REQUIRED for all errors and issues:
a) GATK version used: 4.3
b) Exact command used: gatk DetermineGermlineContigPloidy -L cohort.gc.filtered.interval_list --interval-merging-rule OVERLAPPING_ONLY -I DGR39.tsv -I DGR43.tsv -I DGR45.tsv -I DGR46.tsv -I DGR47.tsv -I DGR48.tsv -I DGR49.tsv -I DGR50.tsv -I DGR51.tsv -I DGR53.tsv -I DGR54.tsv -I DGR55.tsv -I DGR56.tsv -I DGR57.tsv -I DGR598.tsv -I DGR601.tsv -I DGR602.tsv -I DGR60.tsv --contig-ploidy-priors /home/machadog/isadora-project/ref/contig_ploidy_prior_hg38_c.tsv --output /home/machadog/isadora-project/gCNV  --output-prefix ploidy  --verbosity DEBUG

c) Entire program log:
14:20:57.028 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR39.tsv (1 / 18)
14:20:57.315 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR43.tsv (2 / 18)
14:20:57.704 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR45.tsv (3 / 18)
14:20:58.207 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR46.tsv (4 / 18)
14:20:58.559 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR47.tsv (5 / 18)
14:20:58.927 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR48.tsv (6 / 18)
14:20:59.284 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR49.tsv (7 / 18)
14:20:59.646 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR50.tsv (8 / 18)
14:20:59.998 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR51.tsv (9 / 18)
14:21:00.373 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR53.tsv (10 / 18)
14:21:00.730 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR54.tsv (11 / 18)
14:21:01.106 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR55.tsv (12 / 18)
14:21:01.458 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR56.tsv (13 / 18)
14:21:01.827 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR57.tsv (14 / 18)
14:21:02.187 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR598.tsv (15 / 18)
14:21:02.549 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR601.tsv (16 / 18)
14:21:02.971 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR602.tsv (17 / 18)
14:21:03.315 INFO  DetermineGermlineContigPloidy - Aggregating read-count file DGR60.tsv (18 / 18)
14:21:03.684 DEBUG ScriptExecutor - Executing:
14:21:03.684 DEBUG ScriptExecutor -   python
14:21:03.684 DEBUG ScriptExecutor -   /tmp/cohort_determine_ploidy_and_depth.8630416474338381794.py
14:21:03.684 DEBUG ScriptExecutor -   --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig1402167937170341908.tsv
14:21:03.684 DEBUG ScriptExecutor -   --output_calls_path=/mnt/hpccs01/home/machadog/isadora-project/gCNV/ploidy-calls
14:21:03.684 DEBUG ScriptExecutor -   --mapping_error_rate=1.000000e-02
14:21:03.684 DEBUG ScriptExecutor -   --psi_s_scale=1.000000e-04
14:21:03.684 DEBUG ScriptExecutor -   --mean_bias_sd=1.000000e-02
14:21:03.684 DEBUG ScriptExecutor -   --psi_j_scale=1.000000e-03
14:21:03.684 DEBUG ScriptExecutor -   --learning_rate=5.000000e-02
14:21:03.684 DEBUG ScriptExecutor -   --adamax_beta1=9.000000e-01
14:21:03.684 DEBUG ScriptExecutor -   --adamax_beta2=9.990000e-01
14:21:03.684 DEBUG ScriptExecutor -   --log_emission_samples_per_round=2000
14:21:03.684 DEBUG ScriptExecutor -   --log_emission_sampling_rounds=100
14:21:03.684 DEBUG ScriptExecutor -   --log_emission_sampling_median_rel_error=5.000000e-04
14:21:03.684 DEBUG ScriptExecutor -   --max_advi_iter_first_epoch=1000
14:21:03.684 DEBUG ScriptExecutor -   --max_advi_iter_subsequent_epochs=1000
14:21:03.684 DEBUG ScriptExecutor -   --min_training_epochs=20
14:21:03.684 DEBUG ScriptExecutor -   --max_training_epochs=100
14:21:03.685 DEBUG ScriptExecutor -   --initial_temperature=2.000000e+00
14:21:03.685 DEBUG ScriptExecutor -   --num_thermal_advi_iters=5000
14:21:03.685 DEBUG ScriptExecutor -   --convergence_snr_averaging_window=5000
14:21:03.685 DEBUG ScriptExecutor -   --convergence_snr_trigger_threshold=1.000000e-01
14:21:03.685 DEBUG ScriptExecutor -   --convergence_snr_countdown_window=10
14:21:03.685 DEBUG ScriptExecutor -   --max_calling_iters=1
14:21:03.685 DEBUG ScriptExecutor -   --caller_update_convergence_threshold=1.000000e-03
14:21:03.685 DEBUG ScriptExecutor -   --caller_internal_admixing_rate=7.500000e-01
14:21:03.685 DEBUG ScriptExecutor -   --caller_external_admixing_rate=7.500000e-01
14:21:03.685 DEBUG ScriptExecutor -   --disable_caller=false
14:21:03.685 DEBUG ScriptExecutor -   --disable_sampler=false
14:21:03.685 DEBUG ScriptExecutor -   --disable_annealing=false
14:21:03.685 DEBUG ScriptExecutor -   --interval_list=/tmp/intervals886310001970855612.tsv
14:21:03.685 DEBUG ScriptExecutor -   --contig_ploidy_prior_table=/mnt/hpccs01/home/machadog/isadora-project/ref/contig_ploidy_prior_hg38_c.tsv
14:21:03.685 DEBUG ScriptExecutor -   --output_model_path=/mnt/hpccs01/home/machadog/isadora-project/gCNV/ploidy-model
Traceback (most recent call last):
  File "/tmp/cohort_determine_ploidy_and_depth.8630416474338381794.py", line 101, in <module>
    args.contig_ploidy_prior_table)
  File "/home/machadog/miniconda3/envs/gatk_python_env/lib/python3.6/site-packages/gcnvkernel/io/io_ploidy.py", line 198, in get_contig_ploidy_prior_map_from_tsv_file
    values = [float(x) for x in contig_ploidy_prior_pd[column_name].values]
  File "/home/machadog/miniconda3/envs/gatk_python_env/lib/python3.6/site-packages/gcnvkernel/io/io_ploidy.py", line 198, in <listcomp>
    values = [float(x) for x in contig_ploidy_prior_pd[column_name].values]
ValueError: could not convert string to float: '0       1e-05   0.99998 1e-05'
14:21:08.734 DEBUG ScriptExecutor - Result: 1
14:21:08.734 INFO  DetermineGermlineContigPloidy - Shutting down engine
[April 15, 2024 2:21:08 PM AEST] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 0.85 minutes.
Runtime.totalMemory()=3291480064
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
python exited with 1
Command Line: python /tmp/cohort_determine_ploidy_and_depth.8630416474338381794.py --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig1402167937170341908.tsv --output_calls_path=/mnt/hpccs01/home/machadog/isadora-project/gCNV/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/intervals886310001970855612.tsv --contig_ploidy_prior_table=/mnt/hpccs01/home/machadog/isadora-project/ref/contig_ploidy_prior_hg38_c.tsv --output_model_path=/mnt/hpccs01/home/machadog/isadora-project/gCNV/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 /mnt/hpccs01/home/machadog/miniconda3/envs/gatk_python_env/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 /mnt/hpccs01/home/machadog/miniconda3/envs/gatk_python_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar DetermineGermlineContigPloidy -L cohort.gc.filtered.interval_list --interval-merging-rule OVERLAPPING_ONLY -I DGR39.tsv -I DGR43.tsv -I DGR45.tsv -I DGR46.tsv -I DGR47.tsv -I DGR48.tsv -I DGR49.tsv -I DGR50.tsv -I DGR51.tsv -I DGR53.tsv -I DGR54.tsv -I DGR55.tsv -I DGR56.tsv -I DGR57.tsv -I DGR598.tsv -I DGR601.tsv -I DGR602.tsv -I DGR60.tsv --contig-ploidy-priors /home/machadog/isadora-project/ref/contig_ploidy_prior_hg38_c.tsv --output /home/machadog/isadora-project/gCNV --output-prefix ploidy --verbosity DEBUG