GermlineCNVCaller/denoising_config.json

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Yokofakun

• June 18, 2020 06:58

Hello GATK Team, I'm trying to run **GermlineCNVCaller** in CASE mode but I got the exception below. `File not found denoising_config.json`

I must say, I'm not sure I understand the workflow in "case" mode from the manual page: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants so  I'm sur I'm doing something wrong.

Can you help me please

 

a) GATK version used

gatk-4.1.7.0

b) Exact GATK commands used

 

gatk --java-options "-Xmx15g -Djava.io.tmpdir=." GermlineCNVCaller \
--run-mode CASE \
--contig-ploidy-calls "/path/to/cases-ploidy-calls" \
--model "/path/to/ctrl-ploidy-model" \
-I /path/to/B00I4BM.counts.hdf5 -I /path/to/B00I4BN.counts.hdf5 -I /path/to/B00I4BO.counts.hdf5 
--output . \
--output-prefix "20200616.gatkcnv.out" \
--verbosity DEBUG

 

/path/to/cases-ploidy-calls was generated using DetermineGermlineContigPloidy with my cases vs the cohort model ('control model)

 

gatk --java-options "-Xmx${task.memory.giga}g -Djava.io.tmpdir=." \
DetermineGermlineContigPloidy \
--model /path/to/ctrl-ploidy-model  \
-I /path/to/B00I4BM.counts.hdf5 -I /path/to/B00I4BN.counts.hdf5 -I /path/to/B00I4BO.counts.hdf5 
--output . \
--output-prefix cases-ploidy \
-imr OVERLAPPING_ONLY \
--verbosity DEBUG

 

/path/tp/ctrl-ploidy-model : was generated using

gatk --java-options "-Xmx15g -Djava.io.tmpdir=." DetermineGermlineContigPloidy \
-L "gc.filtered.interval_list" \
-XL "exclude.bed" \
-I /path/to/B00GWDY.counts.hdf5 (... other controls) \
--contig-ploidy-priors priors.tsv \
--output . \
--output-prefix ctrl-ploidy -imr OVERLAPPING_ONLY --verbosity DEBUG

 

c) The entire error log if applicable.

(...)
/sandbox/users/lindenbaum-p/packages/anaconda3/envs/GATK/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File "/sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/68/b613c4f10dd3009fdadfa0e4f5a2c0/./case_denoising_calling.4708873447659675819.py", line 187, in <module>
update_args_dict_from_saved_model(args.input_model_path, args_dict)
File "/sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/68/b613c4f10dd3009fdadfa0e4f5a2c0/./case_denoising_calling.4708873447659675819.py", line 109, in update_args_dict_from_saved_model
with open(os.path.join(input_model_path, "denoising_config.json"), 'r') as fp:
FileNotFoundError: [Errno 2] No such file or directory: '/sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/13/79fd0f3f7f1a16c6227e4a673c0637/ctrl-ploidy-model/denoising_config.json'
22:05:41.135 DEBUG ScriptExecutor - Result: 1
22:05:41.139 INFO GermlineCNVCaller - Shutting down engine
[June 17, 2020 10:05:41 PM CEST] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 13.76 minutes.
Runtime.totalMemory()=4390387712
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
python exited with 1
Command Line: python /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/68/b613c4f10dd3009fdadfa0e4f5a2c0/./case_denoising_calling.4708873447659675819.py --ploidy_calls_path=/sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/ec/8b313dfce764d46bf943174254c1e9/cases-ploidy-calls --output_calls_path=/sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/68/b613c4f10dd3009fdadfa0e4f5a2c0/20200616.gatkcnv.out-calls --output_tracking_path=/sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/68/b613c4f10dd3009fdadfa0e4f5a2c0/20200616.gatkcnv.out-tracking --input_model_path=/sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/13/79fd0f3f7f1a16c6227e4a673c0637/ctrl-ploidy-model --read_count_tsv_files /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/68/b613c4f10dd3009fdadfa0e4f5a2c0/B00I4BM6674837490289290626.tsv /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/68/b613c4f10dd3009fdadfa0e4f5a2c0/B00I4BN8380570089158324775.tsv /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/68/b613c4f10dd3009fdadfa0e4f5a2c0/B00I4BO8426920295833024050.tsv --psi_s_scale=1.000000e-04 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --p_alt=1.000000e-06 --cnv_coherence_length=1.000000e+04 --max_copy_number=5 --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.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:130)
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:438)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:309)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
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:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
Using GATK jar /sandbox/apps/bioinfo/binaries/gatk/0.0.0/gatk-4.1.7.0/gatk-package-4.1.7.0-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 -Xmx15g -Djava.io.tmpdir=. -jar /sandbox/apps/bioinfo/binaries/gatk/0.0.0/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar GermlineCNVCaller --run-mode CASE --contig-ploidy-calls /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/ec/8b313dfce764d46bf943174254c1e9/cases-ploidy-calls --model /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/13/79fd0f3f7f1a16c6227e4a673c0637/ctrl-ploidy-model -I /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/5a/fc4ca250e068d1bd930275e976b252/B00I4BM.counts.hdf5 -I /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/5a/fc4ca250e068d1bd930275e976b252/B00I4BN.counts.hdf5 -I /sandbox/shares/u1087/lindenb/work/NEXTFLOW/20200616.gatkcnv/work/5a/fc4ca250e068d1bd930275e976b252/B00I4BO.counts.hdf5 --output . --output-prefix 20200616.gatkcnv.out --verbosity DEBUG

``

 

0

• 

  Bhanu Gandham

  • June 24, 2020 03:51

  Hi,

   

  Have you run in cohort mode to create the PON? PON is needed for case mode. The doc you shared above has more information on this.

   

  0

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• 

  Heba B abusamra

  • August 06, 2020 11:27

  I have the same error can you explain how to create PON in cohort mode 

  my commands

  /app/Genome/GATK-4.1.8.1/gatk DetermineGermlineContigPloidy -L target.preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY -I PBG-1095-19_S2.tsv -I PBG-1077-19R_S8.tsv -I PBG-1076-19R_S7.tsv -I PBG-1096-19_S1.tsv --contig-ploidy-priors contig_ploidy_priors.tsv --output . --output-prefix ploidy --verbosity DEBUG

  /app/Genome/GATK-4.1.8.1/gatk DetermineGermlineContigPloidy --model ploidy-model -I POCG-490-20_S2.tsv -O . --output-prefix ploidy-case --verbosity DEBUG

  /app/Genome/GATK-4.1.8.1/gatk GermlineCNVCaller --run-mode CASE -I POCG-490-20_S2.tsv --contig-ploidy-calls ploidy-case-calls --model ploidy-model --output POCG-490-20 --output-prefix POCG-490-20 --verbosity DEBUG

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• 

  Genevieve Brandt (she/her)

  • August 06, 2020 17:50

  Please see this document under 3. Call autosomal and allosomal contig ploidy with DetermineGermlineContigPloidy https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants

  0

  Comment actions Permalink
• 

  Dr N Ch

  • November 18, 2021 01:57
  • Edited

  Genevieve Brandt

  Hi... Should we run "GermlineCNVCaller --run-mode COHORT" step first... to make work  GermlineCNVCaller --run-mode CASE?

  1. Initially i tried running case step only and it exited with "FileNotFoundError: [Errno 2] No such file or directory: 'CNV/ploidy-case-calls/denoising_config.json' error

   

  2. To resolve the above error... i ran it in cohort mode ---- and these specific errors pop up.

  a) "Sample 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."

  How to I make this list :"Optionally provide intervals to exclude from analysis with --exclude-intervals or -XL, e.g. pseudoautosomal (PAR) regions, "

  b) 06:09:58.115 INFO gcnvkernel.tasks.task_cohort_denoising_calling - Instantiating the denoising model (warm-up)...
  06:10:05.004 INFO GermlineCNVCaller - Shutting down engine
  [18 November, 2021 6:10:05 AM IST] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 0.38 minutes.
  Runtime.totalMemory()=1178075136
  org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
  python exited with 139
  Command Line: python /tmp/cohort_denoising_calling.8874612537117360904.py --ploidy_calls_path=CohortBuild/ploidy-calls --output_calls_path=cohort5cnv-calls --output_tracking_path=CohortBuild/cohortfivecnv/cohort5cnv-tracking --random_seed=1984 --modeling_interval_list=/tmp/intervals594573086710043408.tsv --output_model_path=CohortBuild/cohortfivecnv/cohort5cnv-model --enable_explicit_gc_bias_modeling=False --read_count_tsv_files /tmp/MMG0067808841026474173153131.tsv /tmp/MMG0067827618115401963325547.tsv /tmp/MMG0067922876341803010914191.tsv /tmp/MMG006877700705929029814375.tsv /tmp/MMG0068793470283993599927353.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)

  no clue what it says about!

  When I download the tutorial data I see that the ploidy model folders include a “denoising_config.json” file, but it doesn’t get created with any commands that I run.

   

  Any help would be appreciated

   

  1

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • November 19, 2021 19:16

  Hi Dr N Ch,

  In order to run case mode, you'll need to use a model already constructed with cohort mode. For cohort mode, the general recommendation is to use around 100 samples or more. Do you have this many samples?

  This information is all covered in the introduction section of our tutorial (How to) Call common and rare germline copy number variants: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants.

  Please let me know if you have further questions.

  Best,

  Genevieve

  0

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• 

  Dr N Ch

  • November 20, 2021 03:47

  Hi, Thank you for the response... I am currently following the protocol as in the link shared above.. I can get hold of 100 samples... but now i am trying with 5 samples... to setup the steps ..

  I am stuck up at the above error and i am unable to find "denoising_config.json" script... and thus the program exits...

  How can we resolve this issue?

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • November 22, 2021 21:19

  Hi Dr N Ch,

  You'll need to do cohort mode first to create the model which is needed for case mode. Could you share the complete command and error message for where you are getting stuck in cohort mode? 

  Best,

  Genevieve

  0

  Comment actions Permalink
• 

  Dr N Ch

  • November 23, 2021 03:34

  The model has been created with "DetermineGermlineContigPloidy" and the command successfully worked...

  the next step is to call GermlineCNVCaller : when i tried to execute it... it is throwing up the error

   

  6:09:58.115 INFO gcnvkernel.tasks.task_cohort_denoising_calling - Instantiating the denoising model (warm-up)...
  06:10:05.004 INFO GermlineCNVCaller - Shutting down engine
  [18 November, 2021 6:10:05 AM IST] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 0.38 minutes.
  Runtime.totalMemory()=1178075136
  org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
  python exited with 139
  Command Line: python /tmp/cohort_denoising_calling.8874612537117360904.py --ploidy_calls_path=CohortBuild/ploidy-calls --output_calls_path=cohort5cnv-calls --output_tracking_path=CohortBuild/cohortfivecnv/cohort5cnv-tracking --random_seed=1984 --modeling_interval_list=/tmp/intervals594573086710043408.tsv --output_model_path=CohortBuild/cohortfivecnv/cohort5cnv-model --enable_explicit_gc_bias_modeling=False --read_count_tsv_files /tmp/MMG0067808841026474173153131.tsv /tmp/MMG0067827618115401963325547.tsv /tmp/MMG0067922876341803010914191.tsv /tmp/MMG006877700705929029814375.tsv /tmp/MMG0068793470283993599927353.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)

  no clue what it says about!

  When I download the tutorial data I see that the ploidy model folders include a “denoising_config.json” file, but it doesn’t get created with any commands that I run.

   

  Any help would be appreciated

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • November 23, 2021 19:09

  Dr N Ch Could you please also share your command?

  Is this for cohort mode?

  0

  Comment actions Permalink
• 

  Dr N Ch

  • November 29, 2021 15:00

   

  Genevieve Brandt

  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
  
  

  ERROR OBTAINED:

  [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)

   

  STUCK UP HERE!

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• 

  Genevieve Brandt (she/her)

  • December 01, 2021 18:15

  Hi Dr N Ch,

  Thank you! This is helpful for determining the problem. The error message I am seeing is this one:

  org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
  python exited with 139

  Could you create a new post for this issue? I don't think that it is the same as the original post we are commenting on. My first thoughts regarding this issue is that it could be a problem with the environment/hardware relating to the python packages (related issue). In the new post, please also include your conda/docker environment details.

  Best,

  Genevieve

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