Genevieve Brandt (she/her)

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:  gatk-4.2.0.0

     conda version used: miniconda3, conda 4.10.3

b) Exact command used:

/home/Applications/gatk-4.2.0.0/gatk GermlineCNVCaller \
--run-mode COHORT \
-L /home/Projects/CNV/5.cohort.interval_list \
-I /home/Projects/CNV/80.tsv -I /home/Projects/CNV/82.tsv -I /home/Projects/CNV/92.tsv -I /home/Projects/CNV/77.tsv -I /home/Projects/CNV/79.tsv --contig-ploidy-calls /home/Projects/CNV/ploidy-calls --interval-merging-rule OVERLAPPING_ONLY --output /home/Projects/CNV/cohortfivecnv --output-prefix cohort5cnv --verbosity DEBUG

c) Entire error log:
[29 November, 2021 8:17:01 PM IST] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 1.12 minutes.
Runtime.totalMemory()=1244659712
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 139
Command Line: python /tmp/cohort_denoising_calling.2460559553786744739.py --ploidy_calls_path=/home/Projects/CNV/ploidy-calls --output_calls_path=/home/Projects/CNV/cohortfivecnv/cohort5cnv-calls --output_tracking_path=/home/Projects/CNV/cohortfivecnv/cohort5cnv-tracking --random_seed=1984 --modeling_interval_list=/tmp/intervals1605665010689778693.tsv --output_model_path=/home/Projects/CNV/cohortfivecnv/cohort5cnv-model --enable_explicit_gc_bias_modeling=False --read_count_tsv_files /tmp/804360048707576940571.tsv /tmp/82883171617448040778.tsv /tmp/921039727042770894278.tsv /tmp/777516631403810019298.tsv /tmp/798364616654579626422.tsv --psi_s_scale=1.000000e-04 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --max_bias_factors=5 --psi_t_scale=1.000000e-03 --log_mean_bias_std=1.000000e-01 --init_ard_rel_unexplained_variance=1.000000e-01 --num_gc_bins=20 --gc_curve_sd=1.000000e+00 --active_class_padding_hybrid_mode=50000 --enable_bias_factors=True --disable_bias_factors_in_active_class=False --p_alt=1.000000e-06 --cnv_coherence_length=1.000000e+04 --max_copy_number=5 --p_active=0.010000 --class_coherence_length=10000.000000 --learning_rate=1.000000e-02 --adamax_beta1=9.000000e-01 --adamax_beta2=9.900000e-01 --log_emission_samples_per_round=50 --log_emission_sampling_rounds=10 --log_emission_sampling_median_rel_error=5.000000e-03 --max_advi_iter_first_epoch=5000 --max_advi_iter_subsequent_epochs=200 --min_training_epochs=10 --max_training_epochs=50 --initial_temperature=1.500000e+00 --num_thermal_advi_iters=2500 --convergence_snr_averaging_window=500 --convergence_snr_trigger_threshold=1.000000e-01 --convergence_snr_countdown_window=10 --max_calling_iters=10 --caller_update_convergence_threshold=1.000000e-03 --caller_internal_admixing_rate=7.500000e-01 --caller_external_admixing_rate=1.000000e+00 --disable_caller=false --disable_sampler=false --disable_annealing=false
at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:340)
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)

Thank you