Thank you for providing excellent pipelines.

Now, I am trying to detect germline CNV according to the tutorial (https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants)

In a certain disease with 50 samples, workflow succeeded to acquire vcf files. However, in the other disease with 235 samples, it didn't work at the same environment(gatk conda env) and settings.

faced following error message, in executing DeterminGermilneContigPloidy.

version and command are as following.
a) GATK version used: 4.2.5.0
b) Exact command used: 

for i in `basename -a ${tsv_dir}/*.tsv`
do
input_tsv+="-I ${tsv_dir}/${i} "
done

### step3 ###

###cohort mode
${gatk} DetermineGermlineContigPloidy \
    -L ${analysis_dir}/exome.cohort.gc.filtered.interval_list \
    --interval-merging-rule OVERLAPPING_ONLY \
    ${input_tsv} \
    --contig-ploidy-priors ${cnv_dir}/contig_ploidy_priors.tsv \
    --output ${analysis_dir} \
    --output-prefix ploidy \
    --verbosity DEBUG

c) Entire program log:

17:00:55.728 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/yshare1/home/inos0304/modules/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
17:00:55.743 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression4191870566001061669.so
Mar 01, 2022 5:00:55 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
17:00:55.868 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
17:00:55.868 INFO  DetermineGermlineContigPloidy - The Genome Analysis Toolkit (GATK) v4.2.5.0
17:00:55.868 INFO  DetermineGermlineContigPloidy - For support and documentation go to https://software.broadinstitute.org/gatk/
17:00:55.869 INFO  DetermineGermlineContigPloidy - Executing as inos0304@gc046i on Linux v3.10.0-1127.18.2.el7.x86_64 amd64
17:00:55.869 INFO  DetermineGermlineContigPloidy - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_181-b13
17:00:55.870 INFO  DetermineGermlineContigPloidy - Start Date/Time: 2022/03/01 17:00:55 JST
17:00:55.870 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
17:00:55.870 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
17:00:55.870 INFO  DetermineGermlineContigPloidy - HTSJDK Version: 2.24.1
17:00:55.870 INFO  DetermineGermlineContigPloidy - Picard Version: 2.25.4
17:00:55.870 INFO  DetermineGermlineContigPloidy - Built for Spark Version: 2.4.5
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.BUFFER_SIZE : 131072
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_INDEX : false
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_MD5 : false
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CUSTOM_READER_FACTORY :
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.REFERENCE_FASTA : null
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:00:55.872 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:00:55.873 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
17:00:55.873 DEBUG ConfigFactory - Configuration file values:
17:00:55.876 DEBUG ConfigFactory -     gcsMaxRetries = 20
17:00:55.876 DEBUG ConfigFactory -     gcsProjectForRequesterPays =
17:00:55.876 DEBUG ConfigFactory -     gatk_stacktrace_on_user_exception = false
17:00:55.876 DEBUG ConfigFactory -     samjdk.use_async_io_read_samtools = false
17:00:55.877 DEBUG ConfigFactory -     samjdk.use_async_io_write_samtools = true
17:00:55.877 DEBUG ConfigFactory -     samjdk.use_async_io_write_tribble = false
17:00:55.877 DEBUG ConfigFactory -     samjdk.compression_level = 2
17:00:55.877 DEBUG ConfigFactory -     spark.kryoserializer.buffer.max = 512m
17:00:55.877 DEBUG ConfigFactory -     spark.driver.maxResultSize = 0
17:00:55.877 DEBUG ConfigFactory -     spark.driver.userClassPathFirst = true
17:00:55.877 DEBUG ConfigFactory -     spark.io.compression.codec = lzf
17:00:55.877 DEBUG ConfigFactory -     spark.executor.memoryOverhead = 600
17:00:55.877 DEBUG ConfigFactory -     spark.driver.extraJavaOptions =
17:00:55.877 DEBUG ConfigFactory -     spark.executor.extraJavaOptions =
17:00:55.877 DEBUG ConfigFactory -     codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
17:00:55.877 DEBUG ConfigFactory -     read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
17:00:55.877 DEBUG ConfigFactory -     annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
17:00:55.877 DEBUG ConfigFactory -     cloudPrefetchBuffer = 40
17:00:55.877 DEBUG ConfigFactory -     cloudIndexPrefetchBuffer = -1
17:00:55.878 DEBUG ConfigFactory -     createOutputBamIndex = true
17:00:55.878 INFO  DetermineGermlineContigPloidy - Deflater: IntelDeflater
17:00:55.878 INFO  DetermineGermlineContigPloidy - Inflater: IntelInflater
17:00:55.878 INFO  DetermineGermlineContigPloidy - GCS max retries/reopens: 20
17:00:55.878 INFO  DetermineGermlineContigPloidy - Requester pays: disabled
17:00:55.878 INFO  DetermineGermlineContigPloidy - Initializing engine
17:00:55.882 DEBUG ScriptExecutor - Executing:
17:00:55.882 DEBUG ScriptExecutor -   python
17:00:55.882 DEBUG ScriptExecutor -   -c
17:00:55.882 DEBUG ScriptExecutor -   import gcnvkernel

17:03:43.401 DEBUG ScriptExecutor - Result: 0
17:03:43.404 INFO  DetermineGermlineContigPloidy - Done initializing engine
17:03:43.438 INFO  DetermineGermlineContigPloidy - No contig-ploidy model was provided, running in cohort mode...
17:03:43.438 INFO  DetermineGermlineContigPloidy - Intervals specified...
17:03:43.893 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
17:03:43.893 DEBUG GenomeLocParser -  chr1 (248956422 bp)
17:03:43.893 DEBUG GenomeLocParser -  chr2 (242193529 bp)
17:03:43.893 DEBUG GenomeLocParser -  chr3 (198295559 bp)
17:03:43.893 DEBUG GenomeLocParser -  chr4 (190214555 bp)
17:03:43.893 DEBUG GenomeLocParser -  chr5 (181538259 bp)
17:03:43.893 DEBUG GenomeLocParser -  chr6 (170805979 bp)
17:03:43.893 DEBUG GenomeLocParser -  chr7 (159345973 bp)
17:03:43.893 DEBUG GenomeLocParser -  chr8 (145138636 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr9 (138394717 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr10 (133797422 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr11 (135086622 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr12 (133275309 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr13 (114364328 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr14 (107043718 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr15 (101991189 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr16 (90338345 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr17 (83257441 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr18 (80373285 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr19 (58617616 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr20 (64444167 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr21 (46709983 bp)
17:03:43.894 DEBUG GenomeLocParser -  chr22 (50818468 bp)
17:03:43.894 DEBUG GenomeLocParser -  chrX (156040895 bp)
17:03:43.894 DEBUG GenomeLocParser -  chrY (57227415 bp)
17:03:43.894 DEBUG GenomeLocParser -  chrM (16569 bp)
17:03:43.894 DEBUG GenomeLocParser -  chrEBV (171823 bp)
17:03:43.894 DEBUG GenomeLocParser -  decoy (6391639 bp)
17:03:44.208 INFO  FeatureManager - Using codec IntervalListCodec to read file file:///home/inos0304/human_genome_analysis/cnv/analysis_dcm/exome.cohort.gc.filtered.interval_list
17:03:45.144 DEBUG FeatureDataSource - Cache statistics for FeatureInput /home/inos0304/human_genome_analysis/cnv/analysis_dcm/exome.cohort.gc.filtered.interval_list:/home/inos0304/human_genome_analysis/cnv/analysis_dcm/exome.cohort.gc.filtered.interval_list:
17:03:45.145 DEBUG FeatureCache - Cache hit rate  was 0.00% (0 out of 0 total queries)
17:03:45.205 INFO  IntervalArgumentCollection - Processing 123080634 bp from intervals
17:03:45.446 INFO  DetermineGermlineContigPloidy - Validating and aggregating coverage per contig from input read-count files...
17:03:45.465 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
17:03:45.466 DEBUG GenomeLocParser -  chr1 (248956422 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr2 (242193529 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr3 (198295559 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr4 (190214555 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr5 (181538259 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr6 (170805979 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr7 (159345973 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr8 (145138636 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr9 (138394717 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr10 (133797422 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr11 (135086622 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr12 (133275309 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr13 (114364328 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr14 (107043718 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr15 (101991189 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr16 (90338345 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr17 (83257441 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr18 (80373285 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr19 (58617616 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr20 (64444167 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr21 (46709983 bp)
17:03:45.466 DEBUG GenomeLocParser -  chr22 (50818468 bp)
17:03:45.466 DEBUG GenomeLocParser -  chrX (156040895 bp)
17:03:45.466 DEBUG GenomeLocParser -  chrY (57227415 bp)
17:03:45.466 DEBUG GenomeLocParser -  chrM (16569 bp)
17:03:45.467 DEBUG GenomeLocParser -  chrEBV (171823 bp)
17:03:45.467 DEBUG GenomeLocParser -  decoy (6391639 bp)
17:03:45.518 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_01.tsv (1 / 235)
17:03:45.837 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_02.tsv (2 / 235)
17:03:46.136 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_07.tsv (3 / 235)
17:03:46.440 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_08.tsv (4 / 235)
17:03:46.795 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_11.tsv (5 / 235)
17:03:47.137 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_12.tsv (6 / 235)
17:03:47.440 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_13.tsv (7 / 235)
17:03:47.721 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_16.tsv (8 / 235)
17:03:48.217 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_17.tsv (9 / 235)
17:03:48.566 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_19.tsv (10 / 235)
17:03:48.845 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_23.tsv (11 / 235)
17:03:49.124 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_24.tsv (12 / 235)
17:03:49.405 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_28.tsv (13 / 235)
17:03:49.684 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_29.tsv (14 / 235)
17:03:49.970 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_34.tsv (15 / 235)
17:03:50.254 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_35.tsv (16 / 235)
17:03:50.536 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_37.tsv (17 / 235)
17:03:50.945 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_38.tsv (18 / 235)
17:03:51.341 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_48.tsv (19 / 235)
17:03:51.623 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_49.tsv (20 / 235)
17:03:51.907 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_50.tsv (21 / 235)
17:03:52.193 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_52.tsv (22 / 235)
17:03:52.475 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_56.tsv (23 / 235)
17:03:52.800 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_57.tsv (24 / 235)
17:03:53.118 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_64.tsv (25 / 235)
17:03:53.431 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_65.tsv (26 / 235)
17:03:53.844 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_71.tsv (27 / 235)
17:03:54.276 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_73.tsv (28 / 235)
17:03:54.614 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_74.tsv (29 / 235)
17:03:54.892 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_76.tsv (30 / 235)
17:03:55.171 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_78.tsv (31 / 235)
17:03:55.447 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_79.tsv (32 / 235)
17:03:55.734 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_81.tsv (33 / 235)
17:03:56.021 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_84.tsv (34 / 235)
17:03:56.297 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_88.tsv (35 / 235)
17:03:56.575 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_89.tsv (36 / 235)
17:03:57.030 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_90.tsv (37 / 235)
17:03:57.386 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/JN6556_95.tsv (38 / 235)
17:03:57.660 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_01.tsv (39 / 235)
17:03:57.937 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_02.tsv (40 / 235)
17:03:58.216 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_10.tsv (41 / 235)
17:03:58.576 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_11.tsv (42 / 235)
17:03:58.894 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_12.tsv (43 / 235)
17:03:59.205 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_14.tsv (44 / 235)
17:03:59.485 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_18.tsv (45 / 235)
17:03:59.871 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_19.tsv (46 / 235)
17:04:00.276 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_22.tsv (47 / 235)
17:04:00.562 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_23.tsv (48 / 235)
17:04:00.840 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_28.tsv (49 / 235)
17:04:01.121 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_29.tsv (50 / 235)
17:04:01.401 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_30.tsv (51 / 235)
17:04:01.686 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_31.tsv (52 / 235)
17:04:01.969 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_36.tsv (53 / 235)
17:04:02.253 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_37.tsv (54 / 235)
17:04:02.580 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_38.tsv (55 / 235)
17:04:03.061 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_39.tsv (56 / 235)
17:04:03.412 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_40.tsv (57 / 235)
17:04:03.693 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_41.tsv (58 / 235)
17:04:03.969 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_42.tsv (59 / 235)
17:04:04.242 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_43.tsv (60 / 235)
17:04:04.522 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_45.tsv (61 / 235)
17:04:04.804 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_46.tsv (62 / 235)
17:04:05.081 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_47.tsv (63 / 235)
17:04:05.356 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_48.tsv (64 / 235)
17:04:05.796 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_51.tsv (65 / 235)
17:04:06.165 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_52.tsv (66 / 235)
17:04:06.441 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_53.tsv (67 / 235)
17:04:06.715 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_55.tsv (68 / 235)
17:04:06.990 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_56.tsv (69 / 235)
17:04:07.268 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_60.tsv (70 / 235)
17:04:07.559 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_61.tsv (71 / 235)
17:04:07.854 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4100_62.tsv (72 / 235)
17:04:08.130 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_01.tsv (73 / 235)
17:04:08.536 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_02.tsv (74 / 235)
17:04:08.933 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_07.tsv (75 / 235)
17:04:09.215 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_09.tsv (76 / 235)
17:04:09.491 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_19.tsv (77 / 235)
17:04:09.769 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_20.tsv (78 / 235)
17:04:10.046 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_21.tsv (79 / 235)
17:04:10.336 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_26.tsv (80 / 235)
17:04:10.619 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_27.tsv (81 / 235)
17:04:10.895 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_29.tsv (82 / 235)
17:04:11.233 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_30.tsv (83 / 235)
17:04:11.630 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_35.tsv (84 / 235)
17:04:11.940 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_36.tsv (85 / 235)
17:04:12.343 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_37.tsv (86 / 235)
17:04:12.781 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_38.tsv (87 / 235)
17:04:13.170 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_41.tsv (88 / 235)
17:04:13.479 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_43.tsv (89 / 235)
17:04:13.783 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_45.tsv (90 / 235)
17:04:14.062 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_48.tsv (91 / 235)
17:04:14.345 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_49.tsv (92 / 235)
17:04:14.795 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_50.tsv (93 / 235)
17:04:15.160 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_51.tsv (94 / 235)
17:04:15.441 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_56.tsv (95 / 235)
17:04:15.718 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_58.tsv (96 / 235)
17:04:15.998 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_59.tsv (97 / 235)
17:04:16.275 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_60.tsv (98 / 235)
17:04:16.559 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_62.tsv (99 / 235)
17:04:16.842 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_63.tsv (100 / 235)
17:04:17.121 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_64.tsv (101 / 235)
17:04:17.497 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_65.tsv (102 / 235)
17:04:17.901 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_66.tsv (103 / 235)
17:04:18.190 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_67.tsv (104 / 235)
17:04:18.495 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_68.tsv (105 / 235)
17:04:18.818 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_69.tsv (106 / 235)
17:04:19.126 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_70.tsv (107 / 235)
17:04:19.444 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_74.tsv (108 / 235)
17:04:19.731 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_77.tsv (109 / 235)
17:04:20.009 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_79.tsv (110 / 235)
17:04:20.531 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_83.tsv (111 / 235)
17:04:20.988 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_88.tsv (112 / 235)
17:04:21.347 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_90.tsv (113 / 235)
17:04:21.640 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_95.tsv (114 / 235)
17:04:21.915 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4213_96.tsv (115 / 235)
17:04:22.189 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_05.tsv (116 / 235)
17:04:22.490 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_06.tsv (117 / 235)
17:04:22.786 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_07.tsv (118 / 235)
17:04:23.080 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_08.tsv (119 / 235)
17:04:23.344 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_09.tsv (120 / 235)
17:04:23.871 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_11.tsv (121 / 235)
17:04:24.244 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_13.tsv (122 / 235)
17:04:24.554 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_14.tsv (123 / 235)
17:04:24.838 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_17.tsv (124 / 235)
17:04:25.123 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_22.tsv (125 / 235)
17:04:25.407 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_24.tsv (126 / 235)
17:04:25.684 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_25.tsv (127 / 235)
17:04:25.962 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_26.tsv (128 / 235)
17:04:26.243 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_27.tsv (129 / 235)
17:04:26.664 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_28.tsv (130 / 235)
17:04:27.065 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_29.tsv (131 / 235)
17:04:27.370 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_32.tsv (132 / 235)
17:04:27.675 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_38.tsv (133 / 235)
17:04:27.954 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_39.tsv (134 / 235)
17:04:28.226 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_41.tsv (135 / 235)
17:04:28.495 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_43.tsv (136 / 235)
17:04:28.763 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_58.tsv (137 / 235)
17:04:29.028 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_63.tsv (138 / 235)
17:04:29.415 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_64.tsv (139 / 235)
17:04:29.813 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_68.tsv (140 / 235)
17:04:30.093 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_69.tsv (141 / 235)
17:04:30.366 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_70.tsv (142 / 235)
17:04:30.640 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_71.tsv (143 / 235)
17:04:30.916 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_73.tsv (144 / 235)
17:04:31.185 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_74.tsv (145 / 235)
17:04:31.455 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_80.tsv (146 / 235)
17:04:31.723 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_86.tsv (147 / 235)
17:04:32.103 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_87.tsv (148 / 235)
17:04:32.497 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_89.tsv (149 / 235)
17:04:32.805 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_91.tsv (150 / 235)
17:04:33.076 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_93.tsv (151 / 235)
17:04:33.351 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_94.tsv (152 / 235)
17:04:33.623 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4344_96.tsv (153 / 235)
17:04:33.897 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_03.tsv (154 / 235)
17:04:34.165 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_07.tsv (155 / 235)
17:04:34.432 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_08.tsv (156 / 235)
17:04:34.698 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_09.tsv (157 / 235)
17:04:35.058 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_10.tsv (158 / 235)
17:04:35.403 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_14.tsv (159 / 235)
17:04:35.677 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_16.tsv (160 / 235)
17:04:35.948 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_17.tsv (161 / 235)
17:04:36.222 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_18.tsv (162 / 235)
17:04:36.492 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_19.tsv (163 / 235)
17:04:36.758 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_20.tsv (164 / 235)
17:04:37.034 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_21.tsv (165 / 235)
17:04:37.299 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_23.tsv (166 / 235)
17:04:37.600 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_24.tsv (167 / 235)
17:04:37.965 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_25.tsv (168 / 235)
17:04:38.243 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_26.tsv (169 / 235)
17:04:38.515 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_29.tsv (170 / 235)
17:04:38.789 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_37.tsv (171 / 235)
17:04:39.060 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_38.tsv (172 / 235)
17:04:39.331 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_39.tsv (173 / 235)
17:04:39.600 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_47.tsv (174 / 235)
17:04:39.865 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_51.tsv (175 / 235)
17:04:40.129 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_52.tsv (176 / 235)
17:04:40.478 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_53.tsv (177 / 235)
17:04:40.793 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_56.tsv (178 / 235)
17:04:41.064 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_57.tsv (179 / 235)
17:04:41.334 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_61.tsv (180 / 235)
17:04:41.608 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_64.tsv (181 / 235)
17:04:41.879 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_66.tsv (182 / 235)
17:04:42.146 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_67.tsv (183 / 235)
17:04:42.416 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_68.tsv (184 / 235)
17:04:42.682 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_70.tsv (185 / 235)
17:04:43.025 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_75.tsv (186 / 235)
17:04:43.367 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_76.tsv (187 / 235)
17:04:43.640 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_78.tsv (188 / 235)
17:04:43.910 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_83.tsv (189 / 235)
17:04:44.182 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_84.tsv (190 / 235)
17:04:44.453 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_85.tsv (191 / 235)
17:04:44.719 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_86.tsv (192 / 235)
17:04:44.987 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_88.tsv (193 / 235)
17:04:45.255 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_92.tsv (194 / 235)
17:04:45.569 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4446_93.tsv (195 / 235)
17:04:45.936 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_04.tsv (196 / 235)
17:04:46.246 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_07.tsv (197 / 235)
17:04:46.520 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_08.tsv (198 / 235)
17:04:46.794 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_14.tsv (199 / 235)
17:04:47.067 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_15.tsv (200 / 235)
17:04:47.338 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_16.tsv (201 / 235)
17:04:47.604 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_17.tsv (202 / 235)
17:04:47.871 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_18.tsv (203 / 235)
17:04:48.138 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_19.tsv (204 / 235)
17:04:48.500 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_20.tsv (205 / 235)
17:04:48.815 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_27.tsv (206 / 235)
17:04:49.085 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_30.tsv (207 / 235)
17:04:49.351 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_32.tsv (208 / 235)
17:04:49.621 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_34.tsv (209 / 235)
17:04:49.893 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_36.tsv (210 / 235)
17:04:50.161 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_37.tsv (211 / 235)
17:04:50.430 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_40.tsv (212 / 235)
17:04:50.699 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_41.tsv (213 / 235)
17:04:51.015 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_46.tsv (214 / 235)
17:04:51.328 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_48.tsv (215 / 235)
17:04:51.599 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_50.tsv (216 / 235)
17:04:51.865 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_51.tsv (217 / 235)
17:04:52.137 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_54.tsv (218 / 235)
17:04:52.407 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_57.tsv (219 / 235)
17:04:52.675 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_68.tsv (220 / 235)
17:04:52.944 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_70.tsv (221 / 235)
17:04:53.211 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_71.tsv (222 / 235)
17:04:53.528 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_74.tsv (223 / 235)
17:04:53.845 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_75.tsv (224 / 235)
17:04:54.121 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_78.tsv (225 / 235)
17:04:54.397 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_81.tsv (226 / 235)
17:04:54.669 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_82.tsv (227 / 235)
17:04:54.942 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_83.tsv (228 / 235)
17:04:55.209 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_84.tsv (229 / 235)
17:04:55.478 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_85.tsv (230 / 235)
17:04:55.746 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_86.tsv (231 / 235)
17:04:56.013 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_88.tsv (232 / 235)
17:04:56.304 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_89.tsv (233 / 235)
17:04:56.592 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_91.tsv (234 / 235)
17:04:56.864 INFO  DetermineGermlineContigPloidy - Aggregating read-count file /home/inos0304/human_genome_analysis/cnv/analysis_dcm/tsv/PG4482_95.tsv (235 / 235)
17:04:57.146 DEBUG ScriptExecutor - Executing:
17:04:57.146 DEBUG ScriptExecutor -   python
17:04:57.146 DEBUG ScriptExecutor -   /tmp/cohort_determine_ploidy_and_depth.4778177910973610252.py
17:04:57.146 DEBUG ScriptExecutor -   --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig6404085200174742121.tsv
17:04:57.146 DEBUG ScriptExecutor -   --output_calls_path=/yshare1/home/inos0304/human_genome_analysis/cnv/analysis_dcm/ploidy-calls
17:04:57.146 DEBUG ScriptExecutor -   --mapping_error_rate=1.000000e-02
17:04:57.146 DEBUG ScriptExecutor -   --psi_s_scale=1.000000e-04
17:04:57.146 DEBUG ScriptExecutor -   --mean_bias_sd=1.000000e-02
17:04:57.146 DEBUG ScriptExecutor -   --psi_j_scale=1.000000e-03
17:04:57.146 DEBUG ScriptExecutor -   --learning_rate=5.000000e-02
17:04:57.146 DEBUG ScriptExecutor -   --adamax_beta1=9.000000e-01
17:04:57.146 DEBUG ScriptExecutor -   --adamax_beta2=9.990000e-01
17:04:57.146 DEBUG ScriptExecutor -   --log_emission_samples_per_round=2000
17:04:57.146 DEBUG ScriptExecutor -   --log_emission_sampling_rounds=100
17:04:57.146 DEBUG ScriptExecutor -   --log_emission_sampling_median_rel_error=5.000000e-04
17:04:57.146 DEBUG ScriptExecutor -   --max_advi_iter_first_epoch=1000
17:04:57.146 DEBUG ScriptExecutor -   --max_advi_iter_subsequent_epochs=1000
17:04:57.146 DEBUG ScriptExecutor -   --min_training_epochs=20
17:04:57.146 DEBUG ScriptExecutor -   --max_training_epochs=100
17:04:57.146 DEBUG ScriptExecutor -   --initial_temperature=2.000000e+00
17:04:57.146 DEBUG ScriptExecutor -   --num_thermal_advi_iters=5000
17:04:57.146 DEBUG ScriptExecutor -   --convergence_snr_averaging_window=5000
17:04:57.146 DEBUG ScriptExecutor -   --convergence_snr_trigger_threshold=1.000000e-01
17:04:57.146 DEBUG ScriptExecutor -   --convergence_snr_countdown_window=10
17:04:57.146 DEBUG ScriptExecutor -   --max_calling_iters=1
17:04:57.146 DEBUG ScriptExecutor -   --caller_update_convergence_threshold=1.000000e-03
17:04:57.147 DEBUG ScriptExecutor -   --caller_internal_admixing_rate=7.500000e-01
17:04:57.147 DEBUG ScriptExecutor -   --caller_external_admixing_rate=7.500000e-01
17:04:57.147 DEBUG ScriptExecutor -   --disable_caller=false
17:04:57.147 DEBUG ScriptExecutor -   --disable_sampler=false
17:04:57.147 DEBUG ScriptExecutor -   --disable_annealing=false
17:04:57.147 DEBUG ScriptExecutor -   --interval_list=/tmp/intervals6571358976594763738.tsv
17:04:57.147 DEBUG ScriptExecutor -   --contig_ploidy_prior_table=/yshare1/A/home/inos0304/human_genome_analysis/cnv/contig_ploidy_priors.tsv
17:04:57.147 DEBUG ScriptExecutor -   --output_model_path=/yshare1/home/inos0304/human_genome_analysis/cnv/analysis_dcm/ploidy-model
Traceback (most recent call last):
  File "/tmp/cohort_determine_ploidy_and_depth.4778177910973610252.py", line 125, in <module>
    ploidy_task.engage()
  File "/home/inos0304/miniconda3/envs/gatk/lib/python3.6/site-packages/gcnvkernel/tasks/inference_task_base.py", line 346, in engage
    converged_continuous = self._update_continuous_posteriors()
  File "/home/inos0304/miniconda3/envs/gatk/lib/python3.6/site-packages/gcnvkernel/tasks/inference_task_base.py", line 403, in _update_continuous_posteriors
    raise ConvergenceError
gcnvkernel.tasks.inference_task_base.ConvergenceError
17:05:39.781 DEBUG ScriptExecutor - Result: 1
17:05:39.782 INFO  DetermineGermlineContigPloidy - Shutting down engine
[2022/03/01 17:05:39 JST] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 4.73 minutes.
Runtime.totalMemory()=6227755008
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python /tmp/cohort_determine_ploidy_and_depth.4778177910973610252.py --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig6404085200174742121.tsv --output_calls_path=/yshare1/home/inos0304/human_genome_analysis/cnv/analysis_dcm/ploidy-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/intervals6571358976594763738.tsv --contig_ploidy_prior_table=/yshare1/home/inos0304/human_genome_analysis/cnv/contig_ploidy_priors.tsv --output_model_path=/yshare1/home/inos0304/human_genome_analysis/cnv/analysis_dcm/ploidy-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 /yshare1/home/inos0304/modules/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar

I cannot infer the reasons of error with a larger samples, while smaller samples could finish the workflow.

Is it the problem with sample size or memory of my workstation?

Shoud I make the sample size giving DetermineGermlineCongitPloisy smaller?

if you have any advice, i hope it will solve my problem.

Best regards