You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am using CNV detection with GATK v4.3.0.0 for quite a while very successfully. Now we changed the enrichment kit and I had to do a new model. Everything worked well for the model phase.
As I now run one sample against this model I got the following error at the CNV detection step:
Using GATK jar /usr/BioinfSoftware/GATK/4.3.0.0/gatk-package-4.3.0.0-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 /usr/BioinfSoftware/GATK/4.3.0.0/gatk-package-4.3.0.0-local.jar GermlineCNVCaller --run-mode CASE -contig-ploidy-calls /media/Ergebnisse/0115-24_Masterpanel_NB501654_0623/0115-24_DGCP_noProbe-calls/ --model /media/Data/MasterV3/GCNV_noProbe-model/ --input /media/Ergebnisse/0115-24_Masterpanel_NB501654_0623/0115-24_noProbe.hdf5 --output /media/Ergebnisse/0115-24_Masterpanel_NB501654_0623/ --output-prefix 0115-24_GCNV_noProbe --tmp-dir /media/Data/tmp/
10:20:01.611 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/BioinfSoftware/GATK/4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:20:01.717 INFO GermlineCNVCaller - ------------------------------------------------------------
10:20:01.718 INFO GermlineCNVCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0
10:20:01.718 INFO GermlineCNVCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
10:20:01.718 INFO GermlineCNVCaller - Executing as die9s@k-hg-srv3 on Linux v5.3.18-24.37-default amd64
10:20:01.718 INFO GermlineCNVCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.11+9-suse-3.56.1-x8664
10:20:01.718 INFO GermlineCNVCaller - Start Date/Time: March 14, 2024 at 10:20:01 AM CET
10:20:01.718 INFO GermlineCNVCaller - ------------------------------------------------------------
10:20:01.718 INFO GermlineCNVCaller - ------------------------------------------------------------
10:20:01.719 INFO GermlineCNVCaller - HTSJDK Version: 3.0.1
10:20:01.719 INFO GermlineCNVCaller - Picard Version: 2.27.5
10:20:01.719 INFO GermlineCNVCaller - Built for Spark Version: 2.4.5
10:20:01.719 INFO GermlineCNVCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:20:01.719 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:20:01.719 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:20:01.719 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:20:01.719 INFO GermlineCNVCaller - Deflater: IntelDeflater
10:20:01.719 INFO GermlineCNVCaller - Inflater: IntelInflater
10:20:01.719 INFO GermlineCNVCaller - GCS max retries/reopens: 20
10:20:01.719 INFO GermlineCNVCaller - Requester pays: disabled
10:20:01.720 INFO GermlineCNVCaller - Initializing engine
10:20:07.111 INFO GermlineCNVCaller - Done initializing engine
10:20:07.207 INFO GermlineCNVCaller - Running the tool in CASE mode...
10:20:07.207 INFO GermlineCNVCaller - Validating and aggregating data from input read-count files...
10:20:07.231 INFO GermlineCNVCaller - Aggregating read-count file /media/Ergebnisse/0115-24_Masterpanel_NB501654_0623/0115-24_noProbe.hdf5 (1 / 1)
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
10:20:25.874 INFO GermlineCNVCaller - Shutting down engine
[March 14, 2024 at 10:20:25 AM CET] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 0.40 minutes.
Runtime.totalMemory()=2147483648
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python /media/Data/tmp/case_denoising_calling.3564509013495540802.py --ploidy_calls_path=/media/Ergebnisse/0115-24_Masterpanel_NB501654_0623/0115-24_DGCP_noProbe-calls --output_calls_path=/media/Ergebnisse/0115-24_Masterpanel_NB501654_0623/0115-24_GCNV_noProbe-calls --output_tracking_path=/media/Ergebnisse/0115-24_Masterpanel_NB501654_0623/0115-24_GCNV_noProbe-tracking --input_model_path=/media/Data/MasterV3/GCNV_noProbe-model --random_seed=1984 --read_count_tsv_files /media/Data/tmp/0115-24.rc16220482177493702615.tsv --psi_s_scale=1.000000e-04 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --num_samples_copy_ratio_approx=200 --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
Stdout: 10:20:12.111 INFO case_denoising_calling - THEANO_FLAGS environment variable has been set to: device=cpu,floatX=float64,optimizer=fast_run,compute_test_value=ignore,openmp=true,blas.ldflags=-lmkl_rt,openmp_elemwise_minsize=10
10:20:12.273 INFO root - Loading modeling interval list from the provided model...
10:20:12.475 INFO gcnvkernel.io.io_intervals_and_counts - The given interval list provides the following interval annotations: {'GC_CONTENT'}
10:20:12.491 INFO root - The model contains 11901 intervals and 23 contig(s)
10:20:12.491 INFO root - Loading 1 read counts file(s)...
10:20:12.545 INFO gcnvkernel.io.io_metadata - Loading germline contig ploidy and global read depth metadata...
10:20:12.554 INFO root - Loading denoising model configuration from the provided model...
10:20:12.555 INFO root - - bias factors enabled: True
10:20:12.555 INFO root - - explicit GC bias modeling enabled: True
10:20:12.555 INFO root - - bias factors in active classes disabled: False
10:20:12.555 INFO root - - maximum number of bias factors: 5
10:20:12.555 INFO root - - number of GC curve knobs: 20
10:20:12.555 INFO root - - GC curve prior standard deviation: 1.0
10:20:12.954 INFO gcnvkernel.tasks.task_case_denoising_calling - Instantiating the denoising model...
10:20:15.806 INFO gcnvkernel.tasks.task_case_denoising_calling - Instantiating the sampler...
10:20:15.807 INFO gcnvkernel.tasks.task_case_denoising_calling - Instantiating the copy number caller...
10:20:18.549 INFO gcnvkernel.models.fancy_model - Global model variables: {'log_mean_bias_t', 'psi_t_log__', 'W_tu', 'ard_u_log__'}
10:20:18.549 INFO gcnvkernel.models.fancy_model - Sample-specific model variables: {'read_depth_s_log__', 'psi_s_log__', 'z_sg', 'z_su'}
10:20:18.549 INFO gcnvkernel.tasks.inference_task_base - Instantiating the convergence tracker...
10:20:18.549 INFO gcnvkernel.tasks.inference_task_base - Setting up DA-ADVI...
10:20:24.995 INFO gcnvkernel.tasks.task_case_denoising_calling - Loading the model and updating the instantiated model and workspace...
10:20:25.005 INFO gcnvkernel.io.io_commons - Reading model parameter values for "log_mean_bias_t"...
Stderr: Traceback (most recent call last):
File "/media/Data/tmp/case_denoising_calling.3564509013495540802.py", line 201, in <module>
shared_workspace, initial_params_supplier, args.input_model_path)
File "/usr/BioinfSoftware/Anaconda/3-2020.11/envs/gatk4.3.0.0/lib/python3.6/site-packages/gcnvkernel/tasks/task_case_denoising_calling.py", line 128, in __init__
self.continuous_model_approx, input_model_path)()
File "/usr/BioinfSoftware/Anaconda/3-2020.11/envs/gatk4.3.0.0/lib/python3.6/site-packages/gcnvkernel/io/io_denoising_calling.py", line 93, in __call__
self.input_path, self.denoising_model_approx, self.denoising_model)
File "/usr/BioinfSoftware/Anaconda/3-2020.11/envs/gatk4.3.0.0/lib/python3.6/site-packages/gcnvkernel/io/io_commons.py", line 471, in read_mean_field_global_params
"expected: {2}".format(var_name, var_mu.shape, vmap.shp)
AssertionError: Loaded mean for "log_mean_bias_t" has an unexpected shape; loaded: (11903,), expected: (11901,)
at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:351)
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) ```
Can you give me some hint where this error comes from?
Thanks in advanve
Stefan
The text was updated successfully, but these errors were encountered:
stefandiederich
changed the title
AssertionError: Loaded mean for "log_mean_bias_t" has an unexpected shape; loaded: (11903,), expected: (11901,)
GCNV: AssertionError: Loaded mean for "log_mean_bias_t" has an unexpected shape; loaded: (11903,), expected: (11901,)
Mar 14, 2024
Hi all,
I am using CNV detection with GATK v4.3.0.0 for quite a while very successfully. Now we changed the enrichment kit and I had to do a new model. Everything worked well for the model phase.
As I now run one sample against this model I got the following error at the CNV detection step:
The text was updated successfully, but these errors were encountered: