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20 hours ago •
broadinstitute
broadinstitute
Germline CNV calling error: Cannot run DetermineGermlineContigPloidy due to intability to install gcnvkernel
Hi,
I tried to run DetermineGermlineContigPloidy in cohort mode and it fails:
06:34:40.112 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
06:34:40.152 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression18318423026447352871.so
06:34:40.685 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
06:34:40.724 INFO DetermineGermlineContigPloidy - The Genome Analysis Toolkit (GATK) v4.6.0.0
06:34:40.724 INFO DetermineGermlineContigPloidy - For support and documentation go to https://software.broadinstitute.org/gatk/
06:34:40.724 INFO DetermineGermlineContigPloidy - Executing as u855h@odcf-cn42u15 on Linux v3.10.0-1160.119.1.el7.x86_64 amd64
06:34:40.724 INFO DetermineGermlineContigPloidy - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
06:34:40.724 INFO DetermineGermlineContigPloidy - Start Date/Time: April 16, 2025 at 6:34:39 AM GMT
06:34:40.724 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
06:34:40.724 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
06:34:40.725 INFO DetermineGermlineContigPloidy - HTSJDK Version: 4.1.1
06:34:40.725 INFO DetermineGermlineContigPloidy - Picard Version: 3.2.0
06:34:40.725 INFO DetermineGermlineContigPloidy - Built for Spark Version: 3.5.0
06:34:40.726 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.BUFFER_SIZE : 131072
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.COMPRESSION_LEVEL : 2
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_INDEX : false
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_MD5 : false
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CUSTOM_READER_FACTORY :
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.REFERENCE_FASTA : null
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
06:34:40.727 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
06:34:40.728 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
06:34:40.728 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
06:34:40.728 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
06:34:40.728 DEBUG ConfigFactory - Configuration file values:
06:34:40.731 DEBUG ConfigFactory - gcsMaxRetries = 20
06:34:40.731 DEBUG ConfigFactory - gcsProjectForRequesterPays =
06:34:40.731 DEBUG ConfigFactory - gatk_stacktrace_on_user_exception = false
06:34:40.731 DEBUG ConfigFactory - samjdk.use_async_io_read_samtools = false
06:34:40.731 DEBUG ConfigFactory - samjdk.use_async_io_write_samtools = true
06:34:40.731 DEBUG ConfigFactory - samjdk.use_async_io_write_tribble = false
06:34:40.731 DEBUG ConfigFactory - samjdk.compression_level = 2
06:34:40.732 DEBUG ConfigFactory - spark.kryoserializer.buffer.max = 512m
06:34:40.732 DEBUG ConfigFactory - spark.driver.maxResultSize = 0
06:34:40.732 DEBUG ConfigFactory - spark.driver.userClassPathFirst = true
06:34:40.732 DEBUG ConfigFactory - spark.io.compression.codec = lzf
06:34:40.732 DEBUG ConfigFactory - spark.executor.memoryOverhead = 600
06:34:40.732 DEBUG ConfigFactory - spark.driver.extraJavaOptions =
06:34:40.732 DEBUG ConfigFactory - spark.executor.extraJavaOptions =
06:34:40.732 DEBUG ConfigFactory - codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
06:34:40.732 DEBUG ConfigFactory - read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
06:34:40.732 DEBUG ConfigFactory - annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
06:34:40.732 DEBUG ConfigFactory - cloudPrefetchBuffer = 40
06:34:40.732 DEBUG ConfigFactory - cloudIndexPrefetchBuffer = -1
06:34:40.732 DEBUG ConfigFactory - createOutputBamIndex = true
06:34:40.732 INFO DetermineGermlineContigPloidy - Deflater: IntelDeflater
06:34:40.733 INFO DetermineGermlineContigPloidy - Inflater: IntelInflater
06:34:40.733 INFO DetermineGermlineContigPloidy - GCS max retries/reopens: 20
06:34:40.733 INFO DetermineGermlineContigPloidy - Requester pays: disabled
06:34:40.733 INFO DetermineGermlineContigPloidy - Initializing engine
06:34:40.735 DEBUG ScriptExecutor - Executing:
06:34:40.735 DEBUG ScriptExecutor - python
06:34:40.735 DEBUG ScriptExecutor - -c
06:34:40.735 DEBUG ScriptExecutor - import gcnvkernel
06:35:27.540 DEBUG ScriptExecutor - Result: 0
06:35:27.541 INFO DetermineGermlineContigPloidy - Done initializing engine
06:35:27.606 INFO DetermineGermlineContigPloidy - No contig-ploidy model was provided, running in cohort mode...
06:35:27.606 INFO DetermineGermlineContigPloidy - Intervals specified...
06:35:30.812 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
06:35:30.812 DEBUG GenomeLocParser - 1 (249250621 bp)
06:35:30.812 DEBUG GenomeLocParser - 2 (243199373 bp)
06:35:30.812 DEBUG GenomeLocParser - 3 (198022430 bp)
06:35:30.812 DEBUG GenomeLocParser - 4 (191154276 bp)
06:35:30.812 DEBUG GenomeLocParser - 5 (180915260 bp)
06:35:30.812 DEBUG GenomeLocParser - 6 (171115067 bp)
06:35:30.813 DEBUG GenomeLocParser - 7 (159138663 bp)
06:35:30.813 DEBUG GenomeLocParser - 8 (146364022 bp)
06:35:30.813 DEBUG GenomeLocParser - 9 (141213431 bp)
06:35:30.813 DEBUG GenomeLocParser - 10 (135534747 bp)
06:35:30.813 DEBUG GenomeLocParser - 11 (135006516 bp)
06:35:30.813 DEBUG GenomeLocParser - 12 (133851895 bp)
06:35:30.813 DEBUG GenomeLocParser - 13 (115169878 bp)
06:35:30.813 DEBUG GenomeLocParser - 14 (107349540 bp)
06:35:30.813 DEBUG GenomeLocParser - 15 (102531392 bp)
06:35:30.813 DEBUG GenomeLocParser - 16 (90354753 bp)
06:35:30.813 DEBUG GenomeLocParser - 17 (81195210 bp)
06:35:30.813 DEBUG GenomeLocParser - 18 (78077248 bp)
06:35:30.813 DEBUG GenomeLocParser - 19 (59128983 bp)
06:35:30.814 DEBUG GenomeLocParser - 20 (63025520 bp)
06:35:30.814 DEBUG GenomeLocParser - 21 (48129895 bp)
06:35:30.814 DEBUG GenomeLocParser - 22 (51304566 bp)
06:35:30.814 DEBUG GenomeLocParser - X (155270560 bp)
06:35:30.814 DEBUG GenomeLocParser - Y (59373566 bp)
06:35:30.814 DEBUG GenomeLocParser - MT (16569 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000207.1 (4262 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000226.1 (15008 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000229.1 (19913 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000231.1 (27386 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000210.1 (27682 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000239.1 (33824 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000235.1 (34474 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000201.1 (36148 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000247.1 (36422 bp)
06:35:30.814 DEBUG GenomeLocParser - GL000245.1 (36651 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000197.1 (37175 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000203.1 (37498 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000246.1 (38154 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000249.1 (38502 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000196.1 (38914 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000248.1 (39786 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000244.1 (39929 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000238.1 (39939 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000202.1 (40103 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000234.1 (40531 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000232.1 (40652 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000206.1 (41001 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000240.1 (41933 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000236.1 (41934 bp)
06:35:30.815 DEBUG GenomeLocParser - GL000241.1 (42152 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000243.1 (43341 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000242.1 (43523 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000230.1 (43691 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000237.1 (45867 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000233.1 (45941 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000204.1 (81310 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000198.1 (90085 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000208.1 (92689 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000191.1 (106433 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000227.1 (128374 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000228.1 (129120 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000214.1 (137718 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000221.1 (155397 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000209.1 (159169 bp)
06:35:30.816 DEBUG GenomeLocParser - GL000218.1 (161147 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000220.1 (161802 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000213.1 (164239 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000211.1 (166566 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000199.1 (169874 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000217.1 (172149 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000216.1 (172294 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000215.1 (172545 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000205.1 (174588 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000219.1 (179198 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000224.1 (179693 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000223.1 (180455 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000195.1 (182896 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000212.1 (186858 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000222.1 (186861 bp)
06:35:30.817 DEBUG GenomeLocParser - GL000200.1 (187035 bp)
06:35:30.818 DEBUG GenomeLocParser - GL000193.1 (189789 bp)
06:35:30.818 DEBUG GenomeLocParser - GL000194.1 (191469 bp)
06:35:30.818 DEBUG GenomeLocParser - GL000225.1 (211173 bp)
06:35:30.818 DEBUG GenomeLocParser - GL000192.1 (547496 bp)
06:35:30.818 DEBUG GenomeLocParser - NC_007605 (171823 bp)
06:35:30.818 DEBUG GenomeLocParser - hs37d5 (35477943 bp)
06:35:30.818 DEBUG GenomeLocParser - phiX174 (5386 bp)
06:35:31.021 INFO FeatureManager - Using codec IntervalListCodec to read file file:///data/filtered_intervals.interval_list
06:35:39.947 DEBUG FeatureDataSource - Cache statistics for FeatureInput /data/filtered_intervals.interval_list:/data/filtered_intervals.interval_list:
06:35:39.948 DEBUG FeatureCache - Cache hit rate was 0.00% (0 out of 0 total queries)
06:35:40.232 INFO IntervalArgumentCollection - Processing 2816223150 bp from intervals
06:35:42.250 INFO DetermineGermlineContigPloidy - Validating and aggregating coverage per contig from input read-count files...
06:35:42.744 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
06:35:42.744 DEBUG GenomeLocParser - 1 (249250621 bp)
06:35:42.745 DEBUG GenomeLocParser - 2 (243199373 bp)
06:35:42.745 DEBUG GenomeLocParser - 3 (198022430 bp)
06:35:42.745 DEBUG GenomeLocParser - 4 (191154276 bp)
06:35:42.745 DEBUG GenomeLocParser - 5 (180915260 bp)
06:35:42.745 DEBUG GenomeLocParser - 6 (171115067 bp)
06:35:42.745 DEBUG GenomeLocParser - 7 (159138663 bp)
06:35:42.745 DEBUG GenomeLocParser - 8 (146364022 bp)
06:35:42.745 DEBUG GenomeLocParser - 9 (141213431 bp)
06:35:42.745 DEBUG GenomeLocParser - 10 (135534747 bp)
06:35:42.745 DEBUG GenomeLocParser - 11 (135006516 bp)
06:35:42.745 DEBUG GenomeLocParser - 12 (133851895 bp)
06:35:42.745 DEBUG GenomeLocParser - 13 (115169878 bp)
06:35:42.745 DEBUG GenomeLocParser - 14 (107349540 bp)
06:35:42.745 DEBUG GenomeLocParser - 15 (102531392 bp)
06:35:42.746 DEBUG GenomeLocParser - 16 (90354753 bp)
06:35:42.746 DEBUG GenomeLocParser - 17 (81195210 bp)
06:35:42.746 DEBUG GenomeLocParser - 18 (78077248 bp)
06:35:42.746 DEBUG GenomeLocParser - 19 (59128983 bp)
06:35:42.746 DEBUG GenomeLocParser - 20 (63025520 bp)
06:35:42.746 DEBUG GenomeLocParser - 21 (48129895 bp)
06:35:42.746 DEBUG GenomeLocParser - 22 (51304566 bp)
06:35:42.746 DEBUG GenomeLocParser - X (155270560 bp)
06:35:42.746 DEBUG GenomeLocParser - Y (59373566 bp)
06:35:42.746 DEBUG GenomeLocParser - MT (16569 bp)
06:35:42.746 DEBUG GenomeLocParser - GL000207.1 (4262 bp)
06:35:42.746 DEBUG GenomeLocParser - GL000226.1 (15008 bp)
06:35:42.746 DEBUG GenomeLocParser - GL000229.1 (19913 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000231.1 (27386 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000210.1 (27682 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000239.1 (33824 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000235.1 (34474 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000201.1 (36148 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000247.1 (36422 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000245.1 (36651 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000197.1 (37175 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000203.1 (37498 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000246.1 (38154 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000249.1 (38502 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000196.1 (38914 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000248.1 (39786 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000244.1 (39929 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000238.1 (39939 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000202.1 (40103 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000234.1 (40531 bp)
06:35:42.747 DEBUG GenomeLocParser - GL000232.1 (40652 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000206.1 (41001 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000240.1 (41933 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000236.1 (41934 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000241.1 (42152 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000243.1 (43341 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000242.1 (43523 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000230.1 (43691 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000237.1 (45867 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000233.1 (45941 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000204.1 (81310 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000198.1 (90085 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000208.1 (92689 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000191.1 (106433 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000227.1 (128374 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000228.1 (129120 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000214.1 (137718 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000221.1 (155397 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000209.1 (159169 bp)
06:35:42.748 DEBUG GenomeLocParser - GL000218.1 (161147 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000220.1 (161802 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000213.1 (164239 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000211.1 (166566 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000199.1 (169874 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000217.1 (172149 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000216.1 (172294 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000215.1 (172545 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000205.1 (174588 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000219.1 (179198 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000224.1 (179693 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000223.1 (180455 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000195.1 (182896 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000212.1 (186858 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000222.1 (186861 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000200.1 (187035 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000193.1 (189789 bp)
06:35:42.749 DEBUG GenomeLocParser - GL000194.1 (191469 bp)
06:35:42.750 DEBUG GenomeLocParser - GL000225.1 (211173 bp)
06:35:42.750 DEBUG GenomeLocParser - GL000192.1 (547496 bp)
06:35:42.750 DEBUG GenomeLocParser - NC_007605 (171823 bp)
06:35:42.750 DEBUG GenomeLocParser - hs37d5 (35477943 bp)
06:35:42.750 DEBUG GenomeLocParser - phiX174 (5386 bp)
06:35:43.312 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS01CP.tsv (1 / 17)
06:35:47.321 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS02CP.tsv (2 / 17)
06:35:51.411 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS03CP.tsv (3 / 17)
06:35:55.558 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS04CP.tsv (4 / 17)
06:35:59.444 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS05CP.tsv (5 / 17)
06:36:03.796 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS06PB.tsv (6 / 17)
06:36:08.025 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS07PB.tsv (7 / 17)
06:36:12.452 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS08PB.tsv (8 / 17)
06:36:16.435 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS09PB.tsv (9 / 17)
06:36:20.685 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS10PB.tsv (10 / 17)
06:36:24.475 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS11PB.tsv (11 / 17)
06:36:28.487 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS12PB.tsv (12 / 17)
06:36:32.608 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS13PB.tsv (13 / 17)
06:36:36.943 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS14PB.tsv (14 / 17)
06:36:41.003 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS15PB.tsv (15 / 17)
06:36:45.048 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/D27H.tsv (16 / 17)
06:36:49.498 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/D28H.tsv (17 / 17)
06:36:53.914 DEBUG ScriptExecutor - Executing:
06:36:53.915 DEBUG ScriptExecutor - python
06:36:53.915 DEBUG ScriptExecutor - /tmp/cohort_determine_ploidy_and_depth.5003572249795548121.py
06:36:53.915 DEBUG ScriptExecutor - --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig2134986486837229873.tsv
06:36:53.915 DEBUG ScriptExecutor - --output_calls_path=/data/ploidy_output/ploidy-calls
06:36:53.915 DEBUG ScriptExecutor - --mapping_error_rate=3.000000e-01
06:36:53.915 DEBUG ScriptExecutor - --psi_s_scale=1.000000e-04
06:36:53.915 DEBUG ScriptExecutor - --mean_bias_sd=1.000000e+00
06:36:53.915 DEBUG ScriptExecutor - --psi_j_scale=1.000000e-03
06:36:53.915 DEBUG ScriptExecutor - --learning_rate=5.000000e-02
06:36:53.915 DEBUG ScriptExecutor - --adamax_beta1=9.000000e-01
06:36:53.915 DEBUG ScriptExecutor - --adamax_beta2=9.990000e-01
06:36:53.915 DEBUG ScriptExecutor - --log_emission_samples_per_round=2000
06:36:53.915 DEBUG ScriptExecutor - --log_emission_sampling_rounds=100
06:36:53.915 DEBUG ScriptExecutor - --log_emission_sampling_median_rel_error=5.000000e-04
06:36:53.915 DEBUG ScriptExecutor - --max_advi_iter_first_epoch=1000
06:36:53.915 DEBUG ScriptExecutor - --max_advi_iter_subsequent_epochs=1000
06:36:53.915 DEBUG ScriptExecutor - --min_training_epochs=20
06:36:53.915 DEBUG ScriptExecutor - --max_training_epochs=100
06:36:53.915 DEBUG ScriptExecutor - --initial_temperature=2.000000e+00
06:36:53.915 DEBUG ScriptExecutor - --num_thermal_advi_iters=5000
06:36:53.915 DEBUG ScriptExecutor - --convergence_snr_averaging_window=5000
06:36:53.915 DEBUG ScriptExecutor - --convergence_snr_trigger_threshold=1.000000e-01
06:36:53.915 DEBUG ScriptExecutor - --convergence_snr_countdown_window=10
06:36:53.915 DEBUG ScriptExecutor - --max_calling_iters=1
06:36:53.915 DEBUG ScriptExecutor - --caller_update_convergence_threshold=1.000000e-03
06:36:53.915 DEBUG ScriptExecutor - --caller_internal_admixing_rate=7.500000e-01
06:36:53.915 DEBUG ScriptExecutor - --caller_external_admixing_rate=7.500000e-01
06:36:53.915 DEBUG ScriptExecutor - --disable_caller=false
06:36:53.915 DEBUG ScriptExecutor - --disable_sampler=false
06:36:53.915 DEBUG ScriptExecutor - --disable_annealing=false
06:36:53.915 DEBUG ScriptExecutor - --interval_list=/tmp/intervals6066040695711768054.tsv
06:36:53.915 DEBUG ScriptExecutor - --contig_ploidy_prior_table=/data/hs37d5_contig_ploidy_priors.tsv
06:36:53.915 DEBUG ScriptExecutor - --output_model_path=/data/ploidy_output/ploidy-model
08:37:15.227 INFO cohort_determine_ploidy_and_depth - 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,base_compiledir=/tmp/theano
08:37:24.638 INFO gcnvkernel.structs.metadata - Generating intervals metadata...
08:37:41.926 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.926 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.926 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.926 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.927 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.927 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.927 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.927 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.927 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.927 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.928 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.928 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.928 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.928 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.928 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.928 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.929 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.929 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.929 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.929 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.929 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.929 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.930 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.930 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.930 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.930 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.930 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.930 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.930 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.931 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.931 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.931 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.931 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.931 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.931 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.931 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.932 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.932 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.932 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.932 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.932 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.932 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.933 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.933 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.933 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.933 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.933 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.933 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.933 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.934 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.934 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.934 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.934 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.934 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.934 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.935 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.935 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.935 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.935 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.935 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.935 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.935 WARNING gcnvkernel.models.commons - The given probability vector ([0. 0. 0. 0.]) is not normalized to unity within the provided tolerance (1e-10); sum = 0.0. Normalization was enforced. However, please check the inputs for unintentional errors.
08:37:41.960 INFO gcnvkernel.tasks.task_cohort_ploidy_determination - Instantiating the germline contig ploidy determination model...
08:38:57.583 INFO gcnvkernel.tasks.task_cohort_ploidy_determination - Instantiating the ploidy emission sampler...
08:38:57.584 INFO gcnvkernel.tasks.task_cohort_ploidy_determination - Instantiating the ploidy caller...
08:39:07.595 INFO gcnvkernel.models.fancy_model - Global model variables: {'mean_bias_j_lowerbound__', 'psi_j_log__'}
08:39:07.595 INFO gcnvkernel.models.fancy_model - Sample-specific model variables: {'psi_s_log__'}
08:39:07.595 INFO gcnvkernel.tasks.inference_task_base - Instantiating the convergence tracker...
08:39:07.595 INFO gcnvkernel.tasks.inference_task_base - Setting up DA-ADVI...
08:40:48.430 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
08:40:48.436 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/tmp/cohort_determine_ploidy_and_depth.5003572249795548121.py", line 125, in <module>
ploidy_task.engage()
File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/gcnvkernel/tasks/inference_task_base.py", line 346, in engage
converged_continuous = self._update_continuous_posteriors()
File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/gcnvkernel/tasks/inference_task_base.py", line 403, in _update_continuous_posteriors
raise ConvergenceError
gcnvkernel.tasks.inference_task_base.ConvergenceError
06:40:50.435 DEBUG ScriptExecutor - Result: 1
06:40:50.435 INFO DetermineGermlineContigPloidy - Shutting down engine
[April 16, 2025 at 6:40:50 AM GMT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 6.18 minutes.
Runtime.totalMemory()=29041360896
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python /tmp/cohort_determine_ploidy_and_depth.5003572249795548121.py --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig2134986486837229873.tsv --output_calls_path=/data/ploidy_output/ploidy-calls --mapping_error_rate=3.000000e-01 --psi_s_scale=1.000000e-04 --mean_bias_sd=1.000000e+00 --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 --call!
er_extern
al_admixing_rate=7.500000e-01 --disable_caller=false --disable_sampler=false --disable_annealing=false --interval_list=/tmp/intervals6066040695711768054.tsv --contig_ploidy_prior_table=/data/hs37d5_contig_ploidy_priors.tsv --output_model_path=/data/ploidy_output/ploidy-model
at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:112)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:193)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:168)
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:139)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.executeDeterminePloidyAndDepthPythonScript(DetermineGermlineContigPloidy.java:427)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.doWork(DetermineGermlineContigPloidy.java:324)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
at org.broadinstitute.hellbender.Main.main(Main.java:306)
Using GATK jar /gatk/gatk-package-4.6.0.0-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 /gatk/gatk-package-4.6.0.0-local.jar DetermineGermlineContigPloidy -L /data/filtered_intervals.interval_list --interval-merging-rule OVERLAPPING_ONLY -I /data/LFS01CP.tsv -I /data/LFS02CP.tsv -I /data/LFS03CP.tsv -I /data/LFS04CP.tsv -I /data/LFS05CP.tsv -I /data/LFS06PB.tsv -I /data/LFS07PB.tsv -I /data/LFS08PB.tsv -I /data/LFS09PB.tsv -I /data/LFS10PB.tsv -I /data/LFS11PB.tsv -I /data/LFS12PB.tsv -I /data/LFS13PB.tsv -I /data/LFS14PB.tsv -I /data/LFS15PB.tsv -I /data/D27H.tsv -I /data/D28H.tsv --contig-ploidy-priors /data/hs37d5_contig_ploidy_priors.tsv --output /data/ploidy_output --output-prefix ploidy --verbosity DEBUG
I realized this was because I did not have the gcnvkernel installed. I tried using Singularity to pull the docker image for gatk but this does not seem to work. I also tried to create a micromamba environment to download gcnvkernel but was unsuccessful.
Key Issues: Dependency Conflicts: gcnvkernel==0.9 requires strict versions (pymc==5.10.0, pytensor==2.18.1, numpy==1.26.2, etc.), which are not available or conflict with common environments and tools (e.g. conda/micromamba).
PyVCF is Deprecated: PyVCF==0.6.8 fails to build due to use of deprecated use_2to3.
Runtime Errors: Even after aligning most dependencies, pytensor>=2.30 leads to:
ImportError: cannot import name 'unbroadcast' from 'pytensor.tensor.shape'
Missing System Libraries: Alternatives like vcfpy require libbz2-dev and others, which are not installable on restricted clusters.
Any help would be appreciated. Thanks!
