Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/666218fbd7a74662096aba02954c8f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_XTN-N1-BDNA-1_A23FG3YLT4_1/869_XTN-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_XTN-N1-BDNA-1_A23FG3YLT4_1/869_XTN-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/666218fbd7a74662096aba02954c8f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (12 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i 869_XTN-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --algo TNhaplotyper2 --tumor_sample 869_XTN-N1-BDNA-1_A23FG3YLT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 869_XTN-N1-BDNA-1_A23FG3YLT4_1 869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 869_XTN-N1-BDNA-1_A23FG3YLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments 869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113724659, elapsed 11.6s, est remaining 220.4s, peak mem 636MB, user 116.1s, sys 2.7s, output queue size 51
progress 10% @chr2:3580010, elapsed 23.8s, est remaining 214.0s, peak mem 728MB, user 230.0s, sys 4.4s, output queue size 10
progress 15% @chr2:178606921, elapsed 37.1s, est remaining 210.5s, peak mem 728MB, user 348.7s, sys 6.1s, output queue size 12
progress 20% @chr3:57503916, elapsed 49.5s, est remaining 198.1s, peak mem 728MB, user 468.9s, sys 7.5s, output queue size 54
progress 25% @chr4:70666327, elapsed 62.3s, est remaining 187.0s, peak mem 760MB, user 575.7s, sys 9.2s, output queue size 44
progress 30% @chr5:135879868, elapsed 71.2s, est remaining 166.2s, peak mem 760MB, user 662.2s, sys 10.7s, output queue size 277
progress 35% @chr6:105376025, elapsed 90.5s, est remaining 168.0s, peak mem 761MB, user 840.4s, sys 12.2s, output queue size 560
progress 40% @chr7:107195734, elapsed 105.3s, est remaining 157.9s, peak mem 789MB, user 968.8s, sys 14.1s, output queue size 550
progress 45% @chr8:143725821, elapsed 121.1s, est remaining 148.1s, peak mem 820MB, user 1115.8s, sys 15.9s, output queue size 47
progress 50% @chr10:21766161, elapsed 135.9s, est remaining 135.9s, peak mem 832MB, user 1249.3s, sys 17.5s, output queue size 21
progress 55% @chr11:34154601, elapsed 150.8s, est remaining 123.4s, peak mem 859MB, user 1370.4s, sys 19.1s, output queue size 187
progress 60% @chr12:14621905, elapsed 164.2s, est remaining 109.5s, peak mem 859MB, user 1493.6s, sys 20.5s, output queue size 176
progress 65% @chr13:25096099, elapsed 175.8s, est remaining 94.6s, peak mem 859MB, user 1602.0s, sys 21.6s, output queue size 372
progress 70% @chr15:37966525, elapsed 186.0s, est remaining 79.7s, peak mem 861MB, user 1696.3s, sys 23.2s, output queue size 299
progress 75% @chr16:28506681, elapsed 199.2s, est remaining 66.4s, peak mem 896MB, user 1830.6s, sys 24.6s, output queue size 140
progress 80% @chr17:40032956, elapsed 210.5s, est remaining 52.6s, peak mem 896MB, user 1943.8s, sys 25.9s, output queue size 21
progress 85% @chr19:1821419, elapsed 221.3s, est remaining 39.0s, peak mem 896MB, user 2052.4s, sys 27.1s, output queue size 38
progress 90% @chr19:54738446, elapsed 234.3s, est remaining 26.0s, peak mem 906MB, user 2173.6s, sys 28.5s, output queue size 306
progress 95% @chr22:32202233, elapsed 245.6s, est remaining 12.9s, peak mem 930MB, user 2286.5s, sys 29.8s, output queue size 68
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 253.2s, est remaining 0.0s, peak mem 930MB, user 2361.6s, sys 31.0s, output queue size 7
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 19367974781
output file size: 2801979
reads: 248903661
contig: 178193 intervals 76355618 bases
"assemble": 18971 calls 108.940 user 0.494 sys 113.485 real
"assemble_addRead": 18971 calls 2.838 user 0.017 sys 2.877 real
"assemble_buildGraph": 42401 calls 49.604 user 0.170 sys 52.192 real
"assemble_computecigar": 27109 calls 7.993 user 0.045 sys 7.992 real
"assemble_kg_build_calcsize": 42401 calls 27.258 user 0.070 sys 28.362 real
"assemble_kg_build_clear": 57105 calls 3.757 user 0.025 sys 4.157 real
"assemble_kg_build_prepare": 84802 calls 29.428 user 0.125 sys 30.130 real
"assemble_kg_build_threading": 27697 calls 20.670 user 0.069 sys 21.858 real
"assemble_kg_op1": 27697 calls 13.599 user 0.073 sys 14.402 real
"assemble_kg_op2": 27697 calls 0.494 user 0.002 sys 0.478 real
"assemble_kg_op3": 27697 calls 0.538 user 0.014 sys 0.559 real
"assemble_sg_clean": 27109 calls 2.314 user 0.003 sys 2.539 real
"assemble_sg_create": 27109 calls 3.797 user 0.004 sys 3.897 real
"checkGraph": 18971 calls 0.047 user 0.000 sys 0.059 real
"findHaplotype": 18971 calls 8.547 user 0.045 sys 8.624 real
advance: 189104 calls 803.997 user 12.260 sys 815.964 real
assemble_region: 18971 calls 120.614 user 0.558 sys 125.257 real
build_pileup: 186576 calls 6.212 user 0.054 sys 6.612 real
build_stats: 187500 calls 220.088 user 1.107 sys 232.476 real
build_variants: 15304 calls 0.080 user 0.000 sys 0.114 real
calc: 364343 calls 118.524 user 0.480 sys 127.445 real
calc_region: 15304 calls 555.822 user 1.367 sys 579.457 real
call_region: 15304 calls 11.544 user 0.025 sys 12.025 real
clip_region: 34275 calls 10.659 user 0.054 sys 10.969 real
done: 1 calls 17.862 user 0.080 sys 17.947 real
execute: 1 calls 0.007 user 0.000 sys 253.249 real
fetch: 743546 calls 194.489 user 0.816 sys 204.732 real
fetch_ref: 764476 calls 26.444 user 1.229 sys 6.108 real
fetch_region: 18971 calls 3.350 user 0.002 sys 3.485 real
fetch_vcf: 189104 calls 54.274 user 1.465 sys 60.544 real
idle: 248 calls 0.058 user 0.002 sys 217.780 real
init: 1 calls 0.056 user 0.018 sys 0.078 real
pairhmm: 141375 calls 1000.930 user 1.751 sys 1009.134 real
realign: 15304 calls 108.362 user 0.271 sys 124.496 real
region: 367297 calls 684.610 user 2.066 sys 713.385 real
tracker: 367297 calls 1.094 user 0.067 sys 1.328 real
trim_region: 18971 calls 0.195 user 0.000 sys 0.260 real
overall: 1093935104 mem 3006.591 user 34.956 sys 271.720 real