Entering edit mode
5.6 years ago
mtkk94
▴
10
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
Could you solve the error? I am stuck with the same error.
Any help please
gcnvkernelcan be installed usingconda.