Question: gCNVKERNEL Error while using GATK 4.1
0
gravatar for mtkk94
17 months ago by
mtkk9410
mtkk9410 wrote:

Hi,

I am trying to run GATK 4.1 on WES data for germline CNV detection, and received an error about gcnvkernel. The error states that we do not have gcnvkernel installed, and we can not figure out how to install it. We have used the command "source activate gatk". We are using Python version 3.6.2. WE are getting this error on the DetermineGermlineContigPloidy step. Here's the error:

    Using GATK jar /mnt/data/BIO/tarun/gatk/gatk-package-4.1.1.0-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/data/BIO/tarun/gatk/gatk-package-4.1.1.0-local.jar DetermineGermlineContigPloidy --interval-merging-rule OVERLAPPING_ONLY -I s_1000702506.igv-sorted.tsv -I s_1020203123.igv-sorted.tsv -I s_1111503550.igv-sorted.tsv -I s_1221909007.igv-sorted.tsv -I s_1221909433.igv-sorted.tsv -I s_1222003926.igv-sorted.tsv -I s_1225518817.igv-sorted.tsv -I s_1225529798.igv-sorted.tsv -I s_29138.igv-sorted.tsv -I s_29224.igv-sorted.tsv -I s_31726.igv-sorted.tsv -I s_33020.igv-sorted.tsv -I s_33503.igv-sorted.tsv -I s_34026.igv-sorted.tsv -I s_36674.igv-sorted.tsv -I s_37101.igv-sorted.tsv -I s_40587.igv-sorted.tsv -I s_55257.igv-sorted.tsv -I s_918800749.igv-sorted.tsv -I s_921801464.igv-sorted.tsv --contig-ploidy-priors contigPloidyPriorsTable.tsv --output . --output-prefix ploidy --verbosity DEBUG

. . . . . .

  11:16:46.473 DEBUG ScriptExecutor -   python
        11:16:46.473 DEBUG ScriptExecutor -   -c
        11:16:46.473 DEBUG ScriptExecutor -   import gcnvkernel

        11:16:51.099 DEBUG ScriptExecutor - Result: 0

    11:16:51.099 INFO  DetermineGermlineContigPloidy - Done initializing engine
    11:16:51.103 INFO  DetermineGermlineContigPloidy - No contig-ploidy model was provided, running in cohort mode...
    11:16:51.752 INFO  DetermineGermlineContigPloidy - Retrieving intervals from read-count file (s_1000702506.igv-sorted.tsv)...
    11:16:52.232 INFO  DetermineGermlineContigPloidy - Validating and aggregating coverage per contig from input read-count files...
    11:16:52.377 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_1000702506.igv-sorted.tsv (1 / 20)
    11:16:53.078 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_1020203123.igv-sorted.tsv (2 / 20)
    11:16:53.636 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_1111503550.igv-sorted.tsv (3 / 20)
    11:16:54.094 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_1221909007.igv-sorted.tsv (4 / 20)
    11:16:54.488 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_1221909433.igv-sorted.tsv (5 / 20)
    11:16:54.845 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_1222003926.igv-sorted.tsv (6 / 20)
    11:16:55.350 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_1225518817.igv-sorted.tsv (7 / 20)
    11:16:55.787 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_1225529798.igv-sorted.tsv (8 / 20)
    11:16:56.225 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_29138.igv-sorted.tsv (9 / 20)
    11:16:56.692 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_29224.igv-sorted.tsv (10 / 20)
    11:16:57.062 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_31726.igv-sorted.tsv (11 / 20)
    11:16:57.443 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_33020.igv-sorted.tsv (12 / 20)
    11:16:57.754 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_33503.igv-sorted.tsv (13 / 20)
    11:16:58.268 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_34026.igv-sorted.tsv (14 / 20)
    11:16:58.743 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_36674.igv-sorted.tsv (15 / 20)
    11:16:59.219 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_37101.igv-sorted.tsv (16 / 20)
    11:16:59.648 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_40587.igv-sorted.tsv (17 / 20)
    11:17:00.009 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_55257.igv-sorted.tsv (18 / 20)
    11:17:00.381 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_918800749.igv-sorted.tsv (19 / 20)
    11:17:00.774 INFO  DetermineGermlineContigPloidy - Aggregating read-count file s_921801464.igv-sorted.tsv (20 / 20)
    11:17:01.327 DEBUG ScriptExecutor - Executing:
    11:17:01.328 DEBUG ScriptExecutor -   python
    11:17:01.328 DEBUG ScriptExecutor -   /tmp/cohort_determine_ploidy_and_depth.5450337803162121334.py
    11:17:01.328 DEBUG ScriptExecutor -   --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig7609824734646765959.tsv
    11:17:01.328 DEBUG ScriptExecutor -   --output_calls_path=/mnt/data/smb_share/Mandal_project/Aim1_10PCa10Con_Data_Mayo/gatk/ploidy-calls
    11:17:01.328 DEBUG ScriptExecutor -   --mapping_error_rate=1.000000e-02
    11:17:01.328 DEBUG ScriptExecutor -   --psi_s_scale=1.000000e-04
    11:17:01.328 DEBUG ScriptExecutor -   --mean_bias_sd=1.000000e-02
    11:17:01.328 DEBUG ScriptExecutor -   --psi_j_scale=1.000000e-03
    11:17:01.328 DEBUG ScriptExecutor -   --learning_rate=5.000000e-02
    11:17:01.328 DEBUG ScriptExecutor -   --adamax_beta1=9.000000e-01
    11:17:01.328 DEBUG ScriptExecutor -   --adamax_beta2=9.990000e-01
    11:17:01.328 DEBUG ScriptExecutor -   --log_emission_samples_per_round=2000
    11:17:01.328 DEBUG ScriptExecutor -   --log_emission_sampling_rounds=100
    11:17:01.328 DEBUG ScriptExecutor -   --log_emission_sampling_median_rel_error=5.000000e-04
    11:17:01.328 DEBUG ScriptExecutor -   --max_advi_iter_first_epoch=1000
    11:17:01.328 DEBUG ScriptExecutor -   --max_advi_iter_subsequent_epochs=1000
    11:17:01.328 DEBUG ScriptExecutor -   --min_training_epochs=20
    11:17:01.328 DEBUG ScriptExecutor -   --max_training_epochs=100
    11:17:01.328 DEBUG ScriptExecutor -   --initial_temperature=2.000000e+00
    11:17:01.328 DEBUG ScriptExecutor -   --num_thermal_advi_iters=5000
    11:17:01.328 DEBUG ScriptExecutor -   --convergence_snr_averaging_window=5000
    11:17:01.328 DEBUG ScriptExecutor -   --convergence_snr_trigger_threshold=1.000000e-01
    11:17:01.328 DEBUG ScriptExecutor -   --convergence_snr_countdown_window=10
    11:17:01.328 DEBUG ScriptExecutor -   --max_calling_iters=1
    11:17:01.328 DEBUG ScriptExecutor -   --caller_update_convergence_threshold=1.000000e-03
    11:17:01.329 DEBUG ScriptExecutor -   --caller_internal_admixing_rate=7.500000e-01
    11:17:01.329 DEBUG ScriptExecutor -   --caller_external_admixing_rate=7.500000e-01
    11:17:01.329 DEBUG ScriptExecutor -   --disable_caller=false
    11:17:01.329 DEBUG ScriptExecutor -   --disable_sampler=false
    11:17:01.329 DEBUG ScriptExecutor -   --disable_annealing=false
    11:17:01.329 DEBUG ScriptExecutor -   --interval_list=/tmp/intervals7394963618998808676.tsv
    11:17:01.329 DEBUG ScriptExecutor -   --contig_ploidy_prior_table=/mnt/data/smb_share/Mandal_project/Aim1_10PCa10Con_Data_Mayo/gatk/contigPloidyPriorsTable.tsv
    11:17:01.329 DEBUG ScriptExecutor -   --output_model_path=/mnt/data/smb_share/Mandal_project/Aim1_10PCa10Con_Data_Mayo/gatk/ploidy-model
    11:17:07.300 INFO gcnvkernel.structs.metadata - Generating intervals metadata...
    Traceback (most recent call last):
      File "/tmp/cohort_determine_ploidy_and_depth.5450337803162121334.py", line 96, in <module>
        ploidy_config = gcnvkernel.PloidyModelConfig.from_args_dict(args_dict)
      File "/usr/miniconda3/envs/gatk/lib/python3.6/site-packages/gcnvkernel/models/model_ploidy.py", line 126, in from_args_dict
        return PloidyModelConfig(**relevant_kwargs)
      File "/usr/miniconda3/envs/gatk/lib/python3.6/site-packages/gcnvkernel/models/model_ploidy.py", line 45, in __init__
        contig_ploidy_prior_map)
      File "/usr/miniconda3/envs/gatk/lib/python3.6/site-packages/gcnvkernel/models/model_ploidy.py", line 60, in _get_validated_contig_ploidy_prior_map
        padded_validated_prior = commons.get_normalized_prob_vector(padded_validated_prior, config.prob_sum_tol)
      File "/usr/miniconda3/envs/gatk/lib/python3.6/site-packages/gcnvkernel/models/commons.py", line 26, in get_normalized_prob_vector
        assert all(prob_vector >= 0), "Probabilities must be non-negative"
    AssertionError: Probabilities must be non-negative
    11:17:08.243 DEBUG ScriptExecutor - Result: 1
    11:17:08.245 INFO  DetermineGermlineContigPloidy - Shutting down engine
    [May 1, 2019 11:17:08 AM CDT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 0.40 minutes.
    Runtime.totalMemory()=2511863808
    org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
    python exited with 1
    Command Line: python /tmp/cohort_determine_ploidy_and_depth.5450337803162121334.py --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig7609824734646765959.tsv --output_calls_path=/mnt/data/smb_share/Mandal_project/Aim1_10PCa10Con_Data_Mayo/gatk/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/intervals7394963618998808676.tsv --contig_ploidy_prior_table=/mnt/data/smb_share/Mandal_project/Aim1_10PCa10Con_Data_Mayo/gatk/contigPloidyPriorsTable.tsv --output_model_path=/mnt/data/smb_share/Mandal_project/Aim1_10PCa10Con_Data_Mayo/gatk/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)

Any help would be appreciated.

Thanks,

Tarun

cnv gcnvkernel gatk • 618 views
ADD COMMENTlink written 17 months ago by mtkk9410
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