Germline CNV calling for bulk WGS data aligned to hs37d5_PhiX.fa
I am trying to run germline CNV calling on a cohort of 17 bulk WGS samples that are aligned to hs37d5_PhiX.fa genome. I am confused regarding the DetermineGermlineContigPloidy step. What contig-ploidy-priors file can I use to run this step?
I would like to run the pipeline in both cohort and case-modes.
Thanks a lot!
-
Hi Urja Parekh
Below is an example contig ploidy priors file that you can try with your samples.
CONTIG_NAME PLOIDY_PRIOR_0 PLOIDY_PRIOR_1 PLOIDY_PRIOR_2 PLOIDY_PRIOR_3
1 0.01 0.01 0.97 0.01
2 0.01 0.01 0.97 0.01
3 0.01 0.01 0.97 0.01
4 0.01 0.01 0.97 0.01
5 0.01 0.01 0.97 0.01
6 0.01 0.01 0.97 0.01
7 0.01 0.01 0.97 0.01
8 0.01 0.01 0.97 0.01
9 0.01 0.01 0.97 0.01
10 0.01 0.01 0.97 0.01
11 0.01 0.01 0.97 0.01
12 0.01 0.01 0.97 0.01
13 0.01 0.01 0.97 0.01
14 0.01 0.01 0.97 0.01
15 0.01 0.01 0.97 0.01
16 0.01 0.01 0.97 0.01
17 0.01 0.01 0.97 0.01
18 0.01 0.01 0.97 0.01
19 0.01 0.01 0.97 0.01
20 0.01 0.01 0.97 0.01
21 0.01 0.01 0.97 0.01
22 0.01 0.01 0.97 0.01
X 0.0 0.5 0.5 0.0
Y 0.5 0.5 0.0 0.0This file is only used to predict possible copy states of chromosomes in whole therefore you may change these values to adjust the sensitivity of chromosome copy numbers in your samples. 0 means that particular copy state is never available for your samples. You may add more copy states by adding additional columns with prior probabilities. Regardless GermlineCNVCaller will work on its own to detect copy states of intervals so this file does not change the way GermlineCNVCaller works.
I hope this helps.
Regards.
-
Hi Gökalp,
Thanks a ton for your prompt response. I am trying to run the DetermineGermlineContigPloidy step as follows:singularity exec \
--env THEANO_FLAGS="base_compiledir=/tmp/theano" \
-B /home/u855h/chromothripsis/urja/gatk:/data \
/home/u855h/chromothripsis/urja_python/conda_environments/gatk-cnv/gatk_4.6.0.0.sif \
gatk 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/contig_ploidy_priors.tsv \
--output /data/ploidy_output \
--output-prefix ploidy \
--verbosity DEBUG
I get the following error:08:00:13.164 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
08:00:13.199 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression73529199057688114.so
08:00:13.599 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
08:00:13.624 INFO DetermineGermlineContigPloidy - The Genome Analysis Toolkit (GATK) v4.6.0.0
08:00:13.624 INFO DetermineGermlineContigPloidy - For support and documentation go to https://software.broadinstitute.org/gatk/
08:00:13.624 INFO DetermineGermlineContigPloidy - Executing as u855h@odcf-cn11u13 on Linux v3.10.0-1160.119.1.el7.x86_64 amd64
08:00:13.624 INFO DetermineGermlineContigPloidy - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
08:00:13.624 INFO DetermineGermlineContigPloidy - Start Date/Time: April 16, 2025 at 8:00:12 AM GMT
08:00:13.624 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
08:00:13.624 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
08:00:13.625 INFO DetermineGermlineContigPloidy - HTSJDK Version: 4.1.1
08:00:13.625 INFO DetermineGermlineContigPloidy - Picard Version: 3.2.0
08:00:13.625 INFO DetermineGermlineContigPloidy - Built for Spark Version: 3.5.0
08:00:13.626 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.BUFFER_SIZE : 131072
08:00:13.626 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.COMPRESSION_LEVEL : 2
08:00:13.626 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_INDEX : false
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_MD5 : false
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CUSTOM_READER_FACTORY :
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.REFERENCE_FASTA : null
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
08:00:13.627 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
08:00:13.628 DEBUG ConfigFactory - Configuration file values:
08:00:13.631 DEBUG ConfigFactory - gcsMaxRetries = 20
08:00:13.631 DEBUG ConfigFactory - gcsProjectForRequesterPays =
08:00:13.631 DEBUG ConfigFactory - gatk_stacktrace_on_user_exception = false
08:00:13.631 DEBUG ConfigFactory - samjdk.use_async_io_read_samtools = false
08:00:13.631 DEBUG ConfigFactory - samjdk.use_async_io_write_samtools = true
08:00:13.631 DEBUG ConfigFactory - samjdk.use_async_io_write_tribble = false
08:00:13.631 DEBUG ConfigFactory - samjdk.compression_level = 2
08:00:13.632 DEBUG ConfigFactory - spark.kryoserializer.buffer.max = 512m
08:00:13.632 DEBUG ConfigFactory - spark.driver.maxResultSize = 0
08:00:13.632 DEBUG ConfigFactory - spark.driver.userClassPathFirst = true
08:00:13.632 DEBUG ConfigFactory - spark.io.compression.codec = lzf
08:00:13.632 DEBUG ConfigFactory - spark.executor.memoryOverhead = 600
08:00:13.632 DEBUG ConfigFactory - spark.driver.extraJavaOptions =
08:00:13.632 DEBUG ConfigFactory - spark.executor.extraJavaOptions =
08:00:13.632 DEBUG ConfigFactory - codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
08:00:13.632 DEBUG ConfigFactory - read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
08:00:13.632 DEBUG ConfigFactory - annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
08:00:13.632 DEBUG ConfigFactory - cloudPrefetchBuffer = 40
08:00:13.632 DEBUG ConfigFactory - cloudIndexPrefetchBuffer = -1
08:00:13.633 DEBUG ConfigFactory - createOutputBamIndex = true
08:00:13.633 INFO DetermineGermlineContigPloidy - Deflater: IntelDeflater
08:00:13.633 INFO DetermineGermlineContigPloidy - Inflater: IntelInflater
08:00:13.633 INFO DetermineGermlineContigPloidy - GCS max retries/reopens: 20
08:00:13.633 INFO DetermineGermlineContigPloidy - Requester pays: disabled
08:00:13.634 INFO DetermineGermlineContigPloidy - Initializing engine
08:00:13.637 DEBUG ScriptExecutor - Executing:
08:00:13.637 DEBUG ScriptExecutor - python
08:00:13.637 DEBUG ScriptExecutor - -c
08:00:13.637 DEBUG ScriptExecutor - import gcnvkernel
08:00:50.712 DEBUG ScriptExecutor - Result: 0
08:00:50.713 INFO DetermineGermlineContigPloidy - Done initializing engine
08:00:50.735 INFO DetermineGermlineContigPloidy - No contig-ploidy model was provided, running in cohort mode...
08:00:50.735 INFO DetermineGermlineContigPloidy - Intervals specified...
08:00:54.523 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
08:00:54.524 DEBUG GenomeLocParser - 1 (249250621 bp)
08:00:54.524 DEBUG GenomeLocParser - 2 (243199373 bp)
08:00:54.524 DEBUG GenomeLocParser - 3 (198022430 bp)
08:00:54.524 DEBUG GenomeLocParser - 4 (191154276 bp)
08:00:54.524 DEBUG GenomeLocParser - 5 (180915260 bp)
08:00:54.524 DEBUG GenomeLocParser - 6 (171115067 bp)
08:00:54.524 DEBUG GenomeLocParser - 7 (159138663 bp)
08:00:54.524 DEBUG GenomeLocParser - 8 (146364022 bp)
08:00:54.524 DEBUG GenomeLocParser - 9 (141213431 bp)
08:00:54.524 DEBUG GenomeLocParser - 10 (135534747 bp)
08:00:54.524 DEBUG GenomeLocParser - 11 (135006516 bp)
08:00:54.524 DEBUG GenomeLocParser - 12 (133851895 bp)
08:00:54.524 DEBUG GenomeLocParser - 13 (115169878 bp)
08:00:54.524 DEBUG GenomeLocParser - 14 (107349540 bp)
08:00:54.524 DEBUG GenomeLocParser - 15 (102531392 bp)
08:00:54.525 DEBUG GenomeLocParser - 16 (90354753 bp)
08:00:54.525 DEBUG GenomeLocParser - 17 (81195210 bp)
08:00:54.525 DEBUG GenomeLocParser - 18 (78077248 bp)
08:00:54.525 DEBUG GenomeLocParser - 19 (59128983 bp)
08:00:54.525 DEBUG GenomeLocParser - 20 (63025520 bp)
08:00:54.525 DEBUG GenomeLocParser - 21 (48129895 bp)
08:00:54.525 DEBUG GenomeLocParser - 22 (51304566 bp)
08:00:54.525 DEBUG GenomeLocParser - X (155270560 bp)
08:00:54.525 DEBUG GenomeLocParser - Y (59373566 bp)
08:00:54.525 DEBUG GenomeLocParser - MT (16569 bp)
08:00:54.525 DEBUG GenomeLocParser - GL000207.1 (4262 bp)
08:00:54.525 DEBUG GenomeLocParser - GL000226.1 (15008 bp)
08:00:54.525 DEBUG GenomeLocParser - GL000229.1 (19913 bp)
08:00:54.525 DEBUG GenomeLocParser - GL000231.1 (27386 bp)
08:00:54.525 DEBUG GenomeLocParser - GL000210.1 (27682 bp)
08:00:54.525 DEBUG GenomeLocParser - GL000239.1 (33824 bp)
08:00:54.525 DEBUG GenomeLocParser - GL000235.1 (34474 bp)
08:00:54.525 DEBUG GenomeLocParser - GL000201.1 (36148 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000247.1 (36422 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000245.1 (36651 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000197.1 (37175 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000203.1 (37498 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000246.1 (38154 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000249.1 (38502 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000196.1 (38914 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000248.1 (39786 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000244.1 (39929 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000238.1 (39939 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000202.1 (40103 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000234.1 (40531 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000232.1 (40652 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000206.1 (41001 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000240.1 (41933 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000236.1 (41934 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000241.1 (42152 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000243.1 (43341 bp)
08:00:54.526 DEBUG GenomeLocParser - GL000242.1 (43523 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000230.1 (43691 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000237.1 (45867 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000233.1 (45941 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000204.1 (81310 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000198.1 (90085 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000208.1 (92689 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000191.1 (106433 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000227.1 (128374 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000228.1 (129120 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000214.1 (137718 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000221.1 (155397 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000209.1 (159169 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000218.1 (161147 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000220.1 (161802 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000213.1 (164239 bp)
08:00:54.527 DEBUG GenomeLocParser - GL000211.1 (166566 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000199.1 (169874 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000217.1 (172149 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000216.1 (172294 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000215.1 (172545 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000205.1 (174588 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000219.1 (179198 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000224.1 (179693 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000223.1 (180455 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000195.1 (182896 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000212.1 (186858 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000222.1 (186861 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000200.1 (187035 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000193.1 (189789 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000194.1 (191469 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000225.1 (211173 bp)
08:00:54.528 DEBUG GenomeLocParser - GL000192.1 (547496 bp)
08:00:54.528 DEBUG GenomeLocParser - NC_007605 (171823 bp)
08:00:54.528 DEBUG GenomeLocParser - hs37d5 (35477943 bp)
08:00:54.528 DEBUG GenomeLocParser - phiX174 (5386 bp)
08:00:54.726 INFO FeatureManager - Using codec IntervalListCodec to read file file:///data/filtered_intervals.interval_list
08:01:02.285 DEBUG FeatureDataSource - Cache statistics for FeatureInput /data/filtered_intervals.interval_list:/data/filtered_intervals.interval_list:
08:01:02.286 DEBUG FeatureCache - Cache hit rate was 0.00% (0 out of 0 total queries)
08:01:02.665 INFO IntervalArgumentCollection - Processing 2816223150 bp from intervals
08:01:03.915 INFO DetermineGermlineContigPloidy - Validating and aggregating coverage per contig from input read-count files...
08:01:04.455 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
08:01:04.455 DEBUG GenomeLocParser - 1 (249250621 bp)
08:01:04.455 DEBUG GenomeLocParser - 2 (243199373 bp)
08:01:04.455 DEBUG GenomeLocParser - 3 (198022430 bp)
08:01:04.456 DEBUG GenomeLocParser - 4 (191154276 bp)
08:01:04.456 DEBUG GenomeLocParser - 5 (180915260 bp)
08:01:04.456 DEBUG GenomeLocParser - 6 (171115067 bp)
08:01:04.456 DEBUG GenomeLocParser - 7 (159138663 bp)
08:01:04.457 DEBUG GenomeLocParser - 8 (146364022 bp)
08:01:04.457 DEBUG GenomeLocParser - 9 (141213431 bp)
08:01:04.457 DEBUG GenomeLocParser - 10 (135534747 bp)
08:01:04.457 DEBUG GenomeLocParser - 11 (135006516 bp)
08:01:04.457 DEBUG GenomeLocParser - 12 (133851895 bp)
08:01:04.457 DEBUG GenomeLocParser - 13 (115169878 bp)
08:01:04.457 DEBUG GenomeLocParser - 14 (107349540 bp)
08:01:04.457 DEBUG GenomeLocParser - 15 (102531392 bp)
08:01:04.457 DEBUG GenomeLocParser - 16 (90354753 bp)
08:01:04.458 DEBUG GenomeLocParser - 17 (81195210 bp)
08:01:04.458 DEBUG GenomeLocParser - 18 (78077248 bp)
08:01:04.458 DEBUG GenomeLocParser - 19 (59128983 bp)
08:01:04.458 DEBUG GenomeLocParser - 20 (63025520 bp)
08:01:04.458 DEBUG GenomeLocParser - 21 (48129895 bp)
08:01:04.458 DEBUG GenomeLocParser - 22 (51304566 bp)
08:01:04.458 DEBUG GenomeLocParser - X (155270560 bp)
08:01:04.458 DEBUG GenomeLocParser - Y (59373566 bp)
08:01:04.458 DEBUG GenomeLocParser - MT (16569 bp)
08:01:04.458 DEBUG GenomeLocParser - GL000207.1 (4262 bp)
08:01:04.458 DEBUG GenomeLocParser - GL000226.1 (15008 bp)
08:01:04.459 DEBUG GenomeLocParser - GL000229.1 (19913 bp)
08:01:04.460 DEBUG GenomeLocParser - GL000231.1 (27386 bp)
08:01:04.460 DEBUG GenomeLocParser - GL000210.1 (27682 bp)
08:01:04.460 DEBUG GenomeLocParser - GL000239.1 (33824 bp)
08:01:04.460 DEBUG GenomeLocParser - GL000235.1 (34474 bp)
08:01:04.460 DEBUG GenomeLocParser - GL000201.1 (36148 bp)
08:01:04.461 DEBUG GenomeLocParser - GL000247.1 (36422 bp)
08:01:04.461 DEBUG GenomeLocParser - GL000245.1 (36651 bp)
08:01:04.461 DEBUG GenomeLocParser - GL000197.1 (37175 bp)
08:01:04.462 DEBUG GenomeLocParser - GL000203.1 (37498 bp)
08:01:04.462 DEBUG GenomeLocParser - GL000246.1 (38154 bp)
08:01:04.462 DEBUG GenomeLocParser - GL000249.1 (38502 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000196.1 (38914 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000248.1 (39786 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000244.1 (39929 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000238.1 (39939 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000202.1 (40103 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000234.1 (40531 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000232.1 (40652 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000206.1 (41001 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000240.1 (41933 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000236.1 (41934 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000241.1 (42152 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000243.1 (43341 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000242.1 (43523 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000230.1 (43691 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000237.1 (45867 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000233.1 (45941 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000204.1 (81310 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000198.1 (90085 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000208.1 (92689 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000191.1 (106433 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000227.1 (128374 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000228.1 (129120 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000214.1 (137718 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000221.1 (155397 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000209.1 (159169 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000218.1 (161147 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000220.1 (161802 bp)
08:01:04.463 DEBUG GenomeLocParser - GL000213.1 (164239 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000211.1 (166566 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000199.1 (169874 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000217.1 (172149 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000216.1 (172294 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000215.1 (172545 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000205.1 (174588 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000219.1 (179198 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000224.1 (179693 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000223.1 (180455 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000195.1 (182896 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000212.1 (186858 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000222.1 (186861 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000200.1 (187035 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000193.1 (189789 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000194.1 (191469 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000225.1 (211173 bp)
08:01:04.464 DEBUG GenomeLocParser - GL000192.1 (547496 bp)
08:01:04.464 DEBUG GenomeLocParser - NC_007605 (171823 bp)
08:01:04.464 DEBUG GenomeLocParser - hs37d5 (35477943 bp)
08:01:04.464 DEBUG GenomeLocParser - phiX174 (5386 bp)
08:01:04.842 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS01CP.tsv (1 / 17)
08:01:07.711 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS02CP.tsv (2 / 17)
08:01:10.825 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS03CP.tsv (3 / 17)
08:01:13.512 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS04CP.tsv (4 / 17)
08:01:17.110 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS05CP.tsv (5 / 17)
08:01:19.840 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS06PB.tsv (6 / 17)
08:01:23.079 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS07PB.tsv (7 / 17)
08:01:26.493 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS08PB.tsv (8 / 17)
08:01:29.781 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS09PB.tsv (9 / 17)
08:01:33.024 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS10PB.tsv (10 / 17)
08:01:35.909 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS11PB.tsv (11 / 17)
08:01:38.680 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS12PB.tsv (12 / 17)
08:01:41.804 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS13PB.tsv (13 / 17)
08:01:44.511 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS14PB.tsv (14 / 17)
08:01:47.324 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/LFS15PB.tsv (15 / 17)
08:01:50.166 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/D27H.tsv (16 / 17)
08:01:53.070 INFO DetermineGermlineContigPloidy - Aggregating read-count file /data/D28H.tsv (17 / 17)
08:01:55.812 DEBUG ScriptExecutor - Executing:
08:01:55.812 DEBUG ScriptExecutor - python
08:01:55.812 DEBUG ScriptExecutor - /tmp/cohort_determine_ploidy_and_depth.17637993935490488564.py
08:01:55.812 DEBUG ScriptExecutor - --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig11756143612749541858.tsv
08:01:55.812 DEBUG ScriptExecutor - --output_calls_path=/data/ploidy_output/ploidy-calls
08:01:55.812 DEBUG ScriptExecutor - --mapping_error_rate=3.000000e-01
08:01:55.812 DEBUG ScriptExecutor - --psi_s_scale=1.000000e-04
08:01:55.812 DEBUG ScriptExecutor - --mean_bias_sd=1.000000e+00
08:01:55.812 DEBUG ScriptExecutor - --psi_j_scale=1.000000e-03
08:01:55.812 DEBUG ScriptExecutor - --learning_rate=5.000000e-02
08:01:55.812 DEBUG ScriptExecutor - --adamax_beta1=9.000000e-01
08:01:55.812 DEBUG ScriptExecutor - --adamax_beta2=9.990000e-01
08:01:55.812 DEBUG ScriptExecutor - --log_emission_samples_per_round=2000
08:01:55.812 DEBUG ScriptExecutor - --log_emission_sampling_rounds=100
08:01:55.812 DEBUG ScriptExecutor - --log_emission_sampling_median_rel_error=5.000000e-04
08:01:55.812 DEBUG ScriptExecutor - --max_advi_iter_first_epoch=1000
08:01:55.812 DEBUG ScriptExecutor - --max_advi_iter_subsequent_epochs=1000
08:01:55.812 DEBUG ScriptExecutor - --min_training_epochs=20
08:01:55.812 DEBUG ScriptExecutor - --max_training_epochs=100
08:01:55.812 DEBUG ScriptExecutor - --initial_temperature=2.000000e+00
08:01:55.812 DEBUG ScriptExecutor - --num_thermal_advi_iters=5000
08:01:55.812 DEBUG ScriptExecutor - --convergence_snr_averaging_window=5000
08:01:55.812 DEBUG ScriptExecutor - --convergence_snr_trigger_threshold=1.000000e-01
08:01:55.812 DEBUG ScriptExecutor - --convergence_snr_countdown_window=10
08:01:55.812 DEBUG ScriptExecutor - --max_calling_iters=1
08:01:55.812 DEBUG ScriptExecutor - --caller_update_convergence_threshold=1.000000e-03
08:01:55.812 DEBUG ScriptExecutor - --caller_internal_admixing_rate=7.500000e-01
08:01:55.812 DEBUG ScriptExecutor - --caller_external_admixing_rate=7.500000e-01
08:01:55.812 DEBUG ScriptExecutor - --disable_caller=false
08:01:55.813 DEBUG ScriptExecutor - --disable_sampler=false
08:01:55.813 DEBUG ScriptExecutor - --disable_annealing=false
08:01:55.813 DEBUG ScriptExecutor - --interval_list=/tmp/intervals2916554049902894358.tsv
08:01:55.813 DEBUG ScriptExecutor - --contig_ploidy_prior_table=/data/contig_ploidy_priors.tsv
08:01:55.813 DEBUG ScriptExecutor - --output_model_path=/data/ploidy_output/ploidy-model
10:02:13.409 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
10:02:21.142 INFO gcnvkernel.structs.metadata - Generating intervals metadata...
Traceback (most recent call last):
File "/tmp/cohort_determine_ploidy_and_depth.17637993935490488564.py", line 121, in <module>
sample_metadata_collection)
File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/gcnvkernel/models/model_ploidy.py", line 146, in __init__
"Some contigs do not have ploidy priors"
AssertionError: Some contigs do not have ploidy priors
08:02:36.260 DEBUG ScriptExecutor - Result: 1
08:02:36.261 INFO DetermineGermlineContigPloidy - Shutting down engine
[April 16, 2025 at 8:02:36 AM GMT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 2.39 minutes.
Runtime.totalMemory()=29964107776
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python /tmp/cohort_determine_ploidy_and_depth.17637993935490488564.py --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig11756143612749541858.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 --ca!
ller_exte
rnal_admixing_rate=7.500000e-01 --disable_caller=false --disable_sampler=false --disable_annealing=false --interval_list=/tmp/intervals2916554049902894358.tsv --contig_ploidy_prior_table=/data/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/contig_ploidy_priors.tsv --output /data/ploidy_output --output-prefix ploidy --verbosity DEBUG
Over here I used the contig ploidy priors file as you recommended and I believe the pipeline fails because of missing contigs. I used another contigs ploidy prior file where I assigned all alt contigs as 0 and got the following error:
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
What can I do to solve this problem?
Thanks and regards,
Urja
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