I ran the GermlineCNVCaller on the GATK4 docker using data from Illumina WES runs:
I saw one post about this from 2018, but there were no solutions provided. Was hoping someone figured out what might be causing this issue. Is says that there were anomalous ploidy (3) and karyotypes found. Is there a way to circumvent the errors and proceed with the CNV Calls?
Here is the error log on the terminal:
-------------------------------------------------------------------------------------------------------------------------------------------------------
```
[May 30, 2019 9:34:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 42.22 minutes.
Runtime.totalMemory()=309329920
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 137
Command Line: python /tmp/cohort_denoising_calling.2469363531812992060.py --ploidy_calls_path=/gatk/contig_ploidy_out/201to221-calls --output_calls_path=/gatk/cnv_caller_out/201to221-calls --output_tracking_path=/gatk/cnv_caller_out/201to221-tracking --modeling_interval_list=/tmp/intervals5455361474614479137.tsv --output_model_path=/gatk/cnv_caller_out/201to221-model --enable_explicit_gc_bias_modeling=False --read_count_tsv_files /tmp/sample-06897365439090412481.tsv /tmp/sample-14321148589333665336.tsv /tmp/sample-21835961979843646097.tsv /tmp/sample-38074673515857876969.tsv /tmp/sample-43743553031942260664.tsv /tmp/sample-57298179702079672321.tsv /tmp/sample-62031280085994514055.tsv /tmp/sample-75741767774624679683.tsv /tmp/sample-81194219972171310383.tsv /tmp/sample-97680992559618886592.tsv /tmp/sample-107437152082991706984.tsv /tmp/sample-111888210707192633556.tsv /tmp/sample-128036150598221044845.tsv /tmp/sample-138872009798693940440.tsv /tmp/sample-14940235851191146248.tsv /tmp/sample-154069286361387789329.tsv /tmp/sample-166690524464389231566.tsv /tmp/sample-17146091880304952416.tsv /tmp/sample-187389732363112723677.tsv /tmp/sample-192301262323034965667.tsv --psi_s_scale=1.000000e-04 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --max_bias_factors=5 --psi_t_scale=1.000000e-03 --log_mean_bias_std=1.000000e-01 --init_ard_rel_unexplained_variance=1.000000e-01 --num_gc_bins=20 --gc_curve_sd=1.000000e+00 --active_class_padding_hybrid_mode=50000 --enable_bias_factors=True --disable_bias_factors_in_active_class=False --p_alt=1.000000e-06 --cnv_coherence_length=1.000000e+04 --max_copy_number=5 --p_active=0.010000 --class_coherence_length=10000.000000 --learning_rate=1.000000e-02 --adamax_beta1=9.000000e-01 --adamax_beta2=9.900000e-01 --log_emission_samples_per_round=50 --log_emission_sampling_rounds=10 --log_emission_sampling_median_rel_error=5.000000e-03 --max_advi_iter_first_epoch=5000 --max_advi_iter_subsequent_epochs=200 --min_training_epochs=10 --max_training_epochs=50 --initial_temperature=1.500000e+00 --num_thermal_advi_iters=2500 --convergence_snr_averaging_window=500 --convergence_snr_trigger_threshold=1.000000e-01 --convergence_snr_countdown_window=10 --max_calling_iters=10 --caller_update_convergence_threshold=1.000000e-03 --caller_internal_admixing_rate=7.500000e-01 --caller_external_admixing_rate=1.000000e+00 --disable_caller=false --disable_sampler=false --disable_annealing=false
Stdout: 20:52:35.963 INFO cohort_denoising_calling - Loading 20 read counts file(s)...
20:52:57.460 INFO gcnvkernel.io.io_metadata - Loading germline contig ploidy and global read depth metadata...
20:52:57.467 WARNING gcnvkernel.structs.metadata - Sample 219-Exp29_S115 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.468 WARNING gcnvkernel.structs.metadata - Sample 219-Exp29_S115 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.472 WARNING gcnvkernel.structs.metadata - Sample 220-Exp29_S116 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.472 WARNING gcnvkernel.structs.metadata - Sample 220-Exp29_S116 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.476 WARNING gcnvkernel.structs.metadata - Sample 208-Exp29_S104 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.476 WARNING gcnvkernel.structs.metadata - Sample 208-Exp29_S104 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.481 WARNING gcnvkernel.structs.metadata - Sample 221-Exp29_S117 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.481 WARNING gcnvkernel.structs.metadata - Sample 221-Exp29_S117 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.486 WARNING gcnvkernel.structs.metadata - Sample 213-Exp29_S109 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.486 WARNING gcnvkernel.structs.metadata - Sample 213-Exp29_S109 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.491 WARNING gcnvkernel.structs.metadata - Sample 201-Exp29_S97 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.491 WARNING gcnvkernel.structs.metadata - Sample 201-Exp29_S97 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.495 WARNING gcnvkernel.structs.metadata - Sample 209-Exp29_S105 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.495 WARNING gcnvkernel.structs.metadata - Sample 209-Exp29_S105 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.499 WARNING gcnvkernel.structs.metadata - Sample 203-Exp29_S99 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.499 WARNING gcnvkernel.structs.metadata - Sample 203-Exp29_S99 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.504 WARNING gcnvkernel.structs.metadata - Sample 212-Exp29_S108 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.504 WARNING gcnvkernel.structs.metadata - Sample 212-Exp29_S108 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.508 WARNING gcnvkernel.structs.metadata - Sample 204-Exp29_S100 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.509 WARNING gcnvkernel.structs.metadata - Sample 204-Exp29_S100 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.513 WARNING gcnvkernel.structs.metadata - Sample 218-Exp29_S114 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.513 WARNING gcnvkernel.structs.metadata - Sample 218-Exp29_S114 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.517 WARNING gcnvkernel.structs.metadata - Sample 215-Exp29_S111 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.517 WARNING gcnvkernel.structs.metadata - Sample 215-Exp29_S111 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unrelia
Stderr:
at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:126)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:170)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:151)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:121)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.executeGermlineCNVCallerPythonScript(GermlineCNVCaller.java:441)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:288)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
```
---------------------------------------------------------------------------------------------------------------------------------------------------------
I saw one post about this from 2018, but there were no solutions provided. Was hoping someone figured out what might be causing this issue. Is says that there were anomalous ploidy (3) and karyotypes found. Is there a way to circumvent the errors and proceed with the CNV Calls?
Here is the error log on the terminal:
-------------------------------------------------------------------------------------------------------------------------------------------------------
```
[May 30, 2019 9:34:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 42.22 minutes.
Runtime.totalMemory()=309329920
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 137
Command Line: python /tmp/cohort_denoising_calling.2469363531812992060.py --ploidy_calls_path=/gatk/contig_ploidy_out/201to221-calls --output_calls_path=/gatk/cnv_caller_out/201to221-calls --output_tracking_path=/gatk/cnv_caller_out/201to221-tracking --modeling_interval_list=/tmp/intervals5455361474614479137.tsv --output_model_path=/gatk/cnv_caller_out/201to221-model --enable_explicit_gc_bias_modeling=False --read_count_tsv_files /tmp/sample-06897365439090412481.tsv /tmp/sample-14321148589333665336.tsv /tmp/sample-21835961979843646097.tsv /tmp/sample-38074673515857876969.tsv /tmp/sample-43743553031942260664.tsv /tmp/sample-57298179702079672321.tsv /tmp/sample-62031280085994514055.tsv /tmp/sample-75741767774624679683.tsv /tmp/sample-81194219972171310383.tsv /tmp/sample-97680992559618886592.tsv /tmp/sample-107437152082991706984.tsv /tmp/sample-111888210707192633556.tsv /tmp/sample-128036150598221044845.tsv /tmp/sample-138872009798693940440.tsv /tmp/sample-14940235851191146248.tsv /tmp/sample-154069286361387789329.tsv /tmp/sample-166690524464389231566.tsv /tmp/sample-17146091880304952416.tsv /tmp/sample-187389732363112723677.tsv /tmp/sample-192301262323034965667.tsv --psi_s_scale=1.000000e-04 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --max_bias_factors=5 --psi_t_scale=1.000000e-03 --log_mean_bias_std=1.000000e-01 --init_ard_rel_unexplained_variance=1.000000e-01 --num_gc_bins=20 --gc_curve_sd=1.000000e+00 --active_class_padding_hybrid_mode=50000 --enable_bias_factors=True --disable_bias_factors_in_active_class=False --p_alt=1.000000e-06 --cnv_coherence_length=1.000000e+04 --max_copy_number=5 --p_active=0.010000 --class_coherence_length=10000.000000 --learning_rate=1.000000e-02 --adamax_beta1=9.000000e-01 --adamax_beta2=9.900000e-01 --log_emission_samples_per_round=50 --log_emission_sampling_rounds=10 --log_emission_sampling_median_rel_error=5.000000e-03 --max_advi_iter_first_epoch=5000 --max_advi_iter_subsequent_epochs=200 --min_training_epochs=10 --max_training_epochs=50 --initial_temperature=1.500000e+00 --num_thermal_advi_iters=2500 --convergence_snr_averaging_window=500 --convergence_snr_trigger_threshold=1.000000e-01 --convergence_snr_countdown_window=10 --max_calling_iters=10 --caller_update_convergence_threshold=1.000000e-03 --caller_internal_admixing_rate=7.500000e-01 --caller_external_admixing_rate=1.000000e+00 --disable_caller=false --disable_sampler=false --disable_annealing=false
Stdout: 20:52:35.963 INFO cohort_denoising_calling - Loading 20 read counts file(s)...
20:52:57.460 INFO gcnvkernel.io.io_metadata - Loading germline contig ploidy and global read depth metadata...
20:52:57.467 WARNING gcnvkernel.structs.metadata - Sample 219-Exp29_S115 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.468 WARNING gcnvkernel.structs.metadata - Sample 219-Exp29_S115 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.472 WARNING gcnvkernel.structs.metadata - Sample 220-Exp29_S116 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.472 WARNING gcnvkernel.structs.metadata - Sample 220-Exp29_S116 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.476 WARNING gcnvkernel.structs.metadata - Sample 208-Exp29_S104 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.476 WARNING gcnvkernel.structs.metadata - Sample 208-Exp29_S104 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.481 WARNING gcnvkernel.structs.metadata - Sample 221-Exp29_S117 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.481 WARNING gcnvkernel.structs.metadata - Sample 221-Exp29_S117 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.486 WARNING gcnvkernel.structs.metadata - Sample 213-Exp29_S109 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.486 WARNING gcnvkernel.structs.metadata - Sample 213-Exp29_S109 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.491 WARNING gcnvkernel.structs.metadata - Sample 201-Exp29_S97 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.491 WARNING gcnvkernel.structs.metadata - Sample 201-Exp29_S97 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.495 WARNING gcnvkernel.structs.metadata - Sample 209-Exp29_S105 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.495 WARNING gcnvkernel.structs.metadata - Sample 209-Exp29_S105 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.499 WARNING gcnvkernel.structs.metadata - Sample 203-Exp29_S99 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.499 WARNING gcnvkernel.structs.metadata - Sample 203-Exp29_S99 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.504 WARNING gcnvkernel.structs.metadata - Sample 212-Exp29_S108 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.504 WARNING gcnvkernel.structs.metadata - Sample 212-Exp29_S108 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.508 WARNING gcnvkernel.structs.metadata - Sample 204-Exp29_S100 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.509 WARNING gcnvkernel.structs.metadata - Sample 204-Exp29_S100 has an anomalous karyotype ({'Y': 1, 'X': 2}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.513 WARNING gcnvkernel.structs.metadata - Sample 218-Exp29_S114 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.513 WARNING gcnvkernel.structs.metadata - Sample 218-Exp29_S114 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.517 WARNING gcnvkernel.structs.metadata - Sample 215-Exp29_S111 has an anomalous ploidy (3) for contig 19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
20:52:57.517 WARNING gcnvkernel.structs.metadata - Sample 215-Exp29_S111 has an anomalous karyotype ({'Y': 0, 'X': 3}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unrelia
Stderr:
at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:126)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:170)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:151)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:121)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.executeGermlineCNVCallerPythonScript(GermlineCNVCaller.java:441)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:288)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
```
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