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GATK 4 Determine Contig Ploidy Error - Sample "unknown" already has coverage metadata annotations

Hi,

I am running GATK 4.1 for Germline CNV on 200+ WES samples and came across the error below while running the Dtermine Contig Ploidy step. Any help would be appreciated.

15:52:07.627 DEBUG ScriptExecutor - Executing:
15:52:07.627 DEBUG ScriptExecutor - python
15:52:07.627 DEBUG ScriptExecutor - /tmp/cohort_determine_ploidy_and_depth.5271158842796165046.py
15:52:07.628 DEBUG ScriptExecutor - --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig1630545224704572068.tsv
15:52:07.628 DEBUG ScriptExecutor - --output_calls_path=/mnt/data/smb_share/Mandal_project/PCa_WES/mcdowell#Bailey-Wilson_NF_AAPC/SampleBams/ploidy-calls
15:52:07.628 DEBUG ScriptExecutor - --mapping_error_rate=1.000000e-02
15:52:07.628 DEBUG ScriptExecutor - --psi_s_scale=1.000000e-04
15:52:07.628 DEBUG ScriptExecutor - --mean_bias_sd=1.000000e-02
15:52:07.628 DEBUG ScriptExecutor - --psi_j_scale=1.000000e-03
15:52:07.628 DEBUG ScriptExecutor - --learning_rate=5.000000e-02
15:52:07.628 DEBUG ScriptExecutor - --adamax_beta1=9.000000e-01
15:52:07.628 DEBUG ScriptExecutor - --adamax_beta2=9.990000e-01
15:52:07.628 DEBUG ScriptExecutor - --log_emission_samples_per_round=2000
15:52:07.628 DEBUG ScriptExecutor - --log_emission_sampling_rounds=100
15:52:07.628 DEBUG ScriptExecutor - --log_emission_sampling_median_rel_error=5.000000e-04
15:52:07.628 DEBUG ScriptExecutor - --max_advi_iter_first_epoch=1000
15:52:07.628 DEBUG ScriptExecutor - --max_advi_iter_subsequent_epochs=1000
15:52:07.628 DEBUG ScriptExecutor - --min_training_epochs=20
15:52:07.628 DEBUG ScriptExecutor - --max_training_epochs=100
15:52:07.628 DEBUG ScriptExecutor - --initial_temperature=2.000000e+00
15:52:07.628 DEBUG ScriptExecutor - --num_thermal_advi_iters=5000
15:52:07.628 DEBUG ScriptExecutor - --convergence_snr_averaging_window=5000
15:52:07.628 DEBUG ScriptExecutor - --convergence_snr_trigger_threshold=1.000000e-01
15:52:07.628 DEBUG ScriptExecutor - --convergence_snr_countdown_window=10
15:52:07.628 DEBUG ScriptExecutor - --max_calling_iters=1
15:52:07.628 DEBUG ScriptExecutor - --caller_update_convergence_threshold=1.000000e-03
15:52:07.628 DEBUG ScriptExecutor - --caller_internal_admixing_rate=7.500000e-01
15:52:07.628 DEBUG ScriptExecutor - --caller_external_admixing_rate=7.500000e-01
15:52:07.628 DEBUG ScriptExecutor - --disable_caller=false
15:52:07.628 DEBUG ScriptExecutor - --disable_sampler=false
15:52:07.628 DEBUG ScriptExecutor - --disable_annealing=false
15:52:07.628 DEBUG ScriptExecutor - --interval_list=/tmp/intervals5347690040069421909.tsv
15:52:07.628 DEBUG ScriptExecutor - --contig_ploidy_prior_table=/mnt/data/smb_share/Mandal_project/PCa_WES/mcdowell#Bailey-Wilson_NF_AAPC/SampleBams/contigPloidyPriorsTable2.tsv
15:52:07.628 DEBUG ScriptExecutor - --output_model_path=/mnt/data/smb_share/Mandal_project/PCa_WES/mcdowell#Bailey-Wilson_NF_AAPC/SampleBams/ploidy-model
Traceback (most recent call last):
File "/tmp/cohort_determine_ploidy_and_depth.5271158842796165046.py", line 87, in
sample_metadata_collection, args.sample_coverage_metadata)
File "/usr/miniconda3/envs/gatk/lib/python3.6/site-packages/gcnvkernel/io/io_metadata.py", line 78, in read_sample_coverage_metadata
sample_name, n_j, contig_list))
File "/usr/miniconda3/envs/gatk/lib/python3.6/site-packages/gcnvkernel/structs/metadata.py", line 227, in add_sample_coverage_metadata
'Sample "{0}" already has coverage metadata annotations'.format(sample_name))
gcnvkernel.structs.metadata.SampleAlreadyInCollectionException: Sample "unknown" already has coverage metadata annotations
15:52:16.249 DEBUG ScriptExecutor - Result: 1
15:52:16.250 INFO DetermineGermlineContigPloidy - Shutting down engine
[June 21, 2019 3:52:16 PM CDT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 2.55 minutes.
Runtime.totalMemory()=5929172992
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python /tmp/cohort_determine_ploidy_and_depth.5271158842796165046.py --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig1630545224704572068.tsv --output_calls_path=/mnt/data/smb_share/Mandal_project/PCa_WES/mcdowell#Bailey-Wilson_NF_AAPC/SampleBams/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/intervals5347690040069421909.tsv --contig_ploidy_prior_table=/mnt/data/smb_share/Mandal_project/PCa_WES/mcdowell#Bailey-Wilson_NF_AAPC/SampleBams/contigPloidyPriorsTable2.tsv --output_model_path=/mnt/data/smb_share/Mandal_project/PCa_WES/mcdowell#Bailey-Wilson_NF_AAPC/SampleBams/ploidy-model
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.DetermineGermlineContigPloidy.executeDeterminePloidyAndDepthPythonScript(DetermineGermlineContigPloidy.java:411)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.doWork(DetermineGermlineContigPloidy.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)

Thanks,

Tarun

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