GermlineCNVCaller Assertion Error: Some samples do not have read depth metadata
As stated in the subject, I encounter the no sample depth metadata error.
I found a legacy discussion about this in GATK forum here:
I confirmed I do not have any samples (among the inputs) having missing/duplicated names or global read depth and average ploidy meta info. I'm confused right now and really appreciated if you could shed some lights on the real cause here.
(P.S. The same sample batch has been used to join a bigger cohort CNV calling in COHORT mode and it went OK. But run into this assertion error when trying to independently call CNV for this batch in CASE mode)
REQUIRED for all errors and issues:
a) GATK version used:4.2.6.1
b) Exact command used:
${gatk} GermlineCNVCaller \
--java-options"-DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Xmx40G -XX:+UseParallelOldGC -XX:+UseAdaptiveSizePolicy -XX:ActiveProcessorCount=4 -XX:ParallelGCThreads=4" \--run-modeCASE \--model ${gCNV_cohort_model} \--contig-ploidy-calls ${valid_ploidy_call} \--verbosityDEBUG \<Input read count HDF5 files> \--output ${gCNV_case_dir} \--output-prefix ${gCNV_case_calls_prefix} \--p-alt0.0005 \--cnv-coherence-length1000 \--max-copy-number5 \--mapping-error-rate0.01 \--sample-psi-scale0.01 \--depth-correction-tau10000 \--learning-rate0.05 \--adamax-beta-10.9 \--adamax-beta-20.99 \--log-emission-samples-per-round50 \--log-emission-sampling-median-rel-error0.005 \--log-emission-sampling-rounds10 \--max-advi-iter-first-epoch5000 \--max-advi-iter-subsequent-epochs100 \--min-training-epochs10 \--max-training-epochs100 \--initial-temperature2.0 \--num-thermal-advi-iters2500 \--convergence-snr-averaging-window500 \--convergence-snr-trigger-threshold0.1 \--convergence-snr-countdown-window10 \--max-calling-iters10 \--caller-update-convergence-threshold0.001 \--caller-internal-admixing-rate0.75 \--caller-external-admixing-rate1.0 \--active-class-padding-hybrid-mode5000
c) Entire program log:Line 7962: Tue Feb 14 15:23:40 HKT 2023: In function gatk_wrapper: The GATK wrapper get input arguments: gatk DetermineGermlineContigPloidy --java-options -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Xms20G -Xmx60G -XX:+UseParallelOldGC -XX:+UseAdaptiveSizePolicy -XX:ActiveProcessorCount=4 -XX:ParallelGCThreads=4 --model /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_ploidy_model/iGT359V1_ploidy_normal_cohort-model -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-004.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-005.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-380.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-381.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-382.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-080.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-081.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-210.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170421.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170420.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200628.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210104.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210105.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-172.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-173.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-174.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-220.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-166.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-167.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-168.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-006.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-007.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-008.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-009.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-010.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-011.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-162.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-163.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-164.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-165.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210124.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210126.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200621.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210128.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210130.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210121.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210122.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210123.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200272.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200273.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200274.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-001.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-002.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-003.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210118.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210119.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210120.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210100.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210102.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200635.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200637.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200639.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200643.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-021A.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-022.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-023A.counts.hdf5 --output /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy --output-prefix iGT359V1_cases_ploidy_50_samples_20220304 --verbosity DEBUG
07:23:42.949 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
07:23:42.975 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression6954392534273917627.so
07:23:43.116 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
07:23:43.116 INFO DetermineGermlineContigPloidy - The Genome Analysis Toolkit (GATK) v4.3.0.0
07:23:43.116 INFO DetermineGermlineContigPloidy - For support and documentation go to https://software.broadinstitute.org/gatk/
07:23:43.117 INFO DetermineGermlineContigPloidy - Executing as yangyxt@paedyl02 on Linux v3.10.0-1160.11.1.el7.x86_64 amd64
07:23:43.117 INFO DetermineGermlineContigPloidy - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
07:23:43.117 INFO DetermineGermlineContigPloidy - Start Date/Time: February 14, 2023 7:23:42 AM GMT
07:23:43.117 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
07:23:43.117 INFO DetermineGermlineContigPloidy - ------------------------------------------------------------
07:23:43.117 INFO DetermineGermlineContigPloidy - HTSJDK Version: 3.0.1
07:23:43.117 INFO DetermineGermlineContigPloidy - Picard Version: 2.27.5
07:23:43.117 INFO DetermineGermlineContigPloidy - Built for Spark Version: 2.4.5
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.BUFFER_SIZE : 131072
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.COMPRESSION_LEVEL : 2
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_INDEX : false
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CREATE_MD5 : false
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.CUSTOM_READER_FACTORY :
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.REFERENCE_FASTA : null
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
07:23:43.118 INFO DetermineGermlineContigPloidy - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
07:23:43.118 DEBUG ConfigFactory - Configuration file values:
07:23:43.120 DEBUG ConfigFactory - gcsMaxRetries = 20
07:23:43.120 DEBUG ConfigFactory - gcsProjectForRequesterPays =
07:23:43.120 DEBUG ConfigFactory - gatk_stacktrace_on_user_exception = false
07:23:43.120 DEBUG ConfigFactory - samjdk.use_async_io_read_samtools = false
07:23:43.120 DEBUG ConfigFactory - samjdk.use_async_io_write_samtools = true
07:23:43.121 DEBUG ConfigFactory - samjdk.use_async_io_write_tribble = false
07:23:43.121 DEBUG ConfigFactory - samjdk.compression_level = 2
07:23:43.121 DEBUG ConfigFactory - spark.kryoserializer.buffer.max = 512m
07:23:43.121 DEBUG ConfigFactory - spark.driver.maxResultSize = 0
07:23:43.121 DEBUG ConfigFactory - spark.driver.userClassPathFirst = true
07:23:43.121 DEBUG ConfigFactory - spark.io.compression.codec = lzf
07:23:43.121 DEBUG ConfigFactory - spark.executor.memoryOverhead = 600
07:23:43.121 DEBUG ConfigFactory - spark.driver.extraJavaOptions =
07:23:43.121 DEBUG ConfigFactory - spark.executor.extraJavaOptions =
07:23:43.121 DEBUG ConfigFactory - codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
07:23:43.121 DEBUG ConfigFactory - read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
07:23:43.121 DEBUG ConfigFactory - annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
07:23:43.121 DEBUG ConfigFactory - cloudPrefetchBuffer = 40
07:23:43.121 DEBUG ConfigFactory - cloudIndexPrefetchBuffer = -1
07:23:43.121 DEBUG ConfigFactory - createOutputBamIndex = true
07:23:43.121 INFO DetermineGermlineContigPloidy - Deflater: IntelDeflater
07:23:43.121 INFO DetermineGermlineContigPloidy - Inflater: IntelInflater
07:23:43.121 INFO DetermineGermlineContigPloidy - GCS max retries/reopens: 20
07:23:43.121 INFO DetermineGermlineContigPloidy - Requester pays: disabled
07:23:43.121 INFO DetermineGermlineContigPloidy - Initializing engine
07:23:43.123 DEBUG ScriptExecutor - Executing:
07:23:43.123 DEBUG ScriptExecutor - python
07:23:43.123 DEBUG ScriptExecutor - -c
07:23:43.123 DEBUG ScriptExecutor - import gcnvkernel07:23:54.644 DEBUG ScriptExecutor - Result: 0
07:23:54.644 INFO DetermineGermlineContigPloidy - Done initializing engine
07:23:54.660 INFO DetermineGermlineContigPloidy - A contig-ploidy model was provided, running in case mode...
07:23:55.140 INFO DetermineGermlineContigPloidy - Validating and aggregating coverage per contig from input read-count files...
07:23:55.204 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
07:23:55.204 DEBUG GenomeLocParser - chrM (16571 bp)
07:23:55.204 DEBUG GenomeLocParser - chr1 (249250621 bp)
07:23:55.204 DEBUG GenomeLocParser - chr2 (243199373 bp)
07:23:55.204 DEBUG GenomeLocParser - chr3 (198022430 bp)
07:23:55.204 DEBUG GenomeLocParser - chr4 (191154276 bp)
07:23:55.204 DEBUG GenomeLocParser - chr5 (180915260 bp)
07:23:55.204 DEBUG GenomeLocParser - chr6 (171115067 bp)
07:23:55.204 DEBUG GenomeLocParser - chr7 (159138663 bp)
07:23:55.204 DEBUG GenomeLocParser - chr8 (146364022 bp)
07:23:55.204 DEBUG GenomeLocParser - chr9 (141213431 bp)
07:23:55.204 DEBUG GenomeLocParser - chr10 (135534747 bp)
07:23:55.204 DEBUG GenomeLocParser - chr11 (135006516 bp)
07:23:55.204 DEBUG GenomeLocParser - chr12 (133851895 bp)
07:23:55.205 DEBUG GenomeLocParser - chr13 (115169878 bp)
07:23:55.205 DEBUG GenomeLocParser - chr14 (107349540 bp)
07:23:55.205 DEBUG GenomeLocParser - chr15 (102531392 bp)
07:23:55.205 DEBUG GenomeLocParser - chr16 (90354753 bp)
07:23:55.205 DEBUG GenomeLocParser - chr17 (81195210 bp)
07:23:55.205 DEBUG GenomeLocParser - chr18 (78077248 bp)
07:23:55.205 DEBUG GenomeLocParser - chr19 (59128983 bp)
07:23:55.205 DEBUG GenomeLocParser - chr20 (63025520 bp)
07:23:55.205 DEBUG GenomeLocParser - chr21 (48129895 bp)
07:23:55.205 DEBUG GenomeLocParser - chr22 (51304566 bp)
07:23:55.205 DEBUG GenomeLocParser - chrX (155270560 bp)
07:23:55.205 DEBUG GenomeLocParser - chrY (59373566 bp)
07:23:55.205 DEBUG GenomeLocParser - chr1_gl000191_random (106433 bp)
07:23:55.205 DEBUG GenomeLocParser - chr1_gl000192_random (547496 bp)
07:23:55.205 DEBUG GenomeLocParser - chr4_ctg9_hap1 (590426 bp)
07:23:55.205 DEBUG GenomeLocParser - chr4_gl000193_random (189789 bp)
07:23:55.205 DEBUG GenomeLocParser - chr4_gl000194_random (191469 bp)
07:23:55.205 DEBUG GenomeLocParser - chr6_apd_hap1 (4622290 bp)
07:23:55.205 DEBUG GenomeLocParser - chr6_cox_hap2 (4795371 bp)
07:23:55.205 DEBUG GenomeLocParser - chr6_dbb_hap3 (4610396 bp)
07:23:55.205 DEBUG GenomeLocParser - chr6_mann_hap4 (4683263 bp)
07:23:55.205 DEBUG GenomeLocParser - chr6_mcf_hap5 (4833398 bp)
07:23:55.205 DEBUG GenomeLocParser - chr6_qbl_hap6 (4611984 bp)
07:23:55.205 DEBUG GenomeLocParser - chr6_ssto_hap7 (4928567 bp)
07:23:55.205 DEBUG GenomeLocParser - chr7_gl000195_random (182896 bp)
07:23:55.206 DEBUG GenomeLocParser - chr8_gl000196_random (38914 bp)
07:23:55.206 DEBUG GenomeLocParser - chr8_gl000197_random (37175 bp)
07:23:55.206 DEBUG GenomeLocParser - chr9_gl000198_random (90085 bp)
07:23:55.206 DEBUG GenomeLocParser - chr9_gl000199_random (169874 bp)
07:23:55.206 DEBUG GenomeLocParser - chr9_gl000200_random (187035 bp)
07:23:55.206 DEBUG GenomeLocParser - chr9_gl000201_random (36148 bp)
07:23:55.206 DEBUG GenomeLocParser - chr11_gl000202_random (40103 bp)
07:23:55.206 DEBUG GenomeLocParser - chr17_ctg5_hap1 (1680828 bp)
07:23:55.206 DEBUG GenomeLocParser - chr17_gl000203_random (37498 bp)
07:23:55.206 DEBUG GenomeLocParser - chr17_gl000204_random (81310 bp)
07:23:55.206 DEBUG GenomeLocParser - chr17_gl000205_random (174588 bp)
07:23:55.206 DEBUG GenomeLocParser - chr17_gl000206_random (41001 bp)
07:23:55.206 DEBUG GenomeLocParser - chr18_gl000207_random (4262 bp)
07:23:55.206 DEBUG GenomeLocParser - chr19_gl000208_random (92689 bp)
07:23:55.206 DEBUG GenomeLocParser - chr19_gl000209_random (159169 bp)
07:23:55.206 DEBUG GenomeLocParser - chr21_gl000210_random (27682 bp)
07:23:55.206 DEBUG GenomeLocParser - chrUn_gl000211 (166566 bp)
07:23:55.206 DEBUG GenomeLocParser - chrUn_gl000212 (186858 bp)
07:23:55.206 DEBUG GenomeLocParser - chrUn_gl000213 (164239 bp)
07:23:55.206 DEBUG GenomeLocParser - chrUn_gl000214 (137718 bp)
07:23:55.206 DEBUG GenomeLocParser - chrUn_gl000215 (172545 bp)
07:23:55.206 DEBUG GenomeLocParser - chrUn_gl000216 (172294 bp)
07:23:55.206 DEBUG GenomeLocParser - chrUn_gl000217 (172149 bp)
07:23:55.206 DEBUG GenomeLocParser - chrUn_gl000218 (161147 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000219 (179198 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000220 (161802 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000221 (155397 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000222 (186861 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000223 (180455 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000224 (179693 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000225 (211173 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000226 (15008 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000227 (128374 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000228 (129120 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000229 (19913 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000230 (43691 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000231 (27386 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000232 (40652 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000233 (45941 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000234 (40531 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000235 (34474 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000236 (41934 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000237 (45867 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000238 (39939 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000239 (33824 bp)
07:23:55.207 DEBUG GenomeLocParser - chrUn_gl000240 (41933 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000241 (42152 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000242 (43523 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000243 (43341 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000244 (39929 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000245 (36651 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000246 (38154 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000247 (36422 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000248 (39786 bp)
07:23:55.208 DEBUG GenomeLocParser - chrUn_gl000249 (38502 bp)
07:23:55.317 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-004.counts.hdf5 (1 / 56)
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
07:23:55.600 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-005.counts.hdf5 (2 / 56)
07:23:55.725 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-380.counts.hdf5 (3 / 56)
07:23:55.840 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-381.counts.hdf5 (4 / 56)
07:23:55.954 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-382.counts.hdf5 (5 / 56)
07:23:56.067 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-080.counts.hdf5 (6 / 56)
07:23:56.169 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-081.counts.hdf5 (7 / 56)
07:23:56.279 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-210.counts.hdf5 (8 / 56)
07:23:56.388 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170421.counts.hdf5 (9 / 56)
07:23:56.498 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170420.counts.hdf5 (10 / 56)
07:23:56.606 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200628.counts.hdf5 (11 / 56)
07:23:56.716 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210104.counts.hdf5 (12 / 56)
07:23:56.825 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210105.counts.hdf5 (13 / 56)
07:23:56.934 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-172.counts.hdf5 (14 / 56)
07:23:57.043 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-173.counts.hdf5 (15 / 56)
07:23:57.152 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-174.counts.hdf5 (16 / 56)
07:23:57.261 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-220.counts.hdf5 (17 / 56)
07:23:57.371 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-166.counts.hdf5 (18 / 56)
07:23:57.480 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-167.counts.hdf5 (19 / 56)
07:23:57.590 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-168.counts.hdf5 (20 / 56)
07:23:57.699 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-006.counts.hdf5 (21 / 56)
07:23:57.808 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-007.counts.hdf5 (22 / 56)
07:23:57.917 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-008.counts.hdf5 (23 / 56)
07:23:58.079 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-009.counts.hdf5 (24 / 56)
07:23:58.239 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-010.counts.hdf5 (25 / 56)
07:23:58.397 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-011.counts.hdf5 (26 / 56)
07:23:58.554 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-162.counts.hdf5 (27 / 56)
07:23:58.714 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-163.counts.hdf5 (28 / 56)
07:23:58.874 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-164.counts.hdf5 (29 / 56)
07:23:59.034 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-165.counts.hdf5 (30 / 56)
07:23:59.194 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210124.counts.hdf5 (31 / 56)
07:23:59.353 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210126.counts.hdf5 (32 / 56)
07:23:59.513 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200621.counts.hdf5 (33 / 56)
07:23:59.673 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210128.counts.hdf5 (34 / 56)
07:23:59.832 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210130.counts.hdf5 (35 / 56)
07:23:59.992 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210121.counts.hdf5 (36 / 56)
07:24:00.152 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210122.counts.hdf5 (37 / 56)
07:24:00.312 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210123.counts.hdf5 (38 / 56)
07:24:00.488 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200272.counts.hdf5 (39 / 56)
07:24:00.647 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200273.counts.hdf5 (40 / 56)
07:24:00.807 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200274.counts.hdf5 (41 / 56)
07:24:00.968 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-001.counts.hdf5 (42 / 56)
07:24:01.128 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-002.counts.hdf5 (43 / 56)
07:24:01.286 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-003.counts.hdf5 (44 / 56)
07:24:01.446 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210118.counts.hdf5 (45 / 56)
07:24:01.605 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210119.counts.hdf5 (46 / 56)
07:24:01.766 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210120.counts.hdf5 (47 / 56)
07:24:01.925 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210100.counts.hdf5 (48 / 56)
07:24:02.086 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210102.counts.hdf5 (49 / 56)
07:24:02.245 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200635.counts.hdf5 (50 / 56)
07:24:02.406 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200637.counts.hdf5 (51 / 56)
07:24:02.565 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200639.counts.hdf5 (52 / 56)
07:24:02.727 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200643.counts.hdf5 (53 / 56)
07:24:02.888 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-021A.counts.hdf5 (54 / 56)
07:24:03.049 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-022.counts.hdf5 (55 / 56)
07:24:03.209 INFO DetermineGermlineContigPloidy - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-023A.counts.hdf5 (56 / 56)
07:24:03.388 DEBUG ScriptExecutor - Executing:
07:24:03.388 DEBUG ScriptExecutor - python
07:24:03.388 DEBUG ScriptExecutor - /tmp/case_determine_ploidy_and_depth.8293602068552673491.py
07:24:03.388 DEBUG ScriptExecutor - --sample_coverage_metadata=/tmp/samples-by-coverage-per-contig8985829391102663312.tsv
07:24:03.388 DEBUG ScriptExecutor - --output_calls_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls
07:24:03.388 DEBUG ScriptExecutor - --mapping_error_rate=1.000000e-02
07:24:03.388 DEBUG ScriptExecutor - --psi_s_scale=1.000000e-04
07:24:03.388 DEBUG ScriptExecutor - --learning_rate=5.000000e-02
07:24:03.388 DEBUG ScriptExecutor - --adamax_beta1=9.000000e-01
07:24:03.388 DEBUG ScriptExecutor - --adamax_beta2=9.990000e-01
07:24:03.388 DEBUG ScriptExecutor - --log_emission_samples_per_round=2000
07:24:03.388 DEBUG ScriptExecutor - --log_emission_sampling_rounds=100
07:24:03.388 DEBUG ScriptExecutor - --log_emission_sampling_median_rel_error=5.000000e-04
07:24:03.389 DEBUG ScriptExecutor - --max_advi_iter_first_epoch=1000
07:24:03.389 DEBUG ScriptExecutor - --max_advi_iter_subsequent_epochs=1000
07:24:03.389 DEBUG ScriptExecutor - --min_training_epochs=20
07:24:03.389 DEBUG ScriptExecutor - --max_training_epochs=100
07:24:03.389 DEBUG ScriptExecutor - --initial_temperature=2.000000e+00
07:24:03.389 DEBUG ScriptExecutor - --num_thermal_advi_iters=5000
07:24:03.389 DEBUG ScriptExecutor - --convergence_snr_averaging_window=5000
07:24:03.389 DEBUG ScriptExecutor - --convergence_snr_trigger_threshold=1.000000e-01
07:24:03.389 DEBUG ScriptExecutor - --convergence_snr_countdown_window=10
07:24:03.389 DEBUG ScriptExecutor - --max_calling_iters=1
07:24:03.389 DEBUG ScriptExecutor - --caller_update_convergence_threshold=1.000000e-03
07:24:03.389 DEBUG ScriptExecutor - --caller_internal_admixing_rate=7.500000e-01
07:24:03.389 DEBUG ScriptExecutor - --caller_external_admixing_rate=7.500000e-01
07:24:03.389 DEBUG ScriptExecutor - --disable_caller=false
07:24:03.389 DEBUG ScriptExecutor - --disable_sampler=false
07:24:03.389 DEBUG ScriptExecutor - --disable_annealing=false
07:24:03.389 DEBUG ScriptExecutor - --input_model_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_ploidy_model/iGT359V1_ploidy_normal_cohort-model
15:24:17.044 INFO case_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
15:24:18.229 INFO gcnvkernel.structs.metadata - Generating intervals metadata...
15:24:18.654 INFO gcnvkernel.tasks.task_case_ploidy_determination - Instantiating the germline contig ploidy determination model...
15:24:20.767 INFO gcnvkernel.tasks.task_case_ploidy_determination - Instantiating the ploidy emission sampler...
15:24:20.767 INFO gcnvkernel.tasks.task_case_ploidy_determination - Instantiating the ploidy caller...
15:24:20.987 INFO gcnvkernel.models.fancy_model - Global model variables: {'mean_bias_j_lowerbound__', 'psi_j_log__'}
15:24:20.987 INFO gcnvkernel.models.fancy_model - Sample-specific model variables: {'psi_s_log__'}
15:24:20.987 INFO gcnvkernel.tasks.inference_task_base - Instantiating the convergence tracker...
15:24:20.987 INFO gcnvkernel.tasks.inference_task_base - Setting up DA-ADVI...
15:24:27.592 INFO gcnvkernel.tasks.task_case_ploidy_determination - Loading the model and updating the instantiated model and workspace...
15:24:27.593 INFO gcnvkernel.io.io_commons - Reading model parameter values for "mean_bias_j_lowerbound__"...
15:24:27.598 INFO gcnvkernel.io.io_commons - Reading model parameter values for "psi_j_log__"...
15:24:27.602 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:27.702 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -2223.723 +/- 92.065, SNR: 951.7, T: 1.99: 6%|6 | 64/1000 [00:00<00:01, 638.72it/s]
15:24:27.803 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -1718.483 +/- 211.759, SNR: 188.4, T: 1.97: 15%|#5 | 153/1000 [00:00<00:01, 783.01it/s]
15:24:27.904 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -1366.934 +/- 262.457, SNR: 83.8, T: 1.95: 24%|##4 | 242/1000 [00:00<00:00, 828.01it/s]
15:24:28.004 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -1142.256 +/- 279.949, SNR: 50.6, T: 1.93: 33%|###2 | 327/1000 [00:00<00:00, 835.22it/s]
15:24:28.108 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -985.715 +/- 283.944, SNR: 35.0, T: 1.92: 41%|####1 | 411/1000 [00:00<00:00, 826.72it/s]
15:24:28.214 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -869.646 +/- 282.699, SNR: 26.2, T: 1.90: 49%|####9 | 494/1000 [00:00<00:00, 811.15it/s]
15:24:28.323 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -779.963 +/- 279.106, SNR: 20.6, T: 1.88: 58%|#####7 | 576/1000 [00:00<00:00, 791.38it/s]
15:24:28.433 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -709.484 +/- 274.460, SNR: 16.8, T: 1.87: 66%|######5 | 656/1000 [00:00<00:00, 768.57it/s]
15:24:28.553 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -652.501 +/- 269.492, SNR: 14.1, T: 1.85: 73%|#######3 | 734/1000 [00:00<00:00, 729.52it/s]
15:24:28.677 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -606.689 +/- 264.621, SNR: 12.2, T: 1.84: 81%|######## | 808/1000 [00:01<00:00, 686.08it/s]
15:24:28.814 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -569.169 +/- 260.015, SNR: 10.7, T: 1.82: 88%|########7 | 878/1000 [00:01<00:00, 624.98it/s]
15:24:28.921 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -538.948 +/- 255.850, SNR: 9.6, T: 1.81: 94%|#########4| 942/1000 [00:01<00:00, 617.99it/s]
15:24:29.024 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 1) ELBO: -514.387 +/- 252.142, SNR: 8.7, T: 1.80: 100%|##########| 1000/1000 [00:01<00:00, 703.16it/s]
15:24:29.024 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 1): 0%| | 0/100 [00:00<?, ?it/s]
15:24:29.342 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 1) relative error: 1.0000 +/- 0.0000: 1%|1 | 1/100 [00:00<00:31, 3.15it/s]
15:24:29.658 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 1) relative error: 0.0004 +/- 0.0023: 1%|1 | 1/100 [00:00<01:02, 1.58it/s]
15:24:29.658 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 1): 0%| | 0/1 [00:00<?, ?it/s]
15:24:29.659 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 1) ploidy update size: 0.0770775: 100%|##########| 1/1 [00:00<00:00, 2317.30it/s]
15:24:29.659 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:29.760 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -494.069 +/- 247.613, SNR: 8.1, T: 1.79: 6%|6 | 60/1000 [00:00<00:01, 597.34it/s]
15:24:29.862 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -475.135 +/- 243.435, SNR: 7.5, T: 1.78: 12%|#2 | 120/1000 [00:00<00:01, 591.56it/s]
15:24:29.965 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -457.498 +/- 239.544, SNR: 7.0, T: 1.76: 18%|#8 | 180/1000 [00:00<00:01, 587.57it/s]
15:24:30.068 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -441.317 +/- 235.952, SNR: 6.5, T: 1.75: 24%|##3 | 239/1000 [00:00<00:01, 582.41it/s]
15:24:30.173 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -426.208 +/- 232.555, SNR: 6.1, T: 1.74: 30%|##9 | 298/1000 [00:00<00:01, 573.53it/s]
15:24:30.279 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -412.313 +/- 229.382, SNR: 5.8, T: 1.73: 36%|###5 | 356/1000 [00:00<00:01, 565.50it/s]
15:24:30.384 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -399.496 +/- 226.409, SNR: 5.4, T: 1.72: 41%|####1 | 413/1000 [00:00<00:01, 558.29it/s]
15:24:30.488 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -387.664 +/- 223.610, SNR: 5.1, T: 1.71: 47%|####6 | 469/1000 [00:00<00:00, 550.94it/s]
15:24:30.595 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -376.521 +/- 220.920, SNR: 4.9, T: 1.70: 52%|#####2 | 525/1000 [00:00<00:00, 542.68it/s]
15:24:30.701 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -366.195 +/- 218.377, SNR: 4.6, T: 1.68: 58%|#####8 | 580/1000 [00:01<00:00, 534.35it/s]
15:24:30.807 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -356.616 +/- 215.966, SNR: 4.4, T: 1.67: 63%|######3 | 634/1000 [00:01<00:00, 527.24it/s]
15:24:30.913 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -347.708 +/- 213.677, SNR: 4.2, T: 1.66: 69%|######8 | 687/1000 [00:01<00:00, 519.68it/s]
15:24:31.017 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -339.410 +/- 211.501, SNR: 4.0, T: 1.65: 74%|#######3 | 739/1000 [00:01<00:00, 512.96it/s]
15:24:31.123 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -331.518 +/- 209.391, SNR: 3.8, T: 1.64: 79%|#######9 | 791/1000 [00:01<00:00, 506.85it/s]
15:24:31.228 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -324.148 +/- 207.381, SNR: 3.7, T: 1.63: 84%|########4 | 842/1000 [00:01<00:00, 500.27it/s]
15:24:31.335 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -317.121 +/- 205.426, SNR: 3.5, T: 1.62: 89%|########9 | 893/1000 [00:01<00:00, 492.99it/s]
15:24:31.441 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -310.541 +/- 203.562, SNR: 3.4, T: 1.61: 94%|#########4| 943/1000 [00:01<00:00, 486.29it/s]
15:24:31.546 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -304.373 +/- 201.782, SNR: 3.3, T: 1.60: 99%|#########9| 992/1000 [00:01<00:00, 481.10it/s]
15:24:31.563 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 2) ELBO: -303.391 +/- 201.495, SNR: 3.2, T: 1.60: 100%|##########| 1000/1000 [00:01<00:00, 525.30it/s]
15:24:31.563 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 2): 0%| | 0/100 [00:00<?, ?it/s]
15:24:31.886 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 2) relative error: 0.0722 +/- 0.1559: 1%|1 | 1/100 [00:00<00:31, 3.10it/s]
15:24:32.203 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 2) relative error: 0.0006 +/- 0.0018: 2%|2 | 2/100 [00:00<00:31, 3.13it/s]
15:24:32.522 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 2) relative error: 0.0003 +/- 0.0011: 2%|2 | 2/100 [00:00<00:46, 2.09it/s]
15:24:32.523 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 2): 0%| | 0/1 [00:00<?, ?it/s]
15:24:32.523 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 2) ploidy update size: 0.0388346: 100%|##########| 1/1 [00:00<00:00, 2713.00it/s]
15:24:32.523 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:32.625 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -298.257 +/- 199.721, SNR: 3.1, T: 1.59: 5%|4 | 47/1000 [00:00<00:02, 464.01it/s]
15:24:32.728 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -293.318 +/- 197.995, SNR: 3.1, T: 1.58: 9%|9 | 94/1000 [00:00<00:01, 460.37it/s]
15:24:32.831 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -288.556 +/- 196.317, SNR: 3.0, T: 1.57: 14%|#4 | 141/1000 [00:00<00:01, 456.62it/s]
15:24:32.934 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -284.049 +/- 194.720, SNR: 2.9, T: 1.56: 19%|#8 | 187/1000 [00:00<00:01, 454.12it/s]
15:24:33.037 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -279.686 +/- 193.165, SNR: 2.8, T: 1.55: 23%|##3 | 233/1000 [00:00<00:01, 450.80it/s]
15:24:33.141 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -275.458 +/- 191.653, SNR: 2.7, T: 1.54: 28%|##7 | 279/1000 [00:00<00:01, 447.84it/s]
15:24:33.243 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -271.444 +/- 190.212, SNR: 2.7, T: 1.54: 32%|###2 | 324/1000 [00:00<00:01, 445.34it/s]
15:24:33.347 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -267.543 +/- 188.808, SNR: 2.6, T: 1.53: 37%|###6 | 369/1000 [00:00<00:01, 442.05it/s]
15:24:33.451 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -263.752 +/- 187.439, SNR: 2.5, T: 1.52: 41%|####1 | 414/1000 [00:00<00:01, 438.42it/s]
15:24:33.554 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -260.147 +/- 186.132, SNR: 2.5, T: 1.51: 46%|####5 | 458/1000 [00:01<00:01, 434.91it/s]
15:24:33.657 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -256.640 +/- 184.856, SNR: 2.4, T: 1.50: 50%|##### | 502/1000 [00:01<00:01, 432.44it/s]
15:24:33.763 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -253.225 +/- 183.609, SNR: 2.3, T: 1.49: 55%|#####4 | 546/1000 [00:01<00:01, 427.91it/s]
15:24:33.867 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -249.974 +/- 182.417, SNR: 2.3, T: 1.48: 59%|#####8 | 589/1000 [00:01<00:00, 423.64it/s]
15:24:33.971 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -246.807 +/- 181.251, SNR: 2.2, T: 1.47: 63%|######3 | 632/1000 [00:01<00:00, 420.53it/s]
15:24:34.075 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -243.719 +/- 180.109, SNR: 2.2, T: 1.47: 68%|######7 | 675/1000 [00:01<00:00, 417.48it/s]
15:24:34.178 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -240.778 +/- 179.017, SNR: 2.1, T: 1.46: 72%|#######1 | 717/1000 [00:01<00:00, 414.71it/s]
15:24:34.282 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -237.907 +/- 177.946, SNR: 2.1, T: 1.45: 76%|#######5 | 759/1000 [00:01<00:00, 411.82it/s]
15:24:34.387 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -235.107 +/- 176.895, SNR: 2.1, T: 1.44: 80%|######## | 801/1000 [00:01<00:00, 408.60it/s]
15:24:34.490 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -232.439 +/- 175.889, SNR: 2.0, T: 1.43: 84%|########4 | 842/1000 [00:01<00:00, 404.86it/s]
15:24:34.594 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -229.832 +/- 174.901, SNR: 2.0, T: 1.42: 88%|########8 | 883/1000 [00:02<00:00, 401.83it/s]
15:24:34.699 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -227.286 +/- 173.930, SNR: 1.9, T: 1.42: 92%|#########2| 924/1000 [00:02<00:00, 398.77it/s]
15:24:34.801 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -224.857 +/- 173.000, SNR: 1.9, T: 1.41: 96%|#########6| 964/1000 [00:02<00:00, 396.10it/s]
15:24:34.894 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 3) ELBO: -222.717 +/- 172.176, SNR: 1.9, T: 1.40: 100%|##########| 1000/1000 [00:02<00:00, 421.87it/s]
15:24:34.894 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 3): 0%| | 0/100 [00:00<?, ?it/s]
15:24:35.189 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 3) relative error: 0.1688 +/- 0.1845: 1%|1 | 1/100 [00:00<00:29, 3.40it/s]
15:24:35.481 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 3) relative error: 0.0007 +/- 0.0013: 2%|2 | 2/100 [00:00<00:28, 3.41it/s]
15:24:35.776 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 3) relative error: 0.0004 +/- 0.0008: 2%|2 | 2/100 [00:00<00:43, 2.27it/s]
15:24:35.776 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 3): 0%| | 0/1 [00:00<?, ?it/s]
15:24:35.777 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 3) ploidy update size: 0.0217134: 100%|##########| 1/1 [00:00<00:00, 3460.65it/s]
15:24:35.777 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:35.878 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -220.587 +/- 171.269, SNR: 1.8, T: 1.39: 4%|3 | 39/1000 [00:00<00:02, 387.22it/s]
15:24:35.978 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -218.506 +/- 170.376, SNR: 1.8, T: 1.38: 8%|7 | 78/1000 [00:00<00:02, 388.27it/s]
15:24:36.079 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -216.468 +/- 169.499, SNR: 1.8, T: 1.38: 12%|#1 | 117/1000 [00:00<00:02, 387.30it/s]
15:24:36.181 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -214.472 +/- 168.635, SNR: 1.7, T: 1.37: 16%|#5 | 156/1000 [00:00<00:02, 386.00it/s]
15:24:36.283 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -212.514 +/- 167.786, SNR: 1.7, T: 1.36: 20%|#9 | 195/1000 [00:00<00:02, 384.01it/s]
15:24:36.386 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -210.592 +/- 166.950, SNR: 1.7, T: 1.35: 23%|##3 | 234/1000 [00:00<00:02, 382.13it/s]
15:24:36.490 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -208.705 +/- 166.129, SNR: 1.7, T: 1.35: 27%|##7 | 273/1000 [00:00<00:01, 379.75it/s]
15:24:36.593 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -206.897 +/- 165.341, SNR: 1.6, T: 1.34: 31%|###1 | 311/1000 [00:00<00:01, 376.18it/s]
15:24:36.697 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -205.121 +/- 164.566, SNR: 1.6, T: 1.33: 35%|###4 | 349/1000 [00:00<00:01, 372.94it/s]
15:24:36.802 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -203.375 +/- 163.803, SNR: 1.6, T: 1.32: 39%|###8 | 387/1000 [00:01<00:01, 369.88it/s]
15:24:36.904 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -201.702 +/- 163.072, SNR: 1.6, T: 1.32: 42%|####2 | 424/1000 [00:01<00:01, 367.23it/s]
15:24:37.008 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -200.056 +/- 162.351, SNR: 1.5, T: 1.31: 46%|####6 | 461/1000 [00:01<00:01, 364.42it/s]
15:24:37.112 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -198.437 +/- 161.641, SNR: 1.5, T: 1.30: 50%|####9 | 498/1000 [00:01<00:01, 361.44it/s]
15:24:37.216 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -196.843 +/- 160.941, SNR: 1.5, T: 1.29: 54%|#####3 | 535/1000 [00:01<00:01, 359.25it/s]
15:24:37.320 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -195.316 +/- 160.269, SNR: 1.5, T: 1.29: 57%|#####7 | 571/1000 [00:01<00:01, 355.79it/s]
15:24:37.424 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -193.813 +/- 159.607, SNR: 1.5, T: 1.28: 61%|###### | 607/1000 [00:01<00:01, 352.87it/s]
15:24:37.528 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -192.332 +/- 158.953, SNR: 1.4, T: 1.27: 64%|######4 | 643/1000 [00:01<00:01, 350.55it/s]
15:24:37.634 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -190.874 +/- 158.309, SNR: 1.4, T: 1.26: 68%|######7 | 679/1000 [00:01<00:00, 347.89it/s]
15:24:37.737 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -189.478 +/- 157.690, SNR: 1.4, T: 1.26: 71%|#######1 | 714/1000 [00:01<00:00, 345.18it/s]
15:24:37.840 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -188.102 +/- 157.080, SNR: 1.4, T: 1.25: 75%|#######4 | 749/1000 [00:02<00:00, 343.28it/s]
15:24:37.944 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -186.746 +/- 156.477, SNR: 1.4, T: 1.24: 78%|#######8 | 784/1000 [00:02<00:00, 341.58it/s]
15:24:38.048 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -185.409 +/- 155.881, SNR: 1.3, T: 1.24: 82%|########1 | 819/1000 [00:02<00:00, 339.37it/s]
15:24:38.150 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -184.130 +/- 155.309, SNR: 1.3, T: 1.23: 85%|########5 | 853/1000 [00:02<00:00, 337.66it/s]
15:24:38.253 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -182.868 +/- 154.745, SNR: 1.3, T: 1.22: 89%|########8 | 887/1000 [00:02<00:00, 335.52it/s]
15:24:38.356 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -181.624 +/- 154.186, SNR: 1.3, T: 1.22: 92%|#########2| 921/1000 [00:02<00:00, 334.29it/s]
15:24:38.459 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -180.397 +/- 153.635, SNR: 1.3, T: 1.21: 96%|#########5| 955/1000 [00:02<00:00, 332.47it/s]
15:24:38.563 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -179.187 +/- 153.089, SNR: 1.3, T: 1.20: 99%|#########8| 989/1000 [00:02<00:00, 331.51it/s]
15:24:38.596 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 4) ELBO: -178.799 +/- 152.914, SNR: 1.3, T: 1.20: 100%|##########| 1000/1000 [00:02<00:00, 354.73it/s]
15:24:38.596 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 4): 0%| | 0/100 [00:00<?, ?it/s]
15:24:38.893 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 4) relative error: 0.2732 +/- 0.1886: 1%|1 | 1/100 [00:00<00:29, 3.37it/s]
15:24:39.191 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 4) relative error: 0.0006 +/- 0.0011: 2%|2 | 2/100 [00:00<00:29, 3.36it/s]
15:24:39.489 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 4) relative error: 0.0004 +/- 0.0008: 2%|2 | 2/100 [00:00<00:43, 2.24it/s]
15:24:39.489 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 4): 0%| | 0/1 [00:00<?, ?it/s]
15:24:39.490 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 4) ploidy update size: 0.0115504: 100%|##########| 1/1 [00:00<00:00, 3189.58it/s]
15:24:39.490 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:39.591 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -177.691 +/- 152.384, SNR: 1.3, T: 1.19: 3%|3 | 33/1000 [00:00<00:02, 328.88it/s]
15:24:39.691 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -176.599 +/- 151.860, SNR: 1.2, T: 1.19: 7%|6 | 66/1000 [00:00<00:02, 327.95it/s]
15:24:39.793 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -175.522 +/- 151.341, SNR: 1.2, T: 1.18: 10%|9 | 99/1000 [00:00<00:02, 325.81it/s]
15:24:39.896 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -174.460 +/- 150.828, SNR: 1.2, T: 1.17: 13%|#3 | 132/1000 [00:00<00:02, 324.42it/s]
15:24:39.999 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -173.411 +/- 150.320, SNR: 1.2, T: 1.17: 16%|#6 | 165/1000 [00:00<00:02, 323.33it/s]
15:24:40.102 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -172.375 +/- 149.818, SNR: 1.2, T: 1.16: 20%|#9 | 198/1000 [00:00<00:02, 322.03it/s]
15:24:40.206 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -171.352 +/- 149.321, SNR: 1.2, T: 1.15: 23%|##3 | 231/1000 [00:00<00:02, 320.66it/s]
15:24:40.311 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -170.342 +/- 148.830, SNR: 1.2, T: 1.15: 26%|##6 | 264/1000 [00:00<00:02, 318.50it/s]
15:24:40.415 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -169.373 +/- 148.358, SNR: 1.2, T: 1.14: 30%|##9 | 296/1000 [00:00<00:02, 314.97it/s]
15:24:40.519 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -168.415 +/- 147.891, SNR: 1.1, T: 1.13: 33%|###2 | 328/1000 [00:01<00:02, 312.42it/s]
15:24:40.622 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -167.468 +/- 147.430, SNR: 1.1, T: 1.13: 36%|###6 | 360/1000 [00:01<00:02, 311.73it/s]
15:24:40.726 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -166.531 +/- 146.972, SNR: 1.1, T: 1.12: 39%|###9 | 392/1000 [00:01<00:01, 310.49it/s]
15:24:40.831 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -165.605 +/- 146.520, SNR: 1.1, T: 1.12: 42%|####2 | 424/1000 [00:01<00:01, 309.26it/s]
15:24:40.932 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -164.718 +/- 146.086, SNR: 1.1, T: 1.11: 46%|####5 | 455/1000 [00:01<00:01, 308.23it/s]
15:24:41.034 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -163.839 +/- 145.656, SNR: 1.1, T: 1.10: 49%|####8 | 486/1000 [00:01<00:01, 306.75it/s]
15:24:41.137 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -162.971 +/- 145.230, SNR: 1.1, T: 1.10: 52%|#####1 | 517/1000 [00:01<00:01, 305.17it/s]
15:24:41.240 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -162.111 +/- 144.808, SNR: 1.1, T: 1.09: 55%|#####4 | 548/1000 [00:01<00:01, 303.76it/s]
15:24:41.344 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -161.260 +/- 144.390, SNR: 1.1, T: 1.08: 58%|#####7 | 579/1000 [00:01<00:01, 302.71it/s]
15:24:41.448 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -160.419 +/- 143.976, SNR: 1.0, T: 1.08: 61%|######1 | 610/1000 [00:01<00:01, 300.92it/s]
15:24:41.553 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -159.586 +/- 143.566, SNR: 1.0, T: 1.07: 64%|######4 | 641/1000 [00:02<00:01, 299.27it/s]
15:24:41.655 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -158.788 +/- 143.173, SNR: 1.0, T: 1.07: 67%|######7 | 671/1000 [00:02<00:01, 297.94it/s]
15:24:41.757 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -157.999 +/- 142.783, SNR: 1.0, T: 1.06: 70%|####### | 701/1000 [00:02<00:01, 296.22it/s]
15:24:41.861 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -157.217 +/- 142.397, SNR: 1.0, T: 1.05: 73%|#######3 | 731/1000 [00:02<00:00, 294.61it/s]
15:24:41.964 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -156.443 +/- 142.013, SNR: 1.0, T: 1.05: 76%|#######6 | 761/1000 [00:02<00:00, 293.50it/s]
15:24:42.067 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -155.677 +/- 141.634, SNR: 1.0, T: 1.04: 79%|#######9 | 791/1000 [00:02<00:00, 292.68it/s]
15:24:42.171 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -154.919 +/- 141.257, SNR: 1.0, T: 1.04: 82%|########2 | 821/1000 [00:02<00:00, 291.66it/s]
15:24:42.275 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -154.168 +/- 140.884, SNR: 1.0, T: 1.03: 85%|########5 | 851/1000 [00:02<00:00, 290.10it/s]
15:24:42.380 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -153.424 +/- 140.513, SNR: 1.0, T: 1.02: 88%|########8 | 881/1000 [00:02<00:00, 289.07it/s]
15:24:42.481 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -152.712 +/- 140.158, SNR: 1.0, T: 1.02: 91%|#########1| 910/1000 [00:02<00:00, 288.36it/s]
15:24:42.583 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -152.007 +/- 139.806, SNR: 1.0, T: 1.01: 94%|#########3| 939/1000 [00:03<00:00, 287.48it/s]
15:24:42.685 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -151.309 +/- 139.457, SNR: 0.9, T: 1.01: 97%|#########6| 968/1000 [00:03<00:00, 286.55it/s]
15:24:42.787 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -150.618 +/- 139.111, SNR: 0.9, T: 1.00: 100%|#########9| 997/1000 [00:03<00:00, 285.70it/s]
15:24:42.798 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 5) ELBO: -150.546 +/- 139.075, SNR: 0.9, T: 1.00: 100%|##########| 1000/1000 [00:03<00:00, 302.34it/s]
15:24:42.798 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 5): 0%| | 0/100 [00:00<?, ?it/s]
15:24:43.114 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 5) relative error: 0.2793 +/- 0.1978: 1%|1 | 1/100 [00:00<00:31, 3.17it/s]
15:24:43.426 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 5) relative error: 0.0006 +/- 0.0012: 2%|2 | 2/100 [00:00<00:30, 3.19it/s]
15:24:43.737 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 5) relative error: 0.0003 +/- 0.0007: 2%|2 | 2/100 [00:00<00:45, 2.13it/s]
15:24:43.737 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 5): 0%| | 0/1 [00:00<?, ?it/s]
15:24:43.737 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 5) ploidy update size: 0.00608144: 100%|##########| 1/1 [00:00<00:00, 2038.05it/s]
15:24:43.738 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:43.839 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -88.801 +/- 44.099, SNR: 1.6, T: 1.00: 7%|7 | 71/1000 [00:00<00:01, 706.29it/s]
15:24:43.940 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -69.275 +/- 22.345, SNR: 2.2, T: 1.00: 14%|#4 | 143/1000 [00:00<00:01, 709.06it/s]
15:24:44.040 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -59.865 +/- 14.499, SNR: 2.8, T: 1.00: 21%|##1 | 214/1000 [00:00<00:01, 709.46it/s]
15:24:44.141 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -54.005 +/- 10.747, SNR: 3.3, T: 1.00: 29%|##8 | 286/1000 [00:00<00:01, 710.26it/s]
15:24:44.242 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -49.844 +/- 8.569, SNR: 3.7, T: 1.00: 36%|###5 | 358/1000 [00:00<00:00, 710.27it/s]
15:24:44.344 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -46.780 +/- 7.365, SNR: 3.9, T: 1.00: 43%|####3 | 430/1000 [00:00<00:00, 709.33it/s]
15:24:44.445 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -44.286 +/- 6.571, SNR: 4.0, T: 1.00: 50%|##### | 502/1000 [00:00<00:00, 709.80it/s]
15:24:44.547 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -42.161 +/- 5.997, SNR: 4.1, T: 1.00: 57%|#####7 | 574/1000 [00:00<00:00, 709.96it/s]
15:24:44.647 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -40.304 +/- 5.553, SNR: 4.1, T: 1.00: 64%|######4 | 645/1000 [00:00<00:00, 709.93it/s]
15:24:44.748 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -38.546 +/- 5.128, SNR: 4.2, T: 1.00: 72%|#######1 | 717/1000 [00:01<00:00, 710.24it/s]
15:24:44.850 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -36.868 +/- 4.694, SNR: 4.2, T: 1.00: 79%|#######8 | 789/1000 [00:01<00:00, 710.15it/s]
15:24:44.951 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -35.218 +/- 4.193, SNR: 4.4, T: 1.00: 86%|########6 | 861/1000 [00:01<00:00, 709.77it/s]
15:24:45.052 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -33.583 +/- 3.578, SNR: 4.8, T: 1.00: 93%|#########3| 933/1000 [00:01<00:00, 710.26it/s]
15:24:45.147 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 6) ELBO: -32.060 +/- 2.813, SNR: 5.6, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 709.83it/s]
15:24:45.147 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 6): 0%| | 0/100 [00:00<?, ?it/s]
15:24:45.460 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 6) relative error: 0.2199 +/- 0.2068: 1%|1 | 1/100 [00:00<00:30, 3.20it/s]
15:24:45.772 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 6) relative error: 0.0007 +/- 0.0015: 2%|2 | 2/100 [00:00<00:30, 3.20it/s]
15:24:46.084 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 6) relative error: 0.0005 +/- 0.0008: 3%|3 | 3/100 [00:00<00:30, 3.20it/s]
15:24:46.396 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 6) relative error: 0.0002 +/- 0.0006: 3%|3 | 3/100 [00:01<00:40, 2.40it/s]
15:24:46.396 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 6): 0%| | 0/1 [00:00<?, ?it/s]
15:24:46.397 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 6) ploidy update size: 0.00328327: 100%|##########| 1/1 [00:00<00:00, 2777.68it/s]
15:24:46.397 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:46.497 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -31.357 +/- 2.795, SNR: 5.4, T: 1.00: 7%|7 | 71/1000 [00:00<00:01, 708.93it/s]
15:24:46.598 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -30.672 +/- 2.779, SNR: 5.3, T: 1.00: 14%|#4 | 143/1000 [00:00<00:01, 712.96it/s]
15:24:46.699 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -30.001 +/- 2.763, SNR: 5.1, T: 1.00: 22%|##1 | 215/1000 [00:00<00:01, 713.70it/s]
15:24:46.799 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -29.337 +/- 2.743, SNR: 5.0, T: 1.00: 29%|##8 | 287/1000 [00:00<00:00, 715.29it/s]
15:24:46.900 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -28.674 +/- 2.717, SNR: 4.8, T: 1.00: 36%|###5 | 359/1000 [00:00<00:00, 714.71it/s]
15:24:47.001 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -27.999 +/- 2.679, SNR: 4.7, T: 1.00: 43%|####3 | 431/1000 [00:00<00:00, 715.04it/s]
15:24:47.101 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -27.316 +/- 2.628, SNR: 4.6, T: 1.00: 50%|##### | 503/1000 [00:00<00:00, 716.35it/s]
15:24:47.201 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -26.620 +/- 2.558, SNR: 4.5, T: 1.00: 57%|#####7 | 575/1000 [00:00<00:00, 716.32it/s]
15:24:47.302 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -25.912 +/- 2.467, SNR: 4.4, T: 1.00: 65%|######4 | 647/1000 [00:00<00:00, 715.09it/s]
15:24:47.404 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -25.191 +/- 2.350, SNR: 4.4, T: 1.00: 72%|#######1 | 719/1000 [00:01<00:00, 711.88it/s]
15:24:47.512 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -24.456 +/- 2.198, SNR: 4.4, T: 1.00: 79%|#######9 | 791/1000 [00:01<00:00, 698.87it/s]
15:24:47.612 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -23.718 +/- 2.004, SNR: 4.5, T: 1.00: 86%|########6 | 862/1000 [00:01<00:00, 701.49it/s]
15:24:47.713 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -22.965 +/- 1.746, SNR: 4.8, T: 1.00: 93%|#########3| 933/1000 [00:01<00:00, 702.23it/s]
15:24:47.807 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 7) ELBO: -22.242 +/- 1.410, SNR: 5.5, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 709.40it/s]
15:24:47.807 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 7): 0%| | 0/100 [00:00<?, ?it/s]
15:24:48.127 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 7) relative error: 0.1158 +/- 0.2062: 1%|1 | 1/100 [00:00<00:31, 3.13it/s]
15:24:48.439 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 7) relative error: 0.0009 +/- 0.0020: 2%|2 | 2/100 [00:00<00:30, 3.17it/s]
15:24:48.757 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 7) relative error: 0.0004 +/- 0.0011: 2%|2 | 2/100 [00:00<00:46, 2.11it/s]
15:24:48.757 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 7): 0%| | 0/1 [00:00<?, ?it/s]
15:24:48.758 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 7) ploidy update size: 0.00179471: 100%|##########| 1/1 [00:00<00:00, 2169.84it/s]
15:24:48.758 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:48.859 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -21.864 +/- 1.387, SNR: 5.3, T: 1.00: 7%|7 | 71/1000 [00:00<00:01, 701.41it/s]
15:24:48.960 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -21.517 +/- 1.374, SNR: 5.2, T: 1.00: 14%|#4 | 142/1000 [00:00<00:01, 702.61it/s]
15:24:49.061 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -21.186 +/- 1.364, SNR: 5.0, T: 1.00: 21%|##1 | 213/1000 [00:00<00:01, 703.26it/s]
15:24:49.162 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -20.864 +/- 1.354, SNR: 4.9, T: 1.00: 28%|##8 | 284/1000 [00:00<00:01, 702.33it/s]
15:24:49.263 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -20.542 +/- 1.341, SNR: 4.8, T: 1.00: 36%|###5 | 355/1000 [00:00<00:00, 702.57it/s]
15:24:49.365 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -20.218 +/- 1.324, SNR: 4.6, T: 1.00: 43%|####2 | 426/1000 [00:00<00:00, 702.27it/s]
15:24:49.466 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -19.890 +/- 1.300, SNR: 4.5, T: 1.00: 50%|####9 | 497/1000 [00:00<00:00, 702.81it/s]
15:24:49.566 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -19.556 +/- 1.268, SNR: 4.4, T: 1.00: 57%|#####6 | 568/1000 [00:00<00:00, 704.36it/s]
15:24:49.667 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -19.216 +/- 1.225, SNR: 4.3, T: 1.00: 64%|######3 | 639/1000 [00:00<00:00, 704.24it/s]
15:24:49.767 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -18.868 +/- 1.170, SNR: 4.3, T: 1.00: 71%|#######1 | 710/1000 [00:01<00:00, 704.44it/s]
15:24:49.868 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -18.513 +/- 1.098, SNR: 4.3, T: 1.00: 78%|#######8 | 781/1000 [00:01<00:00, 704.62it/s]
15:24:49.969 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -18.151 +/- 1.005, SNR: 4.4, T: 1.00: 85%|########5 | 852/1000 [00:01<00:00, 705.49it/s]
15:24:50.069 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -17.782 +/- 0.882, SNR: 4.6, T: 1.00: 92%|#########2| 923/1000 [00:01<00:00, 705.97it/s]
15:24:50.169 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -17.406 +/- 0.712, SNR: 5.2, T: 1.00: 99%|#########9| 994/1000 [00:01<00:00, 706.37it/s]
15:24:50.178 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 8) ELBO: -17.374 +/- 0.694, SNR: 5.3, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 704.18it/s]
15:24:50.178 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 8): 0%| | 0/100 [00:00<?, ?it/s]
15:24:50.497 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 8) relative error: 0.0462 +/- 0.1772: 1%|1 | 1/100 [00:00<00:31, 3.14it/s]
15:24:50.861 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 8) relative error: 0.0007 +/- 0.0024: 2%|2 | 2/100 [00:00<00:33, 2.90it/s]
15:24:51.170 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 8) relative error: 0.0004 +/- 0.0013: 2%|2 | 2/100 [00:00<00:48, 2.02it/s]
15:24:51.170 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 8): 0%| | 0/1 [00:00<?, ?it/s]
15:24:51.170 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 8) ploidy update size: 0.00101089: 100%|##########| 1/1 [00:00<00:00, 2152.03it/s]
15:24:51.171 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:51.272 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -17.186 +/- 0.684, SNR: 5.2, T: 1.00: 7%|7 | 73/1000 [00:00<00:01, 723.21it/s]
15:24:51.372 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -17.015 +/- 0.678, SNR: 5.0, T: 1.00: 15%|#4 | 146/1000 [00:00<00:01, 726.75it/s]
15:24:51.472 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -16.850 +/- 0.675, SNR: 4.9, T: 1.00: 22%|##2 | 220/1000 [00:00<00:01, 732.40it/s]
15:24:51.573 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -16.687 +/- 0.671, SNR: 4.7, T: 1.00: 29%|##9 | 294/1000 [00:00<00:00, 731.93it/s]
15:24:51.678 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -16.524 +/- 0.665, SNR: 4.6, T: 1.00: 37%|###6 | 368/1000 [00:00<00:00, 722.86it/s]
15:24:51.781 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -16.361 +/- 0.655, SNR: 4.4, T: 1.00: 44%|####4 | 441/1000 [00:00<00:00, 717.75it/s]
15:24:51.883 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -16.198 +/- 0.643, SNR: 4.3, T: 1.00: 51%|#####1 | 513/1000 [00:00<00:00, 714.29it/s]
15:24:51.983 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -16.031 +/- 0.625, SNR: 4.2, T: 1.00: 58%|#####8 | 585/1000 [00:00<00:00, 715.09it/s]
15:24:52.084 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -15.861 +/- 0.602, SNR: 4.1, T: 1.00: 66%|######5 | 657/1000 [00:00<00:00, 713.95it/s]
15:24:52.188 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -15.687 +/- 0.572, SNR: 4.1, T: 1.00: 73%|#######2 | 729/1000 [00:01<00:00, 707.49it/s]
15:24:52.290 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -15.512 +/- 0.534, SNR: 4.1, T: 1.00: 80%|######## | 800/1000 [00:01<00:00, 704.61it/s]
15:24:52.392 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -15.333 +/- 0.483, SNR: 4.2, T: 1.00: 87%|########7 | 871/1000 [00:01<00:00, 701.48it/s]
15:24:52.496 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -15.151 +/- 0.416, SNR: 4.5, T: 1.00: 94%|#########4| 942/1000 [00:01<00:00, 695.56it/s]
15:24:52.580 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 9) ELBO: -15.000 +/- 0.341, SNR: 5.1, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 709.60it/s]
15:24:52.580 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 9): 0%| | 0/100 [00:00<?, ?it/s]
15:24:52.901 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 9) relative error: 0.0138 +/- 0.1037: 1%|1 | 1/100 [00:00<00:31, 3.12it/s]
15:24:53.223 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 9) relative error: 0.0010 +/- 0.0026: 2%|2 | 2/100 [00:00<00:31, 3.11it/s]
15:24:53.548 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 9) relative error: 0.0005 +/- 0.0011: 2%|2 | 2/100 [00:00<00:47, 2.07it/s]
15:24:53.548 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 9): 0%| | 0/1 [00:00<?, ?it/s]
15:24:53.549 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 9) ploidy update size: 0.000576967: 0%| | 0/1 [00:00<?, ?it/s]
15:24:53.549 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:24:53.649 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.912 +/- 0.337, SNR: 4.9, T: 1.00: 7%|7 | 70/1000 [00:00<00:01, 698.59it/s]
15:24:53.750 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.832 +/- 0.335, SNR: 4.8, T: 1.00: 14%|#4 | 141/1000 [00:00<00:01, 703.25it/s]
15:24:53.850 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.757 +/- 0.333, SNR: 4.6, T: 1.00: 21%|##1 | 212/1000 [00:00<00:01, 704.87it/s]
15:24:53.952 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.682 +/- 0.332, SNR: 4.5, T: 1.00: 28%|##8 | 283/1000 [00:00<00:01, 702.95it/s]
15:24:54.052 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.607 +/- 0.329, SNR: 4.3, T: 1.00: 35%|###5 | 354/1000 [00:00<00:00, 704.79it/s]
15:24:54.153 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.528 +/- 0.325, SNR: 4.2, T: 1.00: 43%|####2 | 427/1000 [00:00<00:00, 710.94it/s]
15:24:54.254 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.449 +/- 0.319, SNR: 4.0, T: 1.00: 50%|##### | 500/1000 [00:00<00:00, 716.01it/s]
15:24:54.355 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.367 +/- 0.310, SNR: 3.9, T: 1.00: 57%|#####7 | 573/1000 [00:00<00:00, 717.75it/s]
15:24:54.455 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.285 +/- 0.299, SNR: 3.8, T: 1.00: 64%|######4 | 645/1000 [00:00<00:00, 718.24it/s]
15:24:54.558 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.201 +/- 0.284, SNR: 3.8, T: 1.00: 72%|#######1 | 717/1000 [00:01<00:00, 712.89it/s]
15:24:54.658 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.115 +/- 0.265, SNR: 3.8, T: 1.00: 79%|#######9 | 790/1000 [00:01<00:00, 716.06it/s]
15:24:54.760 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -14.027 +/- 0.240, SNR: 3.8, T: 1.00: 86%|########6 | 863/1000 [00:01<00:00, 717.98it/s]
15:24:54.861 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -13.937 +/- 0.206, SNR: 4.1, T: 1.00: 94%|#########3| 936/1000 [00:01<00:00, 719.16it/s]
15:24:54.949 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 10) ELBO: -13.857 +/- 0.166, SNR: 4.6, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 714.40it/s]
15:24:54.949 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 10): 0%| | 0/100 [00:00<?, ?it/s]
15:24:55.267 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 10) relative error: 0.0038 +/- 0.0422: 1%|1 | 1/100 [00:00<00:31, 3.15it/s]
15:24:55.584 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 10) relative error: 0.0006 +/- 0.0029: 2%|2 | 2/100 [00:00<00:31, 3.15it/s]
15:24:55.905 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 10) relative error: 0.0006 +/- 0.0013: 3%|3 | 3/100 [00:00<00:30, 3.14it/s]
15:24:56.227 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 10) relative error: 0.0004 +/- 0.0012: 3%|3 | 3/100 [00:01<00:41, 2.35it/s]
15:24:56.227 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 10): 0%| | 0/1 [00:00<?, ?it/s]
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15:24:56.329 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.817 +/- 0.164, SNR: 4.5, T: 1.00: 7%|6 | 69/1000 [00:00<00:01, 685.15it/s]
15:24:56.430 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.780 +/- 0.163, SNR: 4.3, T: 1.00: 14%|#4 | 140/1000 [00:00<00:01, 696.66it/s]
15:24:56.531 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.745 +/- 0.162, SNR: 4.2, T: 1.00: 21%|##1 | 211/1000 [00:00<00:01, 700.03it/s]
15:24:56.632 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.711 +/- 0.161, SNR: 4.0, T: 1.00: 28%|##8 | 282/1000 [00:00<00:01, 700.73it/s]
15:24:56.733 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.675 +/- 0.160, SNR: 3.9, T: 1.00: 35%|###5 | 354/1000 [00:00<00:00, 704.21it/s]
15:24:56.834 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.640 +/- 0.157, SNR: 3.7, T: 1.00: 42%|####2 | 425/1000 [00:00<00:00, 704.25it/s]
15:24:56.937 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.604 +/- 0.154, SNR: 3.6, T: 1.00: 50%|####9 | 496/1000 [00:00<00:00, 700.47it/s]
15:24:57.038 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.567 +/- 0.150, SNR: 3.5, T: 1.00: 57%|#####6 | 568/1000 [00:00<00:00, 704.26it/s]
15:24:57.139 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.529 +/- 0.144, SNR: 3.4, T: 1.00: 64%|######4 | 640/1000 [00:00<00:00, 706.92it/s]
15:24:57.240 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.489 +/- 0.137, SNR: 3.3, T: 1.00: 71%|#######1 | 713/1000 [00:01<00:00, 711.72it/s]
15:24:57.340 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.450 +/- 0.127, SNR: 3.3, T: 1.00: 78%|#######8 | 785/1000 [00:01<00:00, 712.39it/s]
15:24:57.441 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.409 +/- 0.115, SNR: 3.3, T: 1.00: 86%|########5 | 858/1000 [00:01<00:00, 715.91it/s]
15:24:57.543 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.367 +/- 0.098, SNR: 3.5, T: 1.00: 93%|#########3| 931/1000 [00:01<00:00, 717.59it/s]
15:24:57.642 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 11) ELBO: -13.327 +/- 0.077, SNR: 4.0, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 707.60it/s]
15:24:57.642 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 11): 0%| | 0/100 [00:00<?, ?it/s]
15:24:57.967 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 11) relative error: 0.0023 +/- 0.0194: 1%|1 | 1/100 [00:00<00:32, 3.08it/s]
15:24:58.284 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 11) relative error: 0.0008 +/- 0.0024: 2%|2 | 2/100 [00:00<00:31, 3.12it/s]
15:24:58.600 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 11) relative error: 0.0005 +/- 0.0014: 2%|2 | 2/100 [00:00<00:46, 2.09it/s]
15:24:58.600 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 11): 0%| | 0/1 [00:00<?, ?it/s]
15:24:58.601 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 11) ploidy update size: 0.000268689: 0%| | 0/1 [00:00<?, ?it/s]
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15:24:58.702 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.309 +/- 0.075, SNR: 3.9, T: 1.00: 7%|7 | 73/1000 [00:00<00:01, 727.19it/s]
15:24:58.802 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.292 +/- 0.075, SNR: 3.7, T: 1.00: 15%|#4 | 147/1000 [00:00<00:01, 730.92it/s]
15:24:58.903 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.276 +/- 0.074, SNR: 3.6, T: 1.00: 22%|##2 | 221/1000 [00:00<00:01, 731.74it/s]
15:24:59.009 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.261 +/- 0.073, SNR: 3.4, T: 1.00: 30%|##9 | 295/1000 [00:00<00:00, 720.51it/s]
15:24:59.110 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.245 +/- 0.072, SNR: 3.3, T: 1.00: 37%|###6 | 368/1000 [00:00<00:00, 721.24it/s]
15:24:59.210 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.229 +/- 0.070, SNR: 3.2, T: 1.00: 44%|####4 | 442/1000 [00:00<00:00, 725.47it/s]
15:24:59.312 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.213 +/- 0.068, SNR: 3.1, T: 1.00: 52%|#####1 | 516/1000 [00:00<00:00, 727.13it/s]
15:24:59.413 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.196 +/- 0.066, SNR: 2.9, T: 1.00: 59%|#####8 | 590/1000 [00:00<00:00, 728.83it/s]
15:24:59.514 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.179 +/- 0.063, SNR: 2.9, T: 1.00: 66%|######6 | 664/1000 [00:00<00:00, 730.50it/s]
15:24:59.614 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.162 +/- 0.059, SNR: 2.8, T: 1.00: 74%|#######3 | 738/1000 [00:01<00:00, 731.77it/s]
15:24:59.715 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.145 +/- 0.053, SNR: 2.8, T: 1.00: 81%|########1 | 812/1000 [00:01<00:00, 733.00it/s]
15:24:59.815 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.127 +/- 0.047, SNR: 2.8, T: 1.00: 89%|########8 | 886/1000 [00:01<00:00, 734.29it/s]
15:24:59.916 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.109 +/- 0.038, SNR: 3.0, T: 1.00: 96%|#########6| 960/1000 [00:01<00:00, 735.32it/s]
15:24:59.972 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 12) ELBO: -13.099 +/- 0.031, SNR: 3.4, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 729.55it/s]
15:24:59.972 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 12): 0%| | 0/100 [00:00<?, ?it/s]
15:25:00.290 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 12) relative error: 0.0023 +/- 0.0191: 1%|1 | 1/100 [00:00<00:31, 3.15it/s]
15:25:00.611 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 12) relative error: 0.0009 +/- 0.0023: 2%|2 | 2/100 [00:00<00:31, 3.13it/s]
15:25:00.928 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 12) relative error: 0.0004 +/- 0.0016: 2%|2 | 2/100 [00:00<00:46, 2.09it/s]
15:25:00.928 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 12): 0%| | 0/1 [00:00<?, ?it/s]
15:25:00.929 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 12) ploidy update size: 0.000205034: 0%| | 0/1 [00:00<?, ?it/s]
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15:25:01.030 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.093 +/- 0.030, SNR: 3.3, T: 1.00: 7%|7 | 74/1000 [00:00<00:01, 733.11it/s]
15:25:01.131 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.087 +/- 0.030, SNR: 3.1, T: 1.00: 15%|#4 | 148/1000 [00:00<00:01, 736.45it/s]
15:25:01.231 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.081 +/- 0.030, SNR: 3.0, T: 1.00: 22%|##2 | 222/1000 [00:00<00:01, 737.22it/s]
15:25:01.331 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.075 +/- 0.029, SNR: 2.9, T: 1.00: 30%|##9 | 296/1000 [00:00<00:00, 737.66it/s]
15:25:01.443 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.069 +/- 0.029, SNR: 2.7, T: 1.00: 37%|###7 | 370/1000 [00:00<00:00, 707.83it/s]
15:25:01.544 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.064 +/- 0.028, SNR: 2.6, T: 1.00: 44%|####4 | 441/1000 [00:00<00:00, 707.40it/s]
15:25:01.645 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.058 +/- 0.027, SNR: 2.5, T: 1.00: 51%|#####1 | 512/1000 [00:00<00:00, 705.88it/s]
15:25:01.745 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.052 +/- 0.026, SNR: 2.4, T: 1.00: 58%|#####8 | 584/1000 [00:00<00:00, 709.26it/s]
15:25:01.846 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.047 +/- 0.025, SNR: 2.3, T: 1.00: 66%|######5 | 656/1000 [00:00<00:00, 711.28it/s]
15:25:01.946 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.041 +/- 0.024, SNR: 2.2, T: 1.00: 73%|#######2 | 728/1000 [00:01<00:00, 712.42it/s]
15:25:02.048 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.035 +/- 0.022, SNR: 2.1, T: 1.00: 80%|######## | 800/1000 [00:01<00:00, 712.20it/s]
15:25:02.148 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.029 +/- 0.020, SNR: 2.1, T: 1.00: 87%|########7 | 872/1000 [00:01<00:00, 712.69it/s]
15:25:02.250 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.022 +/- 0.017, SNR: 2.0, T: 1.00: 94%|#########4| 944/1000 [00:01<00:00, 712.43it/s]
15:25:02.329 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 13) ELBO: -13.018 +/- 0.014, SNR: 2.1, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 714.65it/s]
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15:25:02.644 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 13) relative error: 0.0023 +/- 0.0170: 1%|1 | 1/100 [00:00<00:31, 3.18it/s]
15:25:02.958 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 13) relative error: 0.0006 +/- 0.0023: 2%|2 | 2/100 [00:00<00:30, 3.18it/s]
15:25:03.273 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 13) relative error: 0.0003 +/- 0.0014: 2%|2 | 2/100 [00:00<00:46, 2.12it/s]
15:25:03.273 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 13): 0%| | 0/1 [00:00<?, ?it/s]
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15:25:03.375 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.016 +/- 0.014, SNR: 2.0, T: 1.00: 7%|7 | 71/1000 [00:00<00:01, 702.77it/s]
15:25:03.476 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.014 +/- 0.014, SNR: 1.9, T: 1.00: 14%|#4 | 142/1000 [00:00<00:01, 703.56it/s]
15:25:03.578 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.012 +/- 0.014, SNR: 1.8, T: 1.00: 21%|##1 | 213/1000 [00:00<00:01, 701.74it/s]
15:25:03.678 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.011 +/- 0.014, SNR: 1.7, T: 1.00: 28%|##8 | 284/1000 [00:00<00:01, 703.13it/s]
15:25:03.778 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.009 +/- 0.014, SNR: 1.6, T: 1.00: 36%|###5 | 359/1000 [00:00<00:00, 719.55it/s]
15:25:03.879 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.007 +/- 0.014, SNR: 1.5, T: 1.00: 43%|####3 | 434/1000 [00:00<00:00, 728.79it/s]
15:25:03.979 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.005 +/- 0.014, SNR: 1.4, T: 1.00: 51%|##### | 509/1000 [00:00<00:00, 735.32it/s]
15:25:04.080 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.004 +/- 0.014, SNR: 1.3, T: 1.00: 58%|#####8 | 584/1000 [00:00<00:00, 737.91it/s]
15:25:04.181 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.002 +/- 0.014, SNR: 1.2, T: 1.00: 66%|######5 | 658/1000 [00:00<00:00, 736.85it/s]
15:25:04.281 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -13.000 +/- 0.014, SNR: 1.1, T: 1.00: 73%|#######3 | 732/1000 [00:01<00:00, 736.14it/s]
15:25:04.383 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -12.998 +/- 0.013, SNR: 1.0, T: 1.00: 81%|######## | 807/1000 [00:01<00:00, 737.49it/s]
15:25:04.484 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -12.996 +/- 0.013, SNR: 0.9, T: 1.00: 88%|########8 | 882/1000 [00:01<00:00, 738.52it/s]
15:25:04.585 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -12.994 +/- 0.013, SNR: 0.7, T: 1.00: 96%|#########5| 957/1000 [00:01<00:00, 739.14it/s]
15:25:04.644 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 14) ELBO: -12.993 +/- 0.012, SNR: 0.7, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 730.31it/s]
15:25:04.644 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 14): 0%| | 0/100 [00:00<?, ?it/s]
15:25:04.959 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 14) relative error: 0.0024 +/- 0.0167: 1%|1 | 1/100 [00:00<00:31, 3.18it/s]
15:25:05.277 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 14) relative error: 0.0006 +/- 0.0024: 2%|2 | 2/100 [00:00<00:31, 3.16it/s]
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15:25:05.916 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 14) relative error: 0.0003 +/- 0.0010: 3%|3 | 3/100 [00:01<00:41, 2.36it/s]
15:25:05.916 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 14): 0%| | 0/1 [00:00<?, ?it/s]
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15:25:06.018 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.993 +/- 0.012, SNR: 0.6, T: 1.00: 7%|7 | 70/1000 [00:00<00:01, 698.58it/s]
15:25:06.118 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.992 +/- 0.012, SNR: 0.6, T: 1.00: 14%|#4 | 141/1000 [00:00<00:01, 703.33it/s]
15:25:06.219 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.992 +/- 0.012, SNR: 0.6, T: 1.00: 21%|##1 | 213/1000 [00:00<00:01, 708.22it/s]
15:25:06.320 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.991 +/- 0.012, SNR: 0.6, T: 1.00: 28%|##8 | 285/1000 [00:00<00:01, 709.30it/s]
15:25:06.421 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.991 +/- 0.012, SNR: 0.5, T: 1.00: 36%|###5 | 357/1000 [00:00<00:00, 710.02it/s]
15:25:06.522 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.991 +/- 0.012, SNR: 0.5, T: 1.00: 43%|####2 | 429/1000 [00:00<00:00, 711.08it/s]
15:25:06.624 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.990 +/- 0.012, SNR: 0.5, T: 1.00: 50%|##### | 501/1000 [00:00<00:00, 711.28it/s]
15:25:06.725 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.990 +/- 0.012, SNR: 0.5, T: 1.00: 57%|#####7 | 573/1000 [00:00<00:00, 711.16it/s]
15:25:06.828 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.989 +/- 0.012, SNR: 0.4, T: 1.00: 64%|######4 | 645/1000 [00:00<00:00, 706.87it/s]
15:25:06.928 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.989 +/- 0.012, SNR: 0.4, T: 1.00: 72%|#######1 | 716/1000 [00:01<00:00, 707.15it/s]
15:25:07.028 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.988 +/- 0.012, SNR: 0.4, T: 1.00: 79%|#######8 | 787/1000 [00:01<00:00, 707.75it/s]
15:25:07.129 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.988 +/- 0.012, SNR: 0.3, T: 1.00: 86%|########5 | 858/1000 [00:01<00:00, 707.82it/s]
15:25:07.231 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.988 +/- 0.012, SNR: 0.3, T: 1.00: 93%|#########2| 929/1000 [00:01<00:00, 704.14it/s]
15:25:07.325 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 15) ELBO: -12.987 +/- 0.012, SNR: 0.3, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 710.51it/s]
15:25:07.325 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 15): 0%| | 0/100 [00:00<?, ?it/s]
15:25:07.641 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 15) relative error: 0.0024 +/- 0.0157: 1%|1 | 1/100 [00:00<00:31, 3.17it/s]
15:25:07.963 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 15) relative error: 0.0009 +/- 0.0025: 2%|2 | 2/100 [00:00<00:31, 3.13it/s]
15:25:08.285 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 15) relative error: 0.0005 +/- 0.0013: 3%|3 | 3/100 [00:00<00:31, 3.12it/s]
15:25:08.611 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 15) relative error: 0.0004 +/- 0.0009: 3%|3 | 3/100 [00:01<00:41, 2.33it/s]
15:25:08.611 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 15): 0%| | 0/1 [00:00<?, ?it/s]
15:25:08.612 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 15) ploidy update size: 8.06557e-05: 0%| | 0/1 [00:00<?, ?it/s]
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15:25:08.713 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.987 +/- 0.012, SNR: 0.3, T: 1.00: 7%|7 | 70/1000 [00:00<00:01, 698.03it/s]
15:25:08.813 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.987 +/- 0.012, SNR: 0.3, T: 1.00: 14%|#4 | 141/1000 [00:00<00:01, 702.97it/s]
15:25:08.914 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.987 +/- 0.012, SNR: 0.3, T: 1.00: 21%|##1 | 212/1000 [00:00<00:01, 704.42it/s]
15:25:09.014 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.987 +/- 0.012, SNR: 0.3, T: 1.00: 28%|##8 | 283/1000 [00:00<00:01, 705.19it/s]
15:25:09.115 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.987 +/- 0.012, SNR: 0.3, T: 1.00: 35%|###5 | 354/1000 [00:00<00:00, 705.84it/s]
15:25:09.215 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.986 +/- 0.012, SNR: 0.3, T: 1.00: 42%|####2 | 425/1000 [00:00<00:00, 705.40it/s]
15:25:09.316 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.986 +/- 0.012, SNR: 0.3, T: 1.00: 50%|####9 | 496/1000 [00:00<00:00, 705.90it/s]
15:25:09.419 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.986 +/- 0.012, SNR: 0.2, T: 1.00: 57%|#####6 | 567/1000 [00:00<00:00, 700.06it/s]
15:25:09.519 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.986 +/- 0.012, SNR: 0.2, T: 1.00: 64%|######3 | 638/1000 [00:00<00:00, 702.14it/s]
15:25:09.620 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.986 +/- 0.012, SNR: 0.2, T: 1.00: 71%|####### | 709/1000 [00:01<00:00, 703.68it/s]
15:25:09.720 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.986 +/- 0.012, SNR: 0.2, T: 1.00: 78%|#######8 | 780/1000 [00:01<00:00, 704.82it/s]
15:25:09.821 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.986 +/- 0.012, SNR: 0.2, T: 1.00: 85%|########5 | 851/1000 [00:01<00:00, 705.04it/s]
15:25:09.922 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 92%|#########2| 922/1000 [00:01<00:00, 704.57it/s]
15:25:10.023 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 99%|#########9| 993/1000 [00:01<00:00, 703.16it/s]
15:25:10.033 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 16) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 703.63it/s]
15:25:10.034 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 16): 0%| | 0/100 [00:00<?, ?it/s]
15:25:10.362 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 16) relative error: 0.0023 +/- 0.0141: 1%|1 | 1/100 [00:00<00:32, 3.05it/s]
15:25:10.687 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 16) relative error: 0.0007 +/- 0.0019: 2%|2 | 2/100 [00:00<00:31, 3.07it/s]
15:25:11.009 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 16) relative error: 0.0005 +/- 0.0014: 3%|3 | 3/100 [00:00<00:31, 3.08it/s]
15:25:11.330 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 16) relative error: 0.0003 +/- 0.0011: 3%|3 | 3/100 [00:01<00:41, 2.31it/s]
15:25:11.331 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 16): 0%| | 0/1 [00:00<?, ?it/s]
15:25:11.331 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 16) ploidy update size: 3.75809e-05: 0%| | 0/1 [00:00<?, ?it/s]
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15:25:11.432 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 7%|6 | 68/1000 [00:00<00:01, 678.63it/s]
15:25:11.533 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 14%|#3 | 139/1000 [00:00<00:01, 691.99it/s]
15:25:11.633 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 21%|## | 209/1000 [00:00<00:01, 694.06it/s]
15:25:11.734 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 28%|##8 | 280/1000 [00:00<00:01, 697.63it/s]
15:25:11.835 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 35%|###5 | 351/1000 [00:00<00:00, 699.80it/s]
15:25:11.936 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 42%|####2 | 422/1000 [00:00<00:00, 701.16it/s]
15:25:12.037 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 49%|####9 | 493/1000 [00:00<00:00, 701.62it/s]
15:25:12.141 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.985 +/- 0.012, SNR: 0.2, T: 1.00: 56%|#####6 | 564/1000 [00:00<00:00, 696.04it/s]
15:25:12.242 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 63%|######3 | 634/1000 [00:00<00:00, 694.81it/s]
15:25:12.343 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 70%|####### | 704/1000 [00:01<00:00, 694.23it/s]
15:25:12.447 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 77%|#######7 | 774/1000 [00:01<00:00, 687.61it/s]
15:25:12.548 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 84%|########4 | 844/1000 [00:01<00:00, 689.15it/s]
15:25:12.650 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 91%|#########1| 914/1000 [00:01<00:00, 689.48it/s]
15:25:12.751 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 98%|#########8| 984/1000 [00:01<00:00, 690.24it/s]
15:25:12.774 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 17) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 693.14it/s]
15:25:12.774 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 17): 0%| | 0/100 [00:00<?, ?it/s]
15:25:13.097 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 17) relative error: 0.0023 +/- 0.0159: 1%|1 | 1/100 [00:00<00:31, 3.10it/s]
15:25:13.420 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 17) relative error: 0.0006 +/- 0.0027: 2%|2 | 2/100 [00:00<00:31, 3.10it/s]
15:25:13.742 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 17) relative error: 0.0004 +/- 0.0016: 2%|2 | 2/100 [00:00<00:47, 2.07it/s]
15:25:13.742 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 17): 0%| | 0/1 [00:00<?, ?it/s]
15:25:13.743 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 17) ploidy update size: 2.26917e-05: 0%| | 0/1 [00:00<?, ?it/s]
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15:25:13.843 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 7%|7 | 71/1000 [00:00<00:01, 707.52it/s]
15:25:13.944 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.2, T: 1.00: 14%|#4 | 142/1000 [00:00<00:01, 708.64it/s]
15:25:14.044 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 21%|##1 | 213/1000 [00:00<00:01, 709.15it/s]
15:25:14.145 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.2, T: 1.00: 28%|##8 | 284/1000 [00:00<00:01, 705.29it/s]
15:25:14.245 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 36%|###5 | 355/1000 [00:00<00:00, 706.40it/s]
15:25:14.345 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 43%|####2 | 426/1000 [00:00<00:00, 707.39it/s]
15:25:14.449 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 50%|####9 | 497/1000 [00:00<00:00, 701.04it/s]
15:25:14.550 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.2, T: 1.00: 57%|#####6 | 569/1000 [00:00<00:00, 704.23it/s]
15:25:14.651 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 64%|######4 | 641/1000 [00:00<00:00, 706.17it/s]
15:25:14.751 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 71%|#######1 | 712/1000 [00:01<00:00, 707.11it/s]
15:25:14.851 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.2, T: 1.00: 78%|#######8 | 783/1000 [00:01<00:00, 707.63it/s]
15:25:14.952 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 85%|########5 | 854/1000 [00:01<00:00, 706.23it/s]
15:25:15.053 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 92%|#########2| 925/1000 [00:01<00:00, 706.73it/s]
15:25:15.153 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 100%|#########9| 996/1000 [00:01<00:00, 707.27it/s]
15:25:15.159 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 18) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 706.36it/s]
15:25:15.159 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 18): 0%| | 0/100 [00:00<?, ?it/s]
15:25:15.481 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 18) relative error: 0.0025 +/- 0.0180: 1%|1 | 1/100 [00:00<00:31, 3.11it/s]
15:25:15.803 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 18) relative error: 0.0007 +/- 0.0023: 2%|2 | 2/100 [00:00<00:31, 3.10it/s]
15:25:16.127 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 18) relative error: 0.0004 +/- 0.0013: 2%|2 | 2/100 [00:00<00:47, 2.07it/s]
15:25:16.127 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 18): 0%| | 0/1 [00:00<?, ?it/s]
15:25:16.127 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 18) ploidy update size: 7.70096e-06: 0%| | 0/1 [00:00<?, ?it/s]
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15:25:16.229 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 7%|7 | 71/1000 [00:00<00:01, 703.36it/s]
15:25:16.329 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.984 +/- 0.012, SNR: 0.1, T: 1.00: 14%|#4 | 142/1000 [00:00<00:01, 706.03it/s]
15:25:16.433 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.1, T: 1.00: 21%|##1 | 213/1000 [00:00<00:01, 696.58it/s]
15:25:16.533 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.1, T: 1.00: 28%|##8 | 284/1000 [00:00<00:01, 699.76it/s]
15:25:16.634 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.1, T: 1.00: 36%|###5 | 355/1000 [00:00<00:00, 701.08it/s]
15:25:16.735 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.1, T: 1.00: 43%|####2 | 426/1000 [00:00<00:00, 702.20it/s]
15:25:16.836 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.1, T: 1.00: 50%|####9 | 497/1000 [00:00<00:00, 703.27it/s]
15:25:16.937 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.1, T: 1.00: 57%|#####6 | 568/1000 [00:00<00:00, 703.48it/s]
15:25:17.037 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.1, T: 1.00: 64%|######3 | 639/1000 [00:00<00:00, 704.32it/s]
15:25:17.138 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.0, T: 1.00: 71%|#######1 | 710/1000 [00:01<00:00, 704.44it/s]
15:25:17.238 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.0, T: 1.00: 78%|#######8 | 781/1000 [00:01<00:00, 705.00it/s]
15:25:17.339 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.0, T: 1.00: 85%|########5 | 852/1000 [00:01<00:00, 705.46it/s]
15:25:17.442 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.983 +/- 0.012, SNR: 0.0, T: 1.00: 92%|#########2| 923/1000 [00:01<00:00, 699.62it/s]
15:25:17.542 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.982 +/- 0.012, SNR: 0.0, T: 1.00: 99%|#########9| 994/1000 [00:01<00:00, 702.71it/s]
15:25:17.551 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 19) ELBO: -12.982 +/- 0.012, SNR: 0.0, T: 1.00: 100%|##########| 1000/1000 [00:01<00:00, 702.65it/s]
15:25:17.551 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 19): 0%| | 0/100 [00:00<?, ?it/s]
15:25:17.873 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 19) relative error: 0.0019 +/- 0.0165: 1%|1 | 1/100 [00:00<00:31, 3.11it/s]
15:25:18.193 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 19) relative error: 0.0009 +/- 0.0023: 2%|2 | 2/100 [00:00<00:31, 3.12it/s]
15:25:18.513 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 19) relative error: 0.0005 +/- 0.0015: 3%|3 | 3/100 [00:00<00:31, 3.12it/s]
15:25:18.831 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 19) relative error: 0.0004 +/- 0.0010: 3%|3 | 3/100 [00:01<00:41, 2.34it/s]
15:25:18.831 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 19): 0%| | 0/1 [00:00<?, ?it/s]
15:25:18.832 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 19) ploidy update size: 8.30884e-05: 0%| | 0/1 [00:00<?, ?it/s]
15:25:18.832 INFO gcnvkernel.tasks.inference_task_base - (denoising) starting...: 0%| | 0/1000 [00:00<?, ?it/s]
15:25:18.847 INFO gcnvkernel.tasks.inference_task_base - (denoising epoch 20) ELBO: -12.982 +/- 0.012, SNR: 0.0, T: 1.00: 1%| | 9/1000 [00:00<00:01, 613.92it/s]
15:25:18.847 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 20): 0%| | 0/100 [00:00<?, ?it/s]
15:25:19.164 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 20) relative error: 0.0016 +/- 0.0070: 1%|1 | 1/100 [00:00<00:31, 3.15it/s]
15:25:19.484 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 20) relative error: 0.0008 +/- 0.0026: 2%|2 | 2/100 [00:00<00:31, 3.14it/s]
15:25:19.801 INFO gcnvkernel.tasks.inference_task_base - (sampling epoch 20) relative error: 0.0004 +/- 0.0014: 2%|2 | 2/100 [00:00<00:46, 2.10it/s]
15:25:19.801 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 20): 0%| | 0/1 [00:00<?, ?it/s]
15:25:19.802 INFO gcnvkernel.tasks.inference_task_base - (ploidy calling epoch 20) ploidy update size: 2.14391e-05: 0%| | 0/1 [00:00<?, ?it/s]
15:25:19.802 INFO gcnvkernel.tasks.inference_task_base - Inference task completed successfully and convergence achieved.
15:25:19.820 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-004" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_0"...
15:25:19.836 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-005" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_1"...
15:25:19.847 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID14-380" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_2"...
15:25:19.858 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID14-381" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_3"...
15:25:19.870 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID14-382" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_4"...
15:25:19.883 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID16-080" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_5"...
15:25:19.896 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID16-081" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_6"...
15:25:19.910 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID20-210" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_7"...
15:25:19.923 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A170421" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_8"...
15:25:19.936 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A170420" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_9"...
15:25:19.949 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200628" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_10"...
15:25:19.962 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210104" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_11"...
15:25:19.975 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210105" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_12"...
15:25:19.988 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-172" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_13"...
15:25:20.001 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-173" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_14"...
15:25:20.015 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-174" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_15"...
15:25:20.028 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID20-220" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_16"...
15:25:20.041 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-166" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_17"...
15:25:20.054 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-167" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_18"...
15:25:20.067 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-168" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_19"...
15:25:20.081 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-006" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_20"...
15:25:20.094 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-007" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_21"...
15:25:20.107 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-008" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_22"...
15:25:20.120 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-009" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_23"...
15:25:20.134 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-010" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_24"...
15:25:20.147 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-011" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_25"...
15:25:20.160 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-162" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_26"...
15:25:20.173 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-163" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_27"...
15:25:20.187 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-164" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_28"...
15:25:20.199 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-165" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_29"...
15:25:20.213 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210124" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_30"...
15:25:20.226 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210126" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_31"...
15:25:20.240 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200621" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_32"...
15:25:20.254 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210128" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_33"...
15:25:20.267 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210130" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_34"...
15:25:20.281 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210121" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_35"...
15:25:20.294 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210122" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_36"...
15:25:20.308 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210123" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_37"...
15:25:20.321 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200272" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_38"...
15:25:20.334 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200273" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_39"...
15:25:20.348 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200274" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_40"...
15:25:20.361 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-001" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_41"...
15:25:20.362 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr16. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:25:20.362 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr17. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:25:20.362 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:25:20.362 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr20. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:25:20.362 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr22. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:25:20.375 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-002" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_42"...
15:25:20.388 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-003" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_43"...
15:25:20.401 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210118" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_44"...
15:25:20.415 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210119" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_45"...
15:25:20.428 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210120" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_46"...
15:25:20.442 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210100" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_47"...
15:25:20.456 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A210102" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_48"...
15:25:20.468 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200635" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_49"...
15:25:20.479 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200637" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_50"...
15:25:20.490 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200639" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_51"...
15:25:20.503 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "A200643" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_52"...
15:25:20.517 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-021A" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_53"...
15:25:20.530 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-022" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_54"...
15:25:20.543 INFO gcnvkernel.io.io_ploidy - Saving posteriors for sample "PID21-023A" in "/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls/SAMPLE_55"...
07:25:22.201 DEBUG ScriptExecutor - Result: 0
07:25:22.203 INFO DetermineGermlineContigPloidy - DetermineGermlineContigPloidy complete.
07:25:22.203 INFO DetermineGermlineContigPloidy - Shutting down engine
[February 14, 2023 7:25:22 AM GMT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 1.65 minutes.
Runtime.totalMemory()=21986541568
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Xms20G -Xmx60G -XX:+UseParallelOldGC -XX:+UseAdaptiveSizePolicy -XX:ActiveProcessorCount=4 -XX:ParallelGCThreads=4 -jar /gatk/gatk-package-4.3.0.0-local.jar DetermineGermlineContigPloidy --model /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_ploidy_model/iGT359V1_ploidy_normal_cohort-model -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-004.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-005.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-380.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-381.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-382.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-080.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-081.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-210.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170421.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170420.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200628.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210104.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210105.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-172.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-173.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-174.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-220.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-166.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-167.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-168.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-006.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-007.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-008.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-009.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-010.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-011.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-162.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-163.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-164.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-165.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210124.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210126.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200621.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210128.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210130.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210121.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210122.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210123.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200272.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200273.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200274.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-001.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-002.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-003.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210118.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210119.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210120.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210100.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210102.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200635.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200637.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200639.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200643.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-021A.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-022.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-023A.counts.hdf5 --output /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy --output-prefix iGT359V1_cases_ploidy_50_samples_20220304 --verbosity DEBUG
singularity/3.7.2 is unloaded
parallel/20210122 is loaded
gcc/9.1.0 is loaded
total 0
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_55
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_54
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_53
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_52
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_51
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_50
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_49
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_48
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_47
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_46
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_45
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_44
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_43
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_42
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_41
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_40
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_39
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_38
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_37
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_36
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_35
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_34
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_33
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_32
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_31
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_30
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_29
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_28
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_27
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_26
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_25
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_24
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_23
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_22
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_21
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_20
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_19
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_18
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_17
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_16
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_15
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_14
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_13
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_12
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_11
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_10
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_9
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_8
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_7
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_6
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_5
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_4
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_3
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_2
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_1
drwxr-xr-x 2 yangyxt wlyang 160 Feb 14 15:25 SAMPLE_0
gcc/9.1.0 is unloaded
parallel/20210122 is loaded
gcnv
Line 97: In function return_to_conda_base: The current conda env is gcnv. Return to base conda env
Line 101: In function return_to_conda_base: After deactivation, The current conda env is base.
Line 257: In function determine_ploidy_case: Tue Feb 14 15:25:27 HKT 2023: ********Determine Ploidies done for all samples in case mode*********
Line 369: In function gCNV_case: Tue Feb 14 15:25:27 HKT 2023: Start running gCNV in case mode
gcc/9.1.0 is loadedLine 7930: Tue Feb 14 15:25:34 HKT 2023: In function gatk_wrapper: Using singularity image to run GATK
singularity/3.7.2 is loaded
building file list ... donesent 2,368 bytes received 12 bytes 4,760.00 bytes/sec
total size is 9,945,084,551 speedup is 4,178,606.95 (DRY RUN)
building file list ... donesent 2,368 bytes received 12 bytes 4,760.00 bytes/sec
total size is 9,945,084,551 speedup is 4,178,606.95Line 7962: Tue Feb 14 15:25:38 HKT 2023: In function gatk_wrapper: The GATK wrapper get input arguments: gatk GermlineCNVCaller --java-options -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Xmx40G -XX:+UseParallelOldGC -XX:+UseAdaptiveSizePolicy -XX:ActiveProcessorCount=4 -XX:ParallelGCThreads=4 --run-mode CASE --model /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_model/iGT359V1_gCNV_normal_cohort-model --contig-ploidy-calls /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_case_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls --verbosity DEBUG -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-004.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-005.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-380.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-381.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-382.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-080.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-081.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-210.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170421.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170420.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200628.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210104.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210105.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-172.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-173.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-174.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-220.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-166.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-167.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-168.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-006.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-007.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-008.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-009.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-010.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-011.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-162.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-163.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-164.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-165.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210124.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210126.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200621.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210128.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210130.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210121.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210122.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210123.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200272.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200273.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200274.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-001.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-002.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-003.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210118.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210119.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210120.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210100.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210102.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200635.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200637.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200639.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200643.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-021A.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-022.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-023A.counts.hdf5 --output /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_cases --output-prefix iGT359V1_gCNV_cases_50_samples_20220304 --p-alt 0.0005 --cnv-coherence-length 1000 --max-copy-number 5 --mapping-error-rate 0.01 --sample-psi-scale 0.01 --depth-correction-tau 10000 --learning-rate 0.05 --adamax-beta-1 0.9 --adamax-beta-2 0.99 --log-emission-samples-per-round 50 --log-emission-sampling-median-rel-error 0.005 --log-emission-sampling-rounds 10 --max-advi-iter-first-epoch 5000 --max-advi-iter-subsequent-epochs 100 --min-training-epochs 10 --max-training-epochs 100 --initial-temperature 2.0 --num-thermal-advi-iters 2500 --convergence-snr-averaging-window 500 --convergence-snr-trigger-threshold 0.1 --convergence-snr-countdown-window 10 --max-calling-iters 10 --caller-update-convergence-threshold 0.001 --caller-internal-admixing-rate 0.75 --caller-external-admixing-rate 1.0 --active-class-padding-hybrid-mode 5000
07:25:41.186 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
07:25:41.214 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression2390803202432716163.so
07:25:41.448 INFO GermlineCNVCaller - ------------------------------------------------------------
07:25:41.448 INFO GermlineCNVCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0
07:25:41.448 INFO GermlineCNVCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
07:25:41.448 INFO GermlineCNVCaller - Executing as yangyxt@paedyl02 on Linux v3.10.0-1160.11.1.el7.x86_64 amd64
07:25:41.448 INFO GermlineCNVCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
07:25:41.448 INFO GermlineCNVCaller - Start Date/Time: February 14, 2023 7:25:41 AM GMT
07:25:41.448 INFO GermlineCNVCaller - ------------------------------------------------------------
07:25:41.448 INFO GermlineCNVCaller - ------------------------------------------------------------
07:25:41.449 INFO GermlineCNVCaller - HTSJDK Version: 3.0.1
07:25:41.449 INFO GermlineCNVCaller - Picard Version: 2.27.5
07:25:41.449 INFO GermlineCNVCaller - Built for Spark Version: 2.4.5
07:25:41.450 INFO GermlineCNVCaller - HTSJDK Defaults.BUFFER_SIZE : 131072
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.CREATE_INDEX : false
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.CREATE_MD5 : false
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.CUSTOM_READER_FACTORY :
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.REFERENCE_FASTA : null
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
07:25:41.451 INFO GermlineCNVCaller - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
07:25:41.451 DEBUG ConfigFactory - Configuration file values:
07:25:41.454 DEBUG ConfigFactory - gcsMaxRetries = 20
07:25:41.455 DEBUG ConfigFactory - gcsProjectForRequesterPays =
07:25:41.455 DEBUG ConfigFactory - gatk_stacktrace_on_user_exception = false
07:25:41.455 DEBUG ConfigFactory - samjdk.use_async_io_read_samtools = false
07:25:41.455 DEBUG ConfigFactory - samjdk.use_async_io_write_samtools = true
07:25:41.455 DEBUG ConfigFactory - samjdk.use_async_io_write_tribble = false
07:25:41.455 DEBUG ConfigFactory - samjdk.compression_level = 2
07:25:41.455 DEBUG ConfigFactory - spark.kryoserializer.buffer.max = 512m
07:25:41.455 DEBUG ConfigFactory - spark.driver.maxResultSize = 0
07:25:41.455 DEBUG ConfigFactory - spark.driver.userClassPathFirst = true
07:25:41.455 DEBUG ConfigFactory - spark.io.compression.codec = lzf
07:25:41.455 DEBUG ConfigFactory - spark.executor.memoryOverhead = 600
07:25:41.455 DEBUG ConfigFactory - spark.driver.extraJavaOptions =
07:25:41.455 DEBUG ConfigFactory - spark.executor.extraJavaOptions =
07:25:41.455 DEBUG ConfigFactory - codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
07:25:41.455 DEBUG ConfigFactory - read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
07:25:41.455 DEBUG ConfigFactory - annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
07:25:41.455 DEBUG ConfigFactory - cloudPrefetchBuffer = 40
07:25:41.455 DEBUG ConfigFactory - cloudIndexPrefetchBuffer = -1
07:25:41.455 DEBUG ConfigFactory - createOutputBamIndex = true
07:25:41.455 INFO GermlineCNVCaller - Deflater: IntelDeflater
07:25:41.455 INFO GermlineCNVCaller - Inflater: IntelInflater
07:25:41.455 INFO GermlineCNVCaller - GCS max retries/reopens: 20
07:25:41.456 INFO GermlineCNVCaller - Requester pays: disabled
07:25:41.456 INFO GermlineCNVCaller - Initializing engine
07:25:41.459 DEBUG ScriptExecutor - Executing:
07:25:41.459 DEBUG ScriptExecutor - python
07:25:41.459 DEBUG ScriptExecutor - -c
07:25:41.459 DEBUG ScriptExecutor - import gcnvkernel07:25:52.616 DEBUG ScriptExecutor - Result: 0
07:25:52.616 INFO GermlineCNVCaller - Done initializing engine
07:25:53.178 INFO GermlineCNVCaller - Running the tool in CASE mode...
07:25:53.178 INFO GermlineCNVCaller - Validating and aggregating data from input read-count files...
07:25:53.243 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
07:25:53.244 DEBUG GenomeLocParser - chrM (16571 bp)
07:25:53.244 DEBUG GenomeLocParser - chr1 (249250621 bp)
07:25:53.244 DEBUG GenomeLocParser - chr2 (243199373 bp)
07:25:53.244 DEBUG GenomeLocParser - chr3 (198022430 bp)
07:25:53.244 DEBUG GenomeLocParser - chr4 (191154276 bp)
07:25:53.244 DEBUG GenomeLocParser - chr5 (180915260 bp)
07:25:53.244 DEBUG GenomeLocParser - chr6 (171115067 bp)
07:25:53.244 DEBUG GenomeLocParser - chr7 (159138663 bp)
07:25:53.244 DEBUG GenomeLocParser - chr8 (146364022 bp)
07:25:53.244 DEBUG GenomeLocParser - chr9 (141213431 bp)
07:25:53.244 DEBUG GenomeLocParser - chr10 (135534747 bp)
07:25:53.244 DEBUG GenomeLocParser - chr11 (135006516 bp)
07:25:53.245 DEBUG GenomeLocParser - chr12 (133851895 bp)
07:25:53.245 DEBUG GenomeLocParser - chr13 (115169878 bp)
07:25:53.245 DEBUG GenomeLocParser - chr14 (107349540 bp)
07:25:53.245 DEBUG GenomeLocParser - chr15 (102531392 bp)
07:25:53.245 DEBUG GenomeLocParser - chr16 (90354753 bp)
07:25:53.245 DEBUG GenomeLocParser - chr17 (81195210 bp)
07:25:53.245 DEBUG GenomeLocParser - chr18 (78077248 bp)
07:25:53.245 DEBUG GenomeLocParser - chr19 (59128983 bp)
07:25:53.245 DEBUG GenomeLocParser - chr20 (63025520 bp)
07:25:53.245 DEBUG GenomeLocParser - chr21 (48129895 bp)
07:25:53.245 DEBUG GenomeLocParser - chr22 (51304566 bp)
07:25:53.245 DEBUG GenomeLocParser - chrX (155270560 bp)
07:25:53.245 DEBUG GenomeLocParser - chrY (59373566 bp)
07:25:53.245 DEBUG GenomeLocParser - chr1_gl000191_random (106433 bp)
07:25:53.245 DEBUG GenomeLocParser - chr1_gl000192_random (547496 bp)
07:25:53.245 DEBUG GenomeLocParser - chr4_ctg9_hap1 (590426 bp)
07:25:53.245 DEBUG GenomeLocParser - chr4_gl000193_random (189789 bp)
07:25:53.245 DEBUG GenomeLocParser - chr4_gl000194_random (191469 bp)
07:25:53.245 DEBUG GenomeLocParser - chr6_apd_hap1 (4622290 bp)
07:25:53.245 DEBUG GenomeLocParser - chr6_cox_hap2 (4795371 bp)
07:25:53.245 DEBUG GenomeLocParser - chr6_dbb_hap3 (4610396 bp)
07:25:53.245 DEBUG GenomeLocParser - chr6_mann_hap4 (4683263 bp)
07:25:53.245 DEBUG GenomeLocParser - chr6_mcf_hap5 (4833398 bp)
07:25:53.245 DEBUG GenomeLocParser - chr6_qbl_hap6 (4611984 bp)
07:25:53.246 DEBUG GenomeLocParser - chr6_ssto_hap7 (4928567 bp)
07:25:53.246 DEBUG GenomeLocParser - chr7_gl000195_random (182896 bp)
07:25:53.246 DEBUG GenomeLocParser - chr8_gl000196_random (38914 bp)
07:25:53.246 DEBUG GenomeLocParser - chr8_gl000197_random (37175 bp)
07:25:53.246 DEBUG GenomeLocParser - chr9_gl000198_random (90085 bp)
07:25:53.246 DEBUG GenomeLocParser - chr9_gl000199_random (169874 bp)
07:25:53.246 DEBUG GenomeLocParser - chr9_gl000200_random (187035 bp)
07:25:53.246 DEBUG GenomeLocParser - chr9_gl000201_random (36148 bp)
07:25:53.246 DEBUG GenomeLocParser - chr11_gl000202_random (40103 bp)
07:25:53.246 DEBUG GenomeLocParser - chr17_ctg5_hap1 (1680828 bp)
07:25:53.246 DEBUG GenomeLocParser - chr17_gl000203_random (37498 bp)
07:25:53.246 DEBUG GenomeLocParser - chr17_gl000204_random (81310 bp)
07:25:53.246 DEBUG GenomeLocParser - chr17_gl000205_random (174588 bp)
07:25:53.246 DEBUG GenomeLocParser - chr17_gl000206_random (41001 bp)
07:25:53.246 DEBUG GenomeLocParser - chr18_gl000207_random (4262 bp)
07:25:53.246 DEBUG GenomeLocParser - chr19_gl000208_random (92689 bp)
07:25:53.246 DEBUG GenomeLocParser - chr19_gl000209_random (159169 bp)
07:25:53.246 DEBUG GenomeLocParser - chr21_gl000210_random (27682 bp)
07:25:53.246 DEBUG GenomeLocParser - chrUn_gl000211 (166566 bp)
07:25:53.246 DEBUG GenomeLocParser - chrUn_gl000212 (186858 bp)
07:25:53.246 DEBUG GenomeLocParser - chrUn_gl000213 (164239 bp)
07:25:53.246 DEBUG GenomeLocParser - chrUn_gl000214 (137718 bp)
07:25:53.246 DEBUG GenomeLocParser - chrUn_gl000215 (172545 bp)
07:25:53.246 DEBUG GenomeLocParser - chrUn_gl000216 (172294 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000217 (172149 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000218 (161147 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000219 (179198 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000220 (161802 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000221 (155397 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000222 (186861 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000223 (180455 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000224 (179693 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000225 (211173 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000226 (15008 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000227 (128374 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000228 (129120 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000229 (19913 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000230 (43691 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000231 (27386 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000232 (40652 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000233 (45941 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000234 (40531 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000235 (34474 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000236 (41934 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000237 (45867 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000238 (39939 bp)
07:25:53.247 DEBUG GenomeLocParser - chrUn_gl000239 (33824 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000240 (41933 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000241 (42152 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000242 (43523 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000243 (43341 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000244 (39929 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000245 (36651 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000246 (38154 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000247 (36422 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000248 (39786 bp)
07:25:53.248 DEBUG GenomeLocParser - chrUn_gl000249 (38502 bp)
07:25:53.398 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-004.counts.hdf5 (1 / 56)
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
07:25:53.951 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-005.counts.hdf5 (2 / 56)
07:25:54.300 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-380.counts.hdf5 (3 / 56)
07:25:54.517 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-381.counts.hdf5 (4 / 56)
07:25:54.736 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-382.counts.hdf5 (5 / 56)
07:25:55.056 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-080.counts.hdf5 (6 / 56)
07:25:55.291 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-081.counts.hdf5 (7 / 56)
07:25:55.487 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-210.counts.hdf5 (8 / 56)
07:25:55.684 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170421.counts.hdf5 (9 / 56)
07:25:55.899 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170420.counts.hdf5 (10 / 56)
07:25:56.170 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200628.counts.hdf5 (11 / 56)
07:25:56.367 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210104.counts.hdf5 (12 / 56)
07:25:56.573 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210105.counts.hdf5 (13 / 56)
07:25:56.770 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-172.counts.hdf5 (14 / 56)
07:25:57.011 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-173.counts.hdf5 (15 / 56)
07:25:57.205 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-174.counts.hdf5 (16 / 56)
07:25:57.400 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-220.counts.hdf5 (17 / 56)
07:25:57.596 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-166.counts.hdf5 (18 / 56)
07:25:57.791 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-167.counts.hdf5 (19 / 56)
07:25:58.041 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-168.counts.hdf5 (20 / 56)
07:25:58.380 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-006.counts.hdf5 (21 / 56)
07:25:58.629 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-007.counts.hdf5 (22 / 56)
07:25:58.819 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-008.counts.hdf5 (23 / 56)
07:25:59.013 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-009.counts.hdf5 (24 / 56)
07:25:59.205 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-010.counts.hdf5 (25 / 56)
07:25:59.398 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-011.counts.hdf5 (26 / 56)
07:25:59.590 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-162.counts.hdf5 (27 / 56)
07:25:59.827 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-163.counts.hdf5 (28 / 56)
07:26:00.020 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-164.counts.hdf5 (29 / 56)
07:26:00.215 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-165.counts.hdf5 (30 / 56)
07:26:00.408 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210124.counts.hdf5 (31 / 56)
07:26:00.601 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210126.counts.hdf5 (32 / 56)
07:26:00.796 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200621.counts.hdf5 (33 / 56)
07:26:00.989 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210128.counts.hdf5 (34 / 56)
07:26:01.292 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210130.counts.hdf5 (35 / 56)
07:26:01.632 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210121.counts.hdf5 (36 / 56)
07:26:01.987 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210122.counts.hdf5 (37 / 56)
07:26:02.200 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210123.counts.hdf5 (38 / 56)
07:26:02.401 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200272.counts.hdf5 (39 / 56)
07:26:02.596 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200273.counts.hdf5 (40 / 56)
07:26:02.794 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200274.counts.hdf5 (41 / 56)
07:26:02.987 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-001.counts.hdf5 (42 / 56)
07:26:03.180 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-002.counts.hdf5 (43 / 56)
07:26:03.372 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-003.counts.hdf5 (44 / 56)
07:26:03.565 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210118.counts.hdf5 (45 / 56)
07:26:03.808 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210119.counts.hdf5 (46 / 56)
07:26:04.003 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210120.counts.hdf5 (47 / 56)
07:26:04.270 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210100.counts.hdf5 (48 / 56)
07:26:04.466 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210102.counts.hdf5 (49 / 56)
07:26:04.662 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200635.counts.hdf5 (50 / 56)
07:26:04.856 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200637.counts.hdf5 (51 / 56)
07:26:05.053 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200639.counts.hdf5 (52 / 56)
07:26:05.249 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200643.counts.hdf5 (53 / 56)
07:26:05.444 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-021A.counts.hdf5 (54 / 56)
07:26:05.639 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-022.counts.hdf5 (55 / 56)
07:26:05.871 INFO GermlineCNVCaller - Aggregating read-count file /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-023A.counts.hdf5 (56 / 56)
07:26:06.225 DEBUG ScriptExecutor - Executing:
07:26:06.225 DEBUG ScriptExecutor - python
07:26:06.225 DEBUG ScriptExecutor - /tmp/case_denoising_calling.8735340376098836158.py
07:26:06.225 DEBUG ScriptExecutor - --ploidy_calls_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_case_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls
07:26:06.225 DEBUG ScriptExecutor - --output_calls_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_cases/iGT359V1_gCNV_cases_50_samples_20220304-calls
07:26:06.225 DEBUG ScriptExecutor - --output_tracking_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_cases/iGT359V1_gCNV_cases_50_samples_20220304-tracking
07:26:06.225 DEBUG ScriptExecutor - --input_model_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_model/iGT359V1_gCNV_normal_cohort-model
07:26:06.225 DEBUG ScriptExecutor - --random_seed=1984
07:26:06.225 DEBUG ScriptExecutor - --read_count_tsv_files
07:26:06.225 DEBUG ScriptExecutor - /tmp/PID21-004.rc3996697127159866848.tsv
07:26:06.225 DEBUG ScriptExecutor - /tmp/PID21-005.rc7520787016139858398.tsv
07:26:06.225 DEBUG ScriptExecutor - /tmp/PID14-380.rc3104612651214575789.tsv
07:26:06.225 DEBUG ScriptExecutor - /tmp/PID14-381.rc6284205699540441810.tsv
07:26:06.225 DEBUG ScriptExecutor - /tmp/PID14-382.rc2973421163991127772.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID16-080.rc4239652385810617246.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID16-081.rc1570300436350134132.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID20-210.rc2585559186618697230.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A170421.rc9092285691624527858.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A170420.rc4457142199329059972.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200628.rc9150974667487554512.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210104.rc2854444899169729178.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210105.rc1019993820445163021.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-172.rc6818770588266119792.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-173.rc7325613598693747038.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-174.rc8459721115893902396.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID20-220.rc9001133265837296431.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-166.rc7563510147985822311.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-167.rc5367453135596286383.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-168.rc2191548041571063666.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-006.rc3440355566996881403.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-007.rc8415064663361381824.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-008.rc8770259091503004957.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-009.rc6245844112743104623.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-010.rc1435663504309056972.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-011.rc7776947346205230307.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-162.rc2867960590379954299.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-163.rc27230547529843574.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-164.rc7007394060982834343.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-165.rc7377586808496616964.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210124.rc7038080625775639732.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210126.rc2907751843360593857.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200621.rc3086182244328727928.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210128.rc9096310227854677387.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210130.rc5236596488700408908.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210121.rc4871634831842774491.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210122.rc5836664007837450144.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210123.rc5963123395737213802.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200272.rc9080921714240172454.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200273.rc3147803468416761695.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200274.rc7854534776612874486.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-001.rc3658668801427587413.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-002.rc2934132621338329904.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-003.rc4532057093596522573.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210118.rc2090207010852485132.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210119.rc1108093825263220878.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210120.rc8900363106472362107.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210100.rc4878952060509326458.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A210102.rc4227625202848691193.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200635.rc6323134288287897533.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200637.rc3682383574246396592.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200639.rc1791725154336064971.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/A200643.rc1410016065850846152.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-021A.rc811870475304660266.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-022.rc8696575780108937791.tsv
07:26:06.226 DEBUG ScriptExecutor - /tmp/PID21-023A.rc5268666594846066657.tsv
07:26:06.226 DEBUG ScriptExecutor - --psi_s_scale=1.000000e-02
07:26:06.226 DEBUG ScriptExecutor - --mapping_error_rate=1.000000e-02
07:26:06.226 DEBUG ScriptExecutor - --depth_correction_tau=1.000000e+04
07:26:06.226 DEBUG ScriptExecutor - --q_c_expectation_mode=hybrid
07:26:06.227 DEBUG ScriptExecutor - --num_samples_copy_ratio_approx=200
07:26:06.227 DEBUG ScriptExecutor - --p_alt=5.000000e-04
07:26:06.227 DEBUG ScriptExecutor - --cnv_coherence_length=1.000000e+03
07:26:06.227 DEBUG ScriptExecutor - --max_copy_number=5
07:26:06.227 DEBUG ScriptExecutor - --learning_rate=5.000000e-02
07:26:06.227 DEBUG ScriptExecutor - --adamax_beta1=9.000000e-01
07:26:06.227 DEBUG ScriptExecutor - --adamax_beta2=9.900000e-01
07:26:06.227 DEBUG ScriptExecutor - --log_emission_samples_per_round=50
07:26:06.227 DEBUG ScriptExecutor - --log_emission_sampling_rounds=10
07:26:06.227 DEBUG ScriptExecutor - --log_emission_sampling_median_rel_error=5.000000e-03
07:26:06.227 DEBUG ScriptExecutor - --max_advi_iter_first_epoch=5000
07:26:06.227 DEBUG ScriptExecutor - --max_advi_iter_subsequent_epochs=100
07:26:06.227 DEBUG ScriptExecutor - --min_training_epochs=10
07:26:06.227 DEBUG ScriptExecutor - --max_training_epochs=100
07:26:06.227 DEBUG ScriptExecutor - --initial_temperature=2.000000e+00
07:26:06.227 DEBUG ScriptExecutor - --num_thermal_advi_iters=2500
07:26:06.227 DEBUG ScriptExecutor - --convergence_snr_averaging_window=500
07:26:06.227 DEBUG ScriptExecutor - --convergence_snr_trigger_threshold=1.000000e-01
07:26:06.227 DEBUG ScriptExecutor - --convergence_snr_countdown_window=10
07:26:06.227 DEBUG ScriptExecutor - --max_calling_iters=10
07:26:06.227 DEBUG ScriptExecutor - --caller_update_convergence_threshold=1.000000e-03
07:26:06.227 DEBUG ScriptExecutor - --caller_internal_admixing_rate=7.500000e-01
07:26:06.227 DEBUG ScriptExecutor - --caller_external_admixing_rate=1.000000e+00
07:26:06.227 DEBUG ScriptExecutor - --disable_caller=false
07:26:06.227 DEBUG ScriptExecutor - --disable_sampler=false
07:26:06.227 DEBUG ScriptExecutor - --disable_annealing=false
15:26:14.881 INFO case_denoising_calling - THEANO_FLAGS environment variable has been set to: device=cpu,floatX=float64,optimizer=fast_run,compute_test_value=ignore,openmp=true,blas.ldflags=-lmkl_rt,openmp_elemwise_minsize=10
15:26:14.907 INFO root - Loading modeling interval list from the provided model...
15:26:16.102 INFO gcnvkernel.io.io_intervals_and_counts - The given interval list provides the following interval annotations: {'GC_CONTENT'}
15:26:17.045 INFO root - The model contains 216085 intervals and 24 contig(s)
15:26:17.045 INFO root - Loading 56 read counts file(s)...
15:26:38.238 INFO gcnvkernel.io.io_metadata - Loading germline contig ploidy and global read depth metadata...
15:26:38.331 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr16. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:26:38.331 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr17. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:26:38.331 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr19. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:26:38.331 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr20. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:26:38.331 WARNING gcnvkernel.structs.metadata - Sample PID21-001 has an anomalous ploidy (3) for contig chr22. The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
15:26:38.436 INFO root - Loading denoising model configuration from the provided model...
15:26:38.437 INFO root - - bias factors enabled: True
15:26:38.437 INFO root - - explicit GC bias modeling enabled: True
15:26:38.437 INFO root - - bias factors in active classes disabled: False
15:26:38.437 INFO root - - maximum number of bias factors: 6
15:26:38.437 INFO root - - number of GC curve knobs: 20
15:26:38.437 INFO root - - GC curve prior standard deviation: 1.0
Traceback (most recent call last):
File "/tmp/case_denoising_calling.8735340376098836158.py", line 194, in <module>
n_st, sample_names, sample_metadata_collection)
File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/gcnvkernel/models/model_denoising_calling.py", line 389, in __init__
sample_metadata_collection, sample_names, self.contig_list)
File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/gcnvkernel/models/model_denoising_calling.py", line 633, in _get_baseline_copy_number_and_read_depth
"Some samples do not have read depth metadata"
AssertionError: Some samples do not have read depth metadata
07:26:40.151 INFO GermlineCNVCaller - Shutting down engine
[February 14, 2023 7:26:40 AM GMT] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 0.98 minutes.
Runtime.totalMemory()=4362076160
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python /tmp/case_denoising_calling.8735340376098836158.py --ploidy_calls_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_case_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls --output_calls_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_cases/iGT359V1_gCNV_cases_50_samples_20220304-calls --output_tracking_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_cases/iGT359V1_gCNV_cases_50_samples_20220304-tracking --input_model_path=/paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_model/iGT359V1_gCNV_normal_cohort-model --random_seed=1984 --read_count_tsv_files /tmp/PID21-004.rc3996697127159866848.tsv /tmp/PID21-005.rc7520787016139858398.tsv /tmp/PID14-380.rc3104612651214575789.tsv /tmp/PID14-381.rc6284205699540441810.tsv /tmp/PID14-382.rc2973421163991127772.tsv /tmp/PID16-080.rc4239652385810617246.tsv /tmp/PID16-081.rc1570300436350134132.tsv /tmp/PID20-210.rc2585559186618697230.tsv /tmp/A170421.rc9092285691624527858.tsv /tmp/A170420.rc4457142199329059972.tsv /tmp/A200628.rc9150974667487554512.tsv /tmp/A210104.rc2854444899169729178.tsv /tmp/A210105.rc1019993820445163021.tsv /tmp/PID21-172.rc6818770588266119792.tsv /tmp/PID21-173.rc7325613598693747038.tsv /tmp/PID21-174.rc8459721115893902396.tsv /tmp/PID20-220.rc9001133265837296431.tsv /tmp/PID21-166.rc7563510147985822311.tsv /tmp/PID21-167.rc5367453135596286383.tsv /tmp/PID21-168.rc2191548041571063666.tsv /tmp/PID21-006.rc3440355566996881403.tsv /tmp/PID21-007.rc8415064663361381824.tsv /tmp/PID21-008.rc8770259091503004957.tsv /tmp/PID21-009.rc6245844112743104623.tsv /tmp/PID21-010.rc1435663504309056972.tsv /tmp/PID21-011.rc7776947346205230307.tsv /tmp/PID21-162.rc2867960590379954299.tsv /tmp/PID21-163.rc27230547529843574.tsv /tmp/PID21-164.rc7007394060982834343.tsv /tmp/PID21-165.rc7377586808496616964.tsv /tmp/A210124.rc7038080625775639732.tsv /tmp/A210126.rc2907751843360593857.tsv /tmp/A200621.rc3086182244328727928.tsv /tmp/A210128.rc9096310227854677387.tsv /tmp/A210130.rc5236596488700408908.tsv /tmp/A210121.rc4871634831842774491.tsv /tmp/A210122.rc5836664007837450144.tsv /tmp/A210123.rc5963123395737213802.tsv /tmp/A200272.rc9080921714240172454.tsv /tmp/A200273.rc3147803468416761695.tsv /tmp/A200274.rc7854534776612874486.tsv /tmp/PID21-001.rc3658668801427587413.tsv /tmp/PID21-002.rc2934132621338329904.tsv /tmp/PID21-003.rc4532057093596522573.tsv /tmp/A210118.rc2090207010852485132.tsv /tmp/A210119.rc1108093825263220878.tsv /tmp/A210120.rc8900363106472362107.tsv /tmp/A210100.rc4878952060509326458.tsv /tmp/A210102.rc4227625202848691193.tsv /tmp/A200635.rc6323134288287897533.tsv /tmp/A200637.rc3682383574246396592.tsv /tmp/A200639.rc1791725154336064971.tsv /tmp/A200643.rc1410016065850846152.tsv /tmp/PID21-021A.rc811870475304660266.tsv /tmp/PID21-022.rc8696575780108937791.tsv /tmp/PID21-023A.rc5268666594846066657.tsv --psi_s_scale=1.000000e-02 --mapping_error_rate=1.000000e-02 --depth_correction_tau=1.000000e+04 --q_c_expectation_mode=hybrid --num_samples_copy_ratio_approx=200 --p_alt=5.000000e-04 --cnv_coherence_length=1.000000e+03 --max_copy_number=5 --learning_rate=5.000000e-02 --adamax_beta1=9.000000e-01 --adamax_beta2=9.900000e-01 --log_emission_samples_per_round=50 --log_emission_sampling_rounds=10 --log_emission_sampling_median_rel_error=5.000000e-03 --max_advi_iter_first_epoch=5000 --max_advi_iter_subsequent_epochs=100 --min_training_epochs=10 --max_training_epochs=100 --initial_temperature=2.000000e+00 --num_thermal_advi_iters=2500 --convergence_snr_averaging_window=500 --convergence_snr_trigger_threshold=1.000000e-01 --convergence_snr_countdown_window=10 --max_calling_iters=10 --caller_update_convergence_threshold=1.000000e-03 --caller_internal_admixing_rate=7.500000e-01 --caller_external_admixing_rate=1.000000e+00 --disable_caller=false --disable_sampler=false --disable_annealing=false
at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:351)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Xmx40G -XX:+UseParallelOldGC -XX:+UseAdaptiveSizePolicy -XX:ActiveProcessorCount=4 -XX:ParallelGCThreads=4 -jar /gatk/gatk-package-4.3.0.0-local.jar GermlineCNVCaller --run-mode CASE --model /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_model/iGT359V1_gCNV_normal_cohort-model --contig-ploidy-calls /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_case_ploidy/iGT359V1_cases_ploidy_50_samples_20220304-calls --verbosity DEBUG -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-004.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-005.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-380.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-381.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID14-382.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-080.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID16-081.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-210.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170421.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A170420.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200628.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210104.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210105.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-172.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-173.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-174.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID20-220.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-166.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-167.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-168.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-006.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-007.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-008.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-009.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-010.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-011.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-162.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-163.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-164.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-165.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210124.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210126.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200621.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210128.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210130.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210121.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210122.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210123.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200272.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200273.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200274.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-001.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-002.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-003.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210118.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210119.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210120.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210100.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A210102.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200635.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200637.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200639.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/A200643.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-021A.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-022.counts.hdf5 -I /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/PID21-023A.counts.hdf5 --output /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_gCNV_cases --output-prefix iGT359V1_gCNV_cases_50_samples_20220304 --p-alt 0.0005 --cnv-coherence-length 1000 --max-copy-number 5 --mapping-error-rate 0.01 --sample-psi-scale 0.01 --depth-correction-tau 10000 --learning-rate 0.05 --adamax-beta-1 0.9 --adamax-beta-2 0.99 --log-emission-samples-per-round 50 --log-emission-sampling-median-rel-error 0.005 --log-emission-sampling-rounds 10 --max-advi-iter-first-epoch 5000 --max-advi-iter-subsequent-epochs 100 --min-training-epochs 10 --max-training-epochs 100 --initial-temperature 2.0 --num-thermal-advi-iters 2500 --convergence-snr-averaging-window 500 --convergence-snr-trigger-threshold 0.1 --convergence-snr-countdown-window 10 --max-calling-iters 10 --caller-update-convergence-threshold 0.001 --caller-internal-admixing-rate 0.75 --caller-external-admixing-rate 1.0 --active-class-padding-hybrid-mode 5000
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I am also having the exact same error. Were you ever able to figure it out? Xscrapert
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Hi Xscrapert,
I apologize for the late response. It looks like in your DetermineContigPloidy command you set path to /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy and as ploidy input GermlineCNVCaller takes /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_case_ploidy - note the difference in the directory spelling.
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