packages/gcnvkernel/models/model_ploidy.py", line 146, in __init__
    "Some contigs do not have ploidy priors"
AssertionError: Some contigs do not have ploidy priors
16:21:25.814 DEBUG ScriptExecutor - Result: 1
16:21:25.815 INFO  DetermineGermlineContigPloidy - Shutting down engine
[December 16, 2024 4:21:25 PM HKT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 15.60 minutes.
Runtime.totalMemory()=3249537024
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
python exited with 1
Command Line: python /tmp/cohort_determine_ploidy_and_depth.4042300543819468421.py --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig4109579850664503560.tsv --output_calls_path=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ploidy-case-calls --mapping_error_rate=1.000000e-02 --psi_s_scale=1.000000e-04 --mean_bias_sd=1.000000e-02 --psi_j_scale=1.000000e-03 --learning_rate=5.000000e-02 --adamax_beta1=9.000000e-01 --adamax_beta2=9.990000e-01 --log_emission_samples_per_round=2000 --log_emission_sampling_rounds=100 --log_emission_sampling_median_rel_error=5.000000e-04 --max_advi_iter_first_epoch=1000 --max_advi_iter_subsequent_epochs=1000 --min_training_epochs=20 --max_training_epochs=100 --initial_temperature=2.000000e+00 --num_thermal_advi_iters=5000 --convergence_snr_averaging_window=5000 --convergence_snr_trigger_threshold=1.000000e-01 --convergence_snr_countdown_window=10 --max_calling_iters=1 --caller_update_convergence_threshold=1.000000e-03 --caller_internal_admixing_rate=7.500000e-01 --caller_external_admixing_rate=7.500000e-01 --disable_caller=false --disable_sampler=false --disable_annealing=false --interval_list=/tmp/intervals6497179731716617468.tsv --contig_ploidy_prior_table=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/contig_ploidy_priors_clean.tsv --output_model_path=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ploidy-case-model
at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:112)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:193)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:168)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:139)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.executeDeterminePloidyAndDepthPythonScript(DetermineGermlineContigPloidy.java:424)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.doWork(DetermineGermlineContigPloidy.java:321)
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 /home/qianrusun/.conda/envs/gatk_20241213/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 /home/qianrusun/.conda/envs/gatk_20241213/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar DetermineGermlineContigPloidy --contig-ploidy-priors /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/contig_ploidy_priors_clean.tsv -I /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A1.hdf5 -I /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A2.hdf5 -O /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ --output-prefix ploidy-case --verbosity DEBUG

16:05:49.999 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/qianrusun/.conda/envs/gatk_20241213/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
16:05:50.112 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression2170316634369124856.so
16:05:50.534 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
16:05:50.534 INFO  DetermineGermlineContigPloidy - The Genome Analysis Toolkit (GATK) v4.3.0.0
16:05:50.534 INFO  DetermineGermlineContigPloidy - For support and documentation go to https://software.broadinstitute.org/gatk/
16:05:50.534 INFO  DetermineGermlineContigPloidy - Executing as qianrusun@rsee on Linux v5.4.0-198-generic amd64
16:05:50.534 INFO  DetermineGermlineContigPloidy - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_412-b08
16:05:50.535 INFO  DetermineGermlineContigPloidy - Start Date/Time: December 16, 2024 4:05:49 PM HKT
16:05:50.535 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
16:05:50.535 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
16:05:50.535 INFO  DetermineGermlineContigPloidy - HTSJDK Version: 3.0.1
16:05:50.535 INFO  DetermineGermlineContigPloidy - Picard Version: 2.27.5
16:05:50.535 INFO  DetermineGermlineContigPloidy - Built for Spark Version: 2.4.5
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.BUFFER_SIZE : 131072
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_INDEX : false
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_MD5 : false
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CUSTOM_READER_FACTORY : 
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
16:05:50.537 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.REFERENCE_FASTA : null
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:05:50.538 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
16:05:50.538 DEBUG ConfigFactory - Configuration file values: 
16:05:50.542 DEBUG ConfigFactory -     gcsMaxRetries = 20
16:05:50.542 DEBUG ConfigFactory -     gcsProjectForRequesterPays = 
16:05:50.542 DEBUG ConfigFactory -     gatk_stacktrace_on_user_exception = false
16:05:50.542 DEBUG ConfigFactory -     samjdk.use_async_io_read_samtools = false
16:05:50.542 DEBUG ConfigFactory -     samjdk.use_async_io_write_samtools = true
16:05:50.542 DEBUG ConfigFactory -     samjdk.use_async_io_write_tribble = false
16:05:50.542 DEBUG ConfigFactory -     samjdk.compression_level = 2
16:05:50.542 DEBUG ConfigFactory -     spark.kryoserializer.buffer.max = 512m
16:05:50.542 DEBUG ConfigFactory -     spark.driver.maxResultSize = 0
16:05:50.543 DEBUG ConfigFactory -     spark.driver.userClassPathFirst = true
16:05:50.543 DEBUG ConfigFactory -     spark.io.compression.codec = lzf
16:05:50.543 DEBUG ConfigFactory -     spark.executor.memoryOverhead = 600
16:05:50.543 DEBUG ConfigFactory -     spark.driver.extraJavaOptions = 
16:05:50.543 DEBUG ConfigFactory -     spark.executor.extraJavaOptions = 
16:05:50.543 DEBUG ConfigFactory -     codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
16:05:50.543 DEBUG ConfigFactory -     read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
16:05:50.543 DEBUG ConfigFactory -     annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
16:05:50.543 DEBUG ConfigFactory -     cloudPrefetchBuffer = 40
16:05:50.543 DEBUG ConfigFactory -     cloudIndexPrefetchBuffer = -1
16:05:50.543 DEBUG ConfigFactory -     createOutputBamIndex = true
16:05:50.543 INFO  DetermineGermlineContigPloidy - Deflater: IntelDeflater
16:05:50.543 INFO  DetermineGermlineContigPloidy - Inflater: IntelInflater
16:05:50.543 INFO  DetermineGermlineContigPloidy - GCS max retries/reopens: 20
16:05:50.544 INFO  DetermineGermlineContigPloidy - Requester pays: disabled
16:05:50.544 INFO  DetermineGermlineContigPloidy - Initializing engine
16:05:50.555 DEBUG ScriptExecutor - Executing:
16:05:50.555 DEBUG ScriptExecutor -   python
16:05:50.555 DEBUG ScriptExecutor -   -c
16:05:50.555 DEBUG ScriptExecutor -   import gcnvkernel

16:06:06.795 DEBUG ScriptExecutor - Result: 0
16:06:06.795 INFO  DetermineGermlineContigPloidy - Done initializing engine
16:06:06.813 INFO  DetermineGermlineContigPloidy - No contig-ploidy model was provided, running in cohort mode...
16:06:06.813 INFO  DetermineGermlineContigPloidy - Retrieving intervals from read-count file (/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A1.hdf5)...
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.
16:06:10.260 INFO  DetermineGermlineContigPloidy - Validating and aggregating coverage per contig from input read-count files...
16:06:10.848 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
16:06:10.849 DEBUG GenomeLocParser -  chr1 (248956422 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr2 (242193529 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr3 (198295559 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr4 (190214555 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr5 (181538259 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr6 (170805979 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr7 (159345973 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr8 (145138636 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr9 (138394717 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr10 (133797422 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr11 (135086622 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr12 (133275309 bp)
16:06:10.849 DEBUG GenomeLocParser -  chr13 (114364328 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr14 (107043718 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr15 (101991189 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr16 (90338345 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr17 (83257441 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr18 (80373285 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr19 (58617616 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr20 (64444167 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr21 (46709983 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr22 (50818468 bp)
16:06:10.850 DEBUG GenomeLocParser -  chrX (156040895 bp)
16:06:10.850 DEBUG GenomeLocParser -  chrY (57227415 bp)
16:06:10.850 DEBUG GenomeLocParser -  chrM (16569 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr1_KI270706v1_random (175055 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr1_KI270707v1_random (32032 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr1_KI270708v1_random (127682 bp)
16:06:10.850 DEBUG GenomeLocParser -  chr1_KI270709v1_random (66860 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr1_KI270710v1_random (40176 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr1_KI270711v1_random (42210 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr1_KI270712v1_random (176043 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr1_KI270713v1_random (40745 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr1_KI270714v1_random (41717 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr2_KI270715v1_random (161471 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr2_KI270716v1_random (153799 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr3_GL000221v1_random (155397 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr4_GL000008v2_random (209709 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr5_GL000208v1_random (92689 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr9_KI270717v1_random (40062 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr9_KI270718v1_random (38054 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr9_KI270719v1_random (176845 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr9_KI270720v1_random (39050 bp)
16:06:10.851 DEBUG GenomeLocParser -  chr11_KI270721v1_random (100316 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr14_GL000009v2_random (201709 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr14_GL000225v1_random (211173 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr14_KI270722v1_random (194050 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr14_GL000194v1_random (191469 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr14_KI270723v1_random (38115 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr14_KI270724v1_random (39555 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr14_KI270725v1_random (172810 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr14_KI270726v1_random (43739 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr15_KI270727v1_random (448248 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr16_KI270728v1_random (1872759 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr17_GL000205v2_random (185591 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr17_KI270729v1_random (280839 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr17_KI270730v1_random (112551 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr22_KI270731v1_random (150754 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr22_KI270732v1_random (41543 bp)
16:06:10.852 DEBUG GenomeLocParser -  chr22_KI270733v1_random (179772 bp)
16:06:10.853 DEBUG GenomeLocParser -  chr22_KI270734v1_random (165050 bp)
16:06:10.853 DEBUG GenomeLocParser -  chr22_KI270735v1_random (42811 bp)
16:06:10.853 DEBUG GenomeLocParser -  chr22_KI270736v1_random (181920 bp)
16:06:10.853 DEBUG GenomeLocParser -  chr22_KI270737v1_random (103838 bp)
16:06:10.853 DEBUG GenomeLocParser -  chr22_KI270738v1_random (99375 bp)
16:06:10.854 DEBUG GenomeLocParser -  chr22_KI270739v1_random (73985 bp)
16:06:10.854 DEBUG GenomeLocParser -  chrY_KI270740v1_random (37240 bp)

...so many unknown I skipped here as the limits
16:06:10.902 DEBUG GenomeLocParser -  HLA-DRB1*16:02:01 (11005 bp)
16:06:11.394 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A1.hdf5 (1 / 2)
16:06:13.320 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A2.hdf5 (2 / 2)
16:06:15.943 DEBUG ScriptExecutor - Executing:
16:06:15.943 DEBUG ScriptExecutor -   python
16:06:15.943 DEBUG ScriptExecutor -   /tmp/cohort_determine_ploidy_and_depth.4042300543819468421.py
16:06:15.943 DEBUG ScriptExecutor -   --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig4109579850664503560.tsv
16:06:15.943 DEBUG ScriptExecutor -   --output_calls_path=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ploidy-case-calls
16:06:15.943 DEBUG ScriptExecutor -   --mapping_error_rate=1.000000e-02
16:06:15.943 DEBUG ScriptExecutor -   --psi_s_scale=1.000000e-04
16:06:15.943 DEBUG ScriptExecutor -   --mean_bias_sd=1.000000e-02
16:06:15.943 DEBUG ScriptExecutor -   --psi_j_scale=1.000000e-03
16:06:15.943 DEBUG ScriptExecutor -   --learning_rate=5.000000e-02
16:06:15.943 DEBUG ScriptExecutor -   --adamax_beta1=9.000000e-01
16:06:15.943 DEBUG ScriptExecutor -   --adamax_beta2=9.990000e-01
16:06:15.943 DEBUG ScriptExecutor -   --log_emission_samples_per_round=2000
16:06:15.943 DEBUG ScriptExecutor -   --log_emission_sampling_rounds=100
16:06:15.943 DEBUG ScriptExecutor -   --log_emission_sampling_median_rel_error=5.000000e-04
16:06:15.943 DEBUG ScriptExecutor -   --max_advi_iter_first_epoch=1000
16:06:15.943 DEBUG ScriptExecutor -   --max_advi_iter_subsequent_epochs=1000
16:06:15.943 DEBUG ScriptExecutor -   --min_training_epochs=20
16:06:15.943 DEBUG ScriptExecutor -   --max_training_epochs=100
16:06:15.943 DEBUG ScriptExecutor -   --initial_temperature=2.000000e+00
16:06:15.943 DEBUG ScriptExecutor -   --num_thermal_advi_iters=5000
16:06:15.943 DEBUG ScriptExecutor -   --convergence_snr_averaging_window=5000
16:06:15.943 DEBUG ScriptExecutor -   --convergence_snr_trigger_threshold=1.000000e-01
16:06:15.943 DEBUG ScriptExecutor -   --convergence_snr_countdown_window=10
16:06:15.943 DEBUG ScriptExecutor -   --max_calling_iters=1
16:06:15.943 DEBUG ScriptExecutor -   --caller_update_convergence_threshold=1.000000e-03
16:06:15.943 DEBUG ScriptExecutor -   --caller_internal_admixing_rate=7.500000e-01
16:06:15.943 DEBUG ScriptExecutor -   --caller_external_admixing_rate=7.500000e-01
16:06:15.943 DEBUG ScriptExecutor -   --disable_caller=false
16:06:15.943 DEBUG ScriptExecutor -   --disable_sampler=false
16:06:15.943 DEBUG ScriptExecutor -   --disable_annealing=false
16:06:15.943 DEBUG ScriptExecutor -   --interval_list=/tmp/intervals6497179731716617468.tsv
16:06:15.943 DEBUG ScriptExecutor -   --contig_ploidy_prior_table=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/contig_ploidy_priors_clean.tsv
16:06:15.943 DEBUG ScriptExecutor -   --output_model_path=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ploidy-case-model
16:06:20.708 INFO cohort_determine_ploidy_and_depth - THEANO_FLAGS environment variable has been set to: device=cpu,floatX=float64,optimizer=fast_run,compute_test_value=ignore,openmp=true,blas.ldflags=-lmkl_rt,openmp_elemwise_minsize=10
16:06:35.368 INFO gcnvkernel.structs.metadata - Generating intervals metadata...
Traceback (most recent call last):
  File "/tmp/cohort_determine_ploidy_and_depth.4042300543819468421.py", line 121, in <module>
    sample_metadata_collection)
  File "/home/qianrusun/.conda/envs/gatk_20241213/lib/python3.6/site-packages/gcnvkernel/models/model_ploidy.py", line 146, in __init__
    "Some contigs do not have ploidy priors"
AssertionError: Some contigs do not have ploidy priors
16:21:25.814 DEBUG ScriptExecutor - Result: 1
16:21:25.815 INFO  DetermineGermlineContigPloidy - Shutting down engine
[December 16, 2024 4:21:25 PM HKT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 15.60 minutes.
Runtime.totalMemory()=3249537024
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
python exited with 1
Command Line: python /tmp/cohort_determine_ploidy_and_depth.4042300543819468421.py --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig4109579850664503560.tsv --output_calls_path=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ploidy-case-calls --mapping_error_rate=1.000000e-02 --psi_s_scale=1.000000e-04 --mean_bias_sd=1.000000e-02 --psi_j_scale=1.000000e-03 --learning_rate=5.000000e-02 --adamax_beta1=9.000000e-01 --adamax_beta2=9.990000e-01 --log_emission_samples_per_round=2000 --log_emission_sampling_rounds=100 --log_emission_sampling_median_rel_error=5.000000e-04 --max_advi_iter_first_epoch=1000 --max_advi_iter_subsequent_epochs=1000 --min_training_epochs=20 --max_training_epochs=100 --initial_temperature=2.000000e+00 --num_thermal_advi_iters=5000 --convergence_snr_averaging_window=5000 --convergence_snr_trigger_threshold=1.000000e-01 --convergence_snr_countdown_window=10 --max_calling_iters=1 --caller_update_convergence_threshold=1.000000e-03 --caller_internal_admixing_rate=7.500000e-01 --caller_external_admixing_rate=7.500000e-01 --disable_caller=false --disable_sampler=false --disable_annealing=false --interval_list=/tmp/intervals6497179731716617468.tsv --contig_ploidy_prior_table=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/contig_ploidy_priors_clean.tsv --output_model_path=/srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ploidy-case-model
    at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
    at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:112)
    at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:193)
    at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:168)
    at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:139)
    at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.executeDeterminePloidyAndDepthPythonScript(DetermineGermlineContigPloidy.java:424)
    at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.doWork(DetermineGermlineContigPloidy.java:321)
    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 /home/qianrusun/.conda/envs/gatk_20241213/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 /home/qianrusun/.conda/envs/gatk_20241213/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar DetermineGermlineContigPloidy --contig-ploidy-priors /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/contig_ploidy_priors_clean.tsv -I /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A1.hdf5 -I /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/02.CollectReadCounts/A2.hdf5 -O /srv/projects/Lenus/cfDNA_2024/WGS_ucfDNA_202409/A2/GATK_CNV/03.DetermineGermlineContigPloidy_CaseMode/ --output-prefix ploidy-case --verbosity DEBUG

 ####Dear gatk developers, the contig.tsv I have checked it is the tab seperated; and the gcnvkernel version is 0.8; the python version is 3.6; the only thing I confused is the R 3.6 version, no idea if the R lower version would affect this? Thank you so much!!

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    Qianru Lenus SUN

    Gökalp Çelik may I bother for your help? thanks! here is my contig.tsv

     

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    Gökalp Çelik

    Hi Qianru Lenus SUN

    We recommend working with main reference contigs only for GCNV workflow. If your read collections contain other unlocalized or alt contigs inside you need to remove them or recollect read counts with only intervals in the main reference contigs. We also recommend running GCNV against chrM with autosomes as chrM may have elevated depths and quite short length for a possible HMM traversal. 

    I hope this helps. 

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