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GATK-4.1.0 GermlineCNVCaller error messages

Hello GATK team,

I have followed the instructions to use conda and created the python environment (gatk conda).
DetermineGermlineContigPloidy went through without error messages but GermlineCNVCaller failed with the following error messages (Several uninformative lines were removed due to a character limit in the body). I would be grateful if you can look into this and help me troubleshoot.

Thank you for your time!
Jungmin

===================
Using GATK jar /ycga-ba/ba_sequencers5/scratch/sz97/Mathieu/jc2545/programs/gatk-4.1.0.0/gatk-package-4.1.0.0-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 -Xmx128g -jar /ycga-ba/ba_sequencers5/scratch/sz97/Mathieu/jc2545/programs/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar GermlineCNVCaller --run-mode COHORT -L /home/wd256/references/capture_coverage/xGen_preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY --contig-ploidy-calls output_dir/normal_cohort-calls --input M_18_SRNS246/M_18_SRNS246.counts.hdf5 --input M_18_SRNS249/M_18_SRNS249.counts.hdf5 --input M_18_SRNS254/M_18_SRNS254.counts.hdf5 --input M_18_SRNS255/M_18_SRNS255.counts.hdf5 ...... --output cohort --output-prefix normal_cohort_run --verbosity DEBUG
17:07:20.126 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/ycga-ba/ba_sequencers5/scratch/sz97/Mathieu/jc2545/programs/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
17:07:20.141 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression8865175445466958388.so
17:07:21.809 INFO GermlineCNVCaller - ------------------------------------------------------------
17:07:21.810 INFO GermlineCNVCaller - The Genome Analysis Toolkit (GATK) v4.1.0.0
17:07:21.811 INFO GermlineCNVCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
17:07:21.811 INFO GermlineCNVCaller - Executing as [email protected] on Linux v3.10.0-693.39.1.el7.x86_64 amd64
17:07:21.811 INFO GermlineCNVCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13
17:07:21.811 INFO GermlineCNVCaller - Start Date/Time: February 15, 2019 5:07:20 PM EST
17:07:21.811 INFO GermlineCNVCaller - ------------------------------------------------------------
17:07:21.811 INFO GermlineCNVCaller - ------------------------------------------------------------
17:07:21.812 INFO GermlineCNVCaller - HTSJDK Version: 2.18.2
17:07:21.812 INFO GermlineCNVCaller - Picard Version: 2.18.25
17:07:21.813 INFO GermlineCNVCaller - HTSJDK Defaults.BUFFER_SIZE : 131072
17:07:21.813 INFO GermlineCNVCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:07:21.813 INFO GermlineCNVCaller - HTSJDK Defaults.CREATE_INDEX : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.CREATE_MD5 : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.CUSTOM_READER_FACTORY :
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.REFERENCE_FASTA : null
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:07:21.814 INFO GermlineCNVCaller - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
17:07:21.814 DEBUG ConfigFactory - Configuration file values:
17:07:21.818 DEBUG ConfigFactory - gcsMaxRetries = 20
17:07:21.818 DEBUG ConfigFactory - gcsProjectForRequesterPays =
17:07:21.818 DEBUG ConfigFactory - gatk_stacktrace_on_user_exception = false
17:07:21.818 DEBUG ConfigFactory - samjdk.use_async_io_read_samtools = false
17:07:21.819 DEBUG ConfigFactory - samjdk.use_async_io_write_samtools = true
17:07:21.819 DEBUG ConfigFactory - samjdk.use_async_io_write_tribble = false
17:07:21.819 DEBUG ConfigFactory - samjdk.compression_level = 2
17:07:21.819 DEBUG ConfigFactory - spark.kryoserializer.buffer.max = 512m
17:07:21.819 DEBUG ConfigFactory - spark.driver.maxResultSize = 0
17:07:21.819 DEBUG ConfigFactory - spark.driver.userClassPathFirst = true
17:07:21.819 DEBUG ConfigFactory - spark.io.compression.codec = lzf
17:07:21.819 DEBUG ConfigFactory - spark.yarn.executor.memoryOverhead = 600
17:07:21.819 DEBUG ConfigFactory - spark.driver.extraJavaOptions =
17:07:21.819 DEBUG ConfigFactory - spark.executor.extraJavaOptions =
17:07:21.819 DEBUG ConfigFactory - codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
17:07:21.819 DEBUG ConfigFactory - read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
17:07:21.819 DEBUG ConfigFactory - annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
17:07:21.819 DEBUG ConfigFactory - cloudPrefetchBuffer = 40
17:07:21.819 DEBUG ConfigFactory - cloudIndexPrefetchBuffer = -1
17:07:21.819 DEBUG ConfigFactory - createOutputBamIndex = true
17:07:21.819 INFO GermlineCNVCaller - Deflater: IntelDeflater
17:07:21.819 INFO GermlineCNVCaller - Inflater: IntelInflater
17:07:21.820 INFO GermlineCNVCaller - GCS max retries/reopens: 20
17:07:21.820 INFO GermlineCNVCaller - Requester pays: disabled
17:07:21.820 INFO GermlineCNVCaller - Initializing engine
17:07:21.824 DEBUG ScriptExecutor - Executing:
17:07:21.824 DEBUG ScriptExecutor - python
17:07:21.824 DEBUG ScriptExecutor - -c
17:07:21.824 DEBUG ScriptExecutor - import gcnvkernel

17:07:27.074 DEBUG ScriptExecutor - Result: 0
17:07:27.074 INFO GermlineCNVCaller - Done initializing engine
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.
17:07:27.511 INFO GermlineCNVCaller - Intervals specified...
17:07:27.512 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
17:07:27.513 DEBUG GenomeLocParser - 1 (249250621 bp)
17:07:27.513 DEBUG GenomeLocParser - 2 (243199373 bp)
.
.
.
17:07:27.521 DEBUG GenomeLocParser - NC_007605 (171823 bp)
17:07:27.521 DEBUG GenomeLocParser - hs37d5 (35477943 bp)
17:07:28.168 INFO IntervalArgumentCollection - Processing 127088123 bp from intervals
17:07:28.260 INFO GermlineCNVCaller - No annotated intervals were provided...
17:07:28.260 INFO GermlineCNVCaller - No GC-content annotations for intervals found; explicit GC-bias correction will not be performed...
17:07:28.440 INFO GermlineCNVCaller - Running the tool in the COHORT mode...
17:07:28.443 INFO GermlineCNVCaller - Validating and aggregating data from input read-count files...
17:07:28.465 INFO GermlineCNVCaller - Aggregating read-count file M_18_SRNS246/M_18_SRNS246.counts.hdf5 (1 / 162)
.
.
.
17:08:07.074 INFO GermlineCNVCaller - Aggregating read-count file M_18_SRNS528/M_18_SRNS528.counts.hdf5 (161 / 162)
17:08:07.334 INFO GermlineCNVCaller - Aggregating read-count file M_18_SRNS531/M_18_SRNS531.counts.hdf5 (162 / 162)
17:08:07.645 DEBUG ScriptExecutor - Executing:
17:08:07.645 DEBUG ScriptExecutor - python
17:08:07.645 DEBUG ScriptExecutor - /tmp/cohort_denoising_calling.9140535429895089708.py
17:08:07.645 DEBUG ScriptExecutor - --ploidy_calls_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/output_dir/normal_cohort-calls
17:08:07.645 DEBUG ScriptExecutor - --output_calls_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-calls
17:08:07.645 DEBUG ScriptExecutor - --output_tracking_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-tracking
17:08:07.645 DEBUG ScriptExecutor - --modeling_interval_list=/tmp/intervals1873462746347841141.tsv
17:08:07.645 DEBUG ScriptExecutor - --output_model_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-model
17:08:07.645 DEBUG ScriptExecutor - --enable_explicit_gc_bias_modeling=False
17:08:07.645 DEBUG ScriptExecutor - --read_count_tsv_files
17:08:07.645 DEBUG ScriptExecutor - /tmp/sample-08612173870077300650.tsv
.
.
.
17:08:07.649 DEBUG ScriptExecutor - /tmp/sample-1605044828027709654690.tsv
17:08:07.649 DEBUG ScriptExecutor - /tmp/sample-1618759982698618716730.tsv
17:08:07.649 DEBUG ScriptExecutor - --psi_s_scale=1.000000e-04
17:08:07.649 DEBUG ScriptExecutor - --mapping_error_rate=1.000000e-02
17:08:07.649 DEBUG ScriptExecutor - --depth_correction_tau=1.000000e+04
17:08:07.649 DEBUG ScriptExecutor - --q_c_expectation_mode=hybrid
17:08:07.649 DEBUG ScriptExecutor - --max_bias_factors=5
17:08:07.649 DEBUG ScriptExecutor - --psi_t_scale=1.000000e-03
17:08:07.649 DEBUG ScriptExecutor - --log_mean_bias_std=1.000000e-01
17:08:07.649 DEBUG ScriptExecutor - --init_ard_rel_unexplained_variance=1.000000e-01
17:08:07.649 DEBUG ScriptExecutor - --num_gc_bins=20
17:08:07.649 DEBUG ScriptExecutor - --gc_curve_sd=1.000000e+00
17:08:07.649 DEBUG ScriptExecutor - --active_class_padding_hybrid_mode=50000
17:08:07.649 DEBUG ScriptExecutor - --enable_bias_factors=True
17:08:07.649 DEBUG ScriptExecutor - --disable_bias_factors_in_active_class=False
17:08:07.649 DEBUG ScriptExecutor - --p_alt=1.000000e-06
17:08:07.649 DEBUG ScriptExecutor - --cnv_coherence_length=1.000000e+04
17:08:07.649 DEBUG ScriptExecutor - --max_copy_number=5
17:08:07.649 DEBUG ScriptExecutor - --p_active=0.010000
17:08:07.649 DEBUG ScriptExecutor - --class_coherence_length=10000.000000
17:08:07.649 DEBUG ScriptExecutor - --learning_rate=1.000000e-02
17:08:07.649 DEBUG ScriptExecutor - --adamax_beta1=9.000000e-01
17:08:07.649 DEBUG ScriptExecutor - --adamax_beta2=9.900000e-01
17:08:07.649 DEBUG ScriptExecutor - --log_emission_samples_per_round=50
17:08:07.649 DEBUG ScriptExecutor - --log_emission_sampling_rounds=10
17:08:07.649 DEBUG ScriptExecutor - --log_emission_sampling_median_rel_error=5.000000e-03
17:08:07.649 DEBUG ScriptExecutor - --max_advi_iter_first_epoch=5000
17:08:07.649 DEBUG ScriptExecutor - --max_advi_iter_subsequent_epochs=200
17:08:07.649 DEBUG ScriptExecutor - --min_training_epochs=10
17:08:07.649 DEBUG ScriptExecutor - --max_training_epochs=50
17:08:07.649 DEBUG ScriptExecutor - --initial_temperature=1.500000e+00
17:08:07.649 DEBUG ScriptExecutor - --num_thermal_advi_iters=2500
17:08:07.649 DEBUG ScriptExecutor - --convergence_snr_averaging_window=500
17:08:07.649 DEBUG ScriptExecutor - --convergence_snr_trigger_threshold=1.000000e-01
17:08:07.649 DEBUG ScriptExecutor - --convergence_snr_countdown_window=10
17:08:07.649 DEBUG ScriptExecutor - --max_calling_iters=10
17:08:07.649 DEBUG ScriptExecutor - --caller_update_convergence_threshold=1.000000e-03
17:08:07.649 DEBUG ScriptExecutor - --caller_internal_admixing_rate=7.500000e-01
17:08:07.649 DEBUG ScriptExecutor - --caller_external_admixing_rate=1.000000e+00
17:08:07.649 DEBUG ScriptExecutor - --disable_caller=false
17:08:07.649 DEBUG ScriptExecutor - --disable_sampler=false
17:08:07.649 DEBUG ScriptExecutor - --disable_annealing=false
17:08:12.398 INFO cohort_denoising_calling - Loading 162 read counts file(s)...
17:09:17.875 INFO gcnvkernel.io.io_metadata - Loading germline contig ploidy and global read depth metadata...
17:09:55.138 INFO gcnvkernel.tasks.task_cohort_denoising_calling - Instantiating the denoising model (warm-up)...
17:11:20.180 DEBUG ScriptExecutor - Result: 137
17:11:20.181 INFO GermlineCNVCaller - Shutting down engine
[February 15, 2019 5:11:20 PM EST] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 4.00 minutes.
Runtime.totalMemory()=6215958528
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 137
Command Line: python /tmp/cohort_denoising_calling.9140535429895089708.py --ploidy_calls_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/output_dir/normal_cohort-calls --output_calls_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-calls --output_tracking_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-tracking --modeling_interval_list=/tmp/intervals1873462746347841141.tsv --output_model_path=/gpfs/ycga/scratch60/ysm/lifton/jc2545/DoC/cohort/cohort/normal_cohort_run-model --enable_explicit_gc_bias_modeling=False --read_count_tsv_files /tmp/sample-08612173870077300650.tsv /tmp/sample-1735339145960625744.tsv /tmp/sample-26703446513270382293.tsv /tmp/sample-35095654387556573137.tsv /tmp/sample-4508962434357349017.tsv /tmp/sample-58460077076107805745.tsv /tmp/sample-6346822365711760370.tsv /tmp/sample-779931899134353312.tsv /tmp/sample-85729935362226663368.tsv /tmp/sample-93257389871598688195.tsv /tmp/sample-1072218606651772505.tsv /tmp/sample-115903914088361457664.tsv /tmp/sample-128235238211199814079.tsv /tmp/sample-137679065752903696578.tsv /tmp/sample-141412526288839282934.tsv /tmp/sample-15519292804984449661.tsv /tmp/sample-161709925844501965417.tsv /tmp/sample-178022787663362200778.tsv /tmp/sample-181125070878149098262.tsv /tmp/sample-194410475879134975275.tsv /tmp/sample-202975550643747300134.tsv /tmp/sample-213009004444143467292.tsv /tmp/sample-221306507585077810612.tsv /tmp/sample-23104024448454209175.tsv /tmp/sample-245133022599306993556.tsv /tmp/sample-25703760885613813312.tsv /tmp/sample-2690774459760965725.tsv /tmp/sample-272313888089716707826.tsv /tmp/sample-288176307810148633677.tsv /tmp/sample-298583951421199428278.tsv /tmp/sample-301692991399952820072.tsv /tmp/sample-317809871850313243733.tsv /tmp/sample-322055164835392021676.tsv /tmp/sample-333188910366149161610.tsv /tmp/sample-341776914456585504962.tsv /tmp/sample-351634383534181696381.tsv /tmp/sample-367781395796149922798.tsv /tmp/sample-3786730386469085354.tsv /tmp/sample-38541771839429688936.tsv /tmp/sample-396058667613341997490.tsv /tmp/sample-402602372245250147133.tsv /tmp/sample-415892540111653423405.tsv /tmp/sample-425671650162117618258.tsv /tmp/sample-437903006633261170767.tsv /tmp/sample-446769403661740456540.tsv /tmp/sample-452807940055394133177.tsv /tmp/sample-468546499565823287044.tsv /tmp/sample-476182160432111186420.tsv /tmp/sample-482196176246104993068.tsv /tmp/sample-497349198039999756481.tsv /tmp/sample-504586740136696693330.tsv /tmp/sample-514629760575640679484.tsv /tmp/sample-521518665764093531540.tsv /tmp/sample-536756030759819452871.tsv /tmp/sample-541814208065030512399.tsv /tmp/sample-557100162055020311558.tsv /tmp/sample-565079065285043205969.tsv /tmp/sample-577473774494155677328.tsv /tmp/sample-585211874134149883927.tsv /tmp/sample-597899152893974380925.tsv /tmp/sample-601774703583028171465.tsv /tmp/sample-615352536760798251526.tsv /tmp/sample-621792155083348440834.tsv /tmp/sample-631065348947130549641.tsv /tmp/sample-641985405380622064199.tsv /tmp/sample-656094636503911408494.tsv /tmp/sample-668415912440582797737.tsv /tmp/sample-676403765944041136118.tsv /tmp/sample-682114045166636957457.tsv /tmp/sample-691095858748617845455.tsv /tmp/sample-701898313659570600550.tsv /tmp/sample-711130096990849289842.tsv /tmp/sample-724909857738488305869.tsv /tmp/sample-733566863875273019740.tsv /tmp/sample-742661156055391989719.tsv /tmp/sample-752900828628492970083.tsv /tmp/sample-767092916011092266094.tsv /tmp/sample-772455948557542008819.tsv /tmp/sample-782509489027797761010.tsv /tmp/sample-796805609730974108586.tsv /tmp/sample-80720962641595403888.tsv /tmp/sample-817173783221065650666.tsv /tmp/sample-822940909550498965708.tsv /tmp/sample-837562722826437020179.tsv /tmp/sample-846265161938613290733.tsv /tmp/sample-853171171276815010438.tsv /tmp/sample-864724444930214959966.tsv /tmp/sample-876678275730001959431.tsv /tmp/sample-887626160582818681387.tsv /tmp/sample-898955761009702615630.tsv /tmp/sample-905439922593393958017.tsv /tmp/sample-912745236161870043640.tsv /tmp/sample-926231084901650523858.tsv /tmp/sample-93935170810944919855.tsv /tmp/sample-9431746064262952062.tsv /tmp/sample-958737018321160287907.tsv /tmp/sample-961802987260101727402.tsv /tmp/sample-977416547149949828041.tsv /tmp/sample-983982274875124448216.tsv /tmp/sample-996198735099776825982.tsv /tmp/sample-1009146208583490663068.tsv /tmp/sample-1018845180303163951595.tsv /tmp/sample-1027135342741286447343.tsv /tmp/sample-1035368514901860687723.tsv /tmp/sample-1042754024539983558009.tsv /tmp/sample-105227740940224097784.tsv /tmp/sample-1067796439126398033702.tsv /tmp/sample-1075076104300625983530.tsv /tmp/sample-1088947366823218733850.tsv /tmp/sample-1096165949344136625979.tsv /tmp/sample-110426075258992495633.tsv /tmp/sample-1116508848571389727702.tsv /tmp/sample-112283331488958653414.tsv /tmp/sample-1132751105099775154028.tsv /tmp/sample-1146473447638075601261.tsv /tmp/sample-1157358912004261216235.tsv /tmp/sample-1163478798295512815260.tsv /tmp/sample-1172106693768918595659.tsv /tmp/sample-1188590848153482833118.tsv /tmp/sample-1193162205698457964430.tsv /tmp/sample-1204202944415748120845.tsv /tmp/sample-121773818989999810769.tsv /tmp/sample-1223745408005714103834.tsv /tmp/sample-1236610659701327035424.tsv /tmp/sample-1245760080493734034654.tsv /tmp/sample-1253807306870096529273.tsv /tmp/sample-1264151487267688408608.tsv /tmp/sample-1277214977153055471289.tsv /tmp/sample-1285224338316659715614.tsv /tmp/sample-1292062026162943299330.tsv /tmp/sample-1301363016348073583379.tsv /tmp/sample-131558554732818920155.tsv /tmp/sample-1325754066569823165479.tsv /tmp/sample-1336042767672212270992.tsv /tmp/sample-1343968514112614746127.tsv /tmp/sample-1355546751716954575927.tsv /tmp/sample-136236845290987331012.tsv /tmp/sample-1374816528101346997220.tsv /tmp/sample-1385317851245406091520.tsv /tmp/sample-1391042137054808258316.tsv /tmp/sample-1403742557849491744561.tsv /tmp/sample-1411502587679797062853.tsv /tmp/sample-1424733541746568284028.tsv /tmp/sample-143238400405838309221.tsv /tmp/sample-1441096103849753405535.tsv /tmp/sample-1452666884939739940900.tsv /tmp/sample-1464156055658986985443.tsv /tmp/sample-1472026389278997599086.tsv /tmp/sample-148589445790255766165.tsv /tmp/sample-1497827386382328631572.tsv /tmp/sample-1504915479842211825427.tsv /tmp/sample-1515203597135250209395.tsv /tmp/sample-1528978682591511597058.tsv /tmp/sample-1535467962477746299596.tsv /tmp/sample-1548510164331176337876.tsv /tmp/sample-1552624811099715500627.tsv /tmp/sample-1562605141662085486436.tsv /tmp/sample-1575754839084389129440.tsv /tmp/sample-1583068624308611691335.tsv /tmp/sample-159139367590923153119.tsv /tmp/sample-1605044828027709654690.tsv /tmp/sample-1618759982698618716730.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.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.GermlineCNVCaller.executeGermlineCNVCallerPythonScript(GermlineCNVCaller.java:441)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.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)

Answers

  • sleeslee Member, Broadie, Dev ✭✭✭

    @crackiee that looks like an out-of-memory error to me. It looks like you are running a decent number (162) of samples. Depending on the number of bins in /home/wd256/references/capture_coverage/xGen_preprocessed.interval_list, you may need to scatter multiple runs of GermlineCNVCaller to bring your memory requirements down. See the WDLs at https://github.com/broadinstitute/gatk/tree/master/scripts/cnv_wdl/germline to see how this done.

  • crackieecrackiee Member

    @slee This is great. Will try to run 25 sample a block and see if i can reproduce an error.

  • sleeslee Member, Broadie, Dev ✭✭✭

    Sorry, just to be clear---I was referring to scattering across shards of intervals, not samples, to bring down memory requirements. The number of bins in each shard x the number of samples is what determines the memory requirement for each shard.

    The scattered-case mode WDL at that link additionally shards across samples when running in case mode, but this is a different matter.

  • mtkk94mtkk94 Member

    We came across the same error. We are working only with 20 samples and still the same error. Is importing gcnvkernel the reason for the error? Please advice.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @mtkk94

    Can you please post the exact command you are using, the version of gatk and the entire error log please.

  • mtkk94mtkk94 Member

    Hi Bhanu,

    We are using GATK 4.1.1.0. Below is the command and the error we received.

    (gatk) BIO\[email protected]:~/disk_big/Mandal_project/Aim1_10PCa10Con_Data_Mayo/gatk$ /home/BIO/tarun/gatk/gatk 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
    
    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
    11:16:44.577 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/data/BIO/tarun/gatk/gatk-package-4.1.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    11:16:44.611 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression252335513312361917.so
    May 01, 2019 11:16:46 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    11:16:46.452 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
    11:16:46.453 INFO  DetermineGermlineContigPloidy - The Genome Analysis Toolkit (GATK) v4.1.1.0
    11:16:46.453 INFO  DetermineGermlineContigPloidy - For support and documentation go to https://software.broadinstitute.org/gatk/
    11:16:46.453 INFO  DetermineGermlineContigPloidy - Executing as BIO\[email protected] on Linux v4.4.0-137-generic amd64
    11:16:46.453 INFO  DetermineGermlineContigPloidy - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_181-8u181-b13-0ubuntu0.16.04.1-b13
    11:16:46.454 INFO  DetermineGermlineContigPloidy - Start Date/Time: May 1, 2019 11:16:44 AM CDT
    11:16:46.454 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
    11:16:46.454 INFO  DetermineGermlineContigPloidy - ------------------------------------------------------------
    11:16:46.455 INFO  DetermineGermlineContigPloidy - HTSJDK Version: 2.19.0
    11:16:46.455 INFO  DetermineGermlineContigPloidy - Picard Version: 2.19.0
    11:16:46.457 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.BUFFER_SIZE : 131072
    11:16:46.457 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_INDEX : false
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_MD5 : false
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.CUSTOM_READER_FACTORY : 
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.REFERENCE_FASTA : null
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    11:16:46.458 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    11:16:46.459 INFO  DetermineGermlineContigPloidy - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
    11:16:46.459 DEBUG ConfigFactory - Configuration file values: 
    11:16:46.466 DEBUG ConfigFactory -  gcsMaxRetries = 20
    11:16:46.466 DEBUG ConfigFactory -  gcsProjectForRequesterPays = 
    11:16:46.466 DEBUG ConfigFactory -  gatk_stacktrace_on_user_exception = false
    11:16:46.466 DEBUG ConfigFactory -  samjdk.use_async_io_read_samtools = false
    11:16:46.466 DEBUG ConfigFactory -  samjdk.use_async_io_write_samtools = true
    11:16:46.466 DEBUG ConfigFactory -  samjdk.use_async_io_write_tribble = false
    11:16:46.466 DEBUG ConfigFactory -  samjdk.compression_level = 2
    11:16:46.467 DEBUG ConfigFactory -  spark.kryoserializer.buffer.max = 512m
    11:16:46.467 DEBUG ConfigFactory -  spark.driver.maxResultSize = 0
    11:16:46.467 DEBUG ConfigFactory -  spark.driver.userClassPathFirst = true
    11:16:46.467 DEBUG ConfigFactory -  spark.io.compression.codec = lzf
    11:16:46.467 DEBUG ConfigFactory -  spark.yarn.executor.memoryOverhead = 600
    11:16:46.467 DEBUG ConfigFactory -  spark.driver.extraJavaOptions = 
    11:16:46.467 DEBUG ConfigFactory -  spark.executor.extraJavaOptions = 
    11:16:46.467 DEBUG ConfigFactory -  codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
    11:16:46.467 DEBUG ConfigFactory -  read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
    11:16:46.467 DEBUG ConfigFactory -  annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
    11:16:46.467 DEBUG ConfigFactory -  cloudPrefetchBuffer = 40
    11:16:46.467 DEBUG ConfigFactory -  cloudIndexPrefetchBuffer = -1
    11:16:46.468 DEBUG ConfigFactory -  createOutputBamIndex = true
    11:16:46.468 INFO  DetermineGermlineContigPloidy - Deflater: IntelDeflater
    11:16:46.468 INFO  DetermineGermlineContigPloidy - Inflater: IntelInflater
    11:16:46.468 INFO  DetermineGermlineContigPloidy - GCS max retries/reopens: 20
    11:16:46.468 INFO  DetermineGermlineContigPloidy - Requester pays: disabled
    11:16:46.468 INFO  DetermineGermlineContigPloidy - Initializing engine
    11:16:46.473 DEBUG ScriptExecutor - Executing:
    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)
    

    Thank you for your help.

    Tarun

  • sleeslee Member, Broadie, Dev ✭✭✭

    @mtkk94 looks like there might be a problem with your contig-ploidy priors (/mnt/data/smb_share/Mandal_project/Aim1_10PCa10Con_Data_Mayo/gatk/contigPloidyPriorsTable.tsv). Do you mind posting the contents of that file?

  • mtkk94mtkk94 Member

    @slee Yes, that is definitely a possibility since we weren't exactly sure how to make this table. Below are the contents of the contig-ploidy priors table that we used.

    CONTIG_NAME PLOIDY_PRIOR_0 PLOIDY_PRIOR_1 PLOIDY_PRIOR_2 PLOIDY_PRIOR_3
    1 0.01 0.02 0.95 0.02
    2 0.01 0.02 0.95 0.02
    3 0.01 0.02 0.95 0.02
    4 0.01 0.02 0.95 0.02
    5 0.01 0.02 0.95 0.02
    6 0.01 0.02 0.95 0.02
    7 0.01 0.02 0.95 0.02
    8 0.01 0.02 0.95 0.02
    9 0.01 0.02 0.95 0.02
    10 0.01 0.02 0.95 0.02
    11 0.01 0.02 0.95 0.02
    12 0.01 0.02 0.95 0.02
    13 0.01 0.02 0.95 0.02
    14 0.01 0.02 0.95 0.02
    15 0.01 0.02 0.95 0.02
    16 0.01 0.02 0.95 0.02
    17 0.01 0.02 0.95 0.02
    18 0.01 0.02 0.95 0.02
    19 0.01 0.02 0.95 0.02
    20 0.01 0.02 0.95 0.02
    21 0.01 0.02 0.95 0.02
    22 0.01 0.02 0.95 0.02
    X 0.01 0.49 0.48 0.02
    Y 0.49 0.49 0.02 0

    Thank you for any help/advice.

    Tarun

  • sleeslee Member, Broadie, Dev ✭✭✭

    OK, thanks @mtkk94. Assuming that you're using a properly formatted TSV (perhaps check for missing tabs or accidental use of other whitespace) and that your contig names are all included correctly, I'm not sure why you should be getting that error. Can you double check? See e.g. https://gatkforums.broadinstitute.org/gatk/discussion/comment/56707 for some further caveats.

  • mtkk94mtkk94 Member

    @slee Thank you for your help. The contig names were different, so we fixed that and the command worked.

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