Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/26d8ca4c41a45f2eb69d9415d7fc56/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  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_VZQ-N1-BDNA-1_A23FG3YLT4_1/869_VZQ-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/8a/26d8ca4c41a45f2eb69d9415d7fc56/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_VZQ-N1-BDNA-1_A23FG3YLT4_1/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
==> 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_VZQ-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_VZQ-N1-BDNA-1_A23FG3YLT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 869_VZQ-N1-BDNA-1_A23FG3YLT4_1 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 869_VZQ-N1-BDNA-1_A23FG3YLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113705733, elapsed 9.8s, est remaining 187.0s, peak mem 602MB, user 101.6s, sys 2.2s, output queue size 29
progress 10% @chr2:3679769, elapsed 24.9s, est remaining 223.9s, peak mem 739MB, user 233.7s, sys 4.2s, output queue size 59
progress 15% @chr2:178588438, elapsed 37.2s, est remaining 210.9s, peak mem 753MB, user 341.8s, sys 5.7s, output queue size 144
progress 20% @chr3:57503916, elapsed 49.1s, est remaining 196.3s, peak mem 771MB, user 453.1s, sys 7.3s, output queue size 53
progress 25% @chr4:70768438, elapsed 61.0s, est remaining 183.0s, peak mem 801MB, user 560.0s, sys 9.0s, output queue size 298
progress 30% @chr5:135879868, elapsed 69.6s, est remaining 162.3s, peak mem 801MB, user 642.4s, sys 10.8s, output queue size 276
progress 35% @chr6:105026198, elapsed 92.4s, est remaining 171.7s, peak mem 801MB, user 851.2s, sys 12.4s, output queue size 26
progress 40% @chr7:107661542, elapsed 109.8s, est remaining 164.8s, peak mem 813MB, user 988.2s, sys 14.3s, output queue size 582
progress 45% @chr8:143791566, elapsed 124.8s, est remaining 152.6s, peak mem 822MB, user 1135.9s, sys 16.1s, output queue size 14
progress 50% @chr10:21733404, elapsed 137.2s, est remaining 137.2s, peak mem 829MB, user 1254.4s, sys 17.6s, output queue size 58
progress 55% @chr11:34152287, elapsed 150.4s, est remaining 123.1s, peak mem 840MB, user 1367.7s, sys 19.1s, output queue size 187
progress 60% @chr12:14882039, elapsed 163.5s, est remaining 109.0s, peak mem 856MB, user 1485.1s, sys 20.7s, output queue size 215
progress 65% @chr13:32201841, elapsed 173.7s, est remaining 93.5s, peak mem 856MB, user 1592.6s, sys 22.0s, output queue size 169
progress 70% @chr15:37950936, elapsed 182.8s, est remaining 78.4s, peak mem 863MB, user 1680.8s, sys 23.5s, output queue size 302
progress 75% @chr16:28537919, elapsed 195.9s, est remaining 65.3s, peak mem 884MB, user 1811.7s, sys 25.1s, output queue size 139
progress 80% @chr17:40053198, elapsed 207.1s, est remaining 51.8s, peak mem 885MB, user 1923.3s, sys 26.6s, output queue size 20
progress 85% @chr19:1817607, elapsed 218.7s, est remaining 38.6s, peak mem 888MB, user 2036.2s, sys 28.2s, output queue size 35
progress 90% @chr19:54725147, elapsed 232.3s, est remaining 25.8s, peak mem 898MB, user 2163.1s, sys 29.8s, output queue size 20
progress 95% @chr22:32154144, elapsed 243.5s, est remaining 12.8s, peak mem 903MB, user 2274.4s, sys 31.1s, output queue size 68
progress 100% @chr6_GL000254v2_alt:3881605, elapsed 256.3s, est remaining 0.0s, peak mem 903MB, user 2391.9s, sys 32.5s, output queue size 19
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: 19049735503
output file size: 2932586
reads: 237599312
contig: 178193 intervals 76355618 bases
"assemble": 19662 calls 116.273 user 0.697 sys 119.755 real
"assemble_addRead": 19662 calls 2.818 user 0.026 sys 2.963 real
"assemble_buildGraph": 44029 calls 53.017 user 0.234 sys 54.918 real
"assemble_computecigar": 28441 calls 7.848 user 0.030 sys 7.901 real
"assemble_kg_build_calcsize": 44029 calls 28.273 user 0.113 sys 29.627 real
"assemble_kg_build_clear": 58940 calls 4.643 user 0.011 sys 4.427 real
"assemble_kg_build_prepare": 88058 calls 31.043 user 0.179 sys 31.516 real
"assemble_kg_build_threading": 29118 calls 22.512 user 0.097 sys 23.254 real
"assemble_kg_op1": 29118 calls 15.198 user 0.073 sys 15.436 real
"assemble_kg_op2": 29118 calls 0.471 user 0.013 sys 0.480 real
"assemble_kg_op3": 29118 calls 0.599 user 0.000 sys 0.590 real
"assemble_sg_clean": 28441 calls 2.439 user 0.000 sys 2.642 real
"assemble_sg_create": 28441 calls 3.926 user 0.025 sys 4.164 real
"checkGraph": 19662 calls 0.063 user 0.015 sys 0.063 real
"findHaplotype": 19662 calls 8.383 user 0.049 sys 8.526 real
advance: 189104 calls 794.032 user 12.658 sys 809.993 real
assemble_region: 19662 calls 127.781 user 0.786 sys 131.519 real
build_pileup: 186582 calls 6.147 user 0.056 sys 6.576 real
build_stats: 187321 calls 218.143 user 1.429 sys 229.705 real
build_variants: 15929 calls 0.076 user 0.000 sys 0.115 real
calc: 363943 calls 119.440 user 0.505 sys 128.151 real
calc_region: 15929 calls 592.796 user 1.395 sys 615.995 real
call_region: 15929 calls 11.879 user 0.048 sys 12.461 real
clip_region: 35591 calls 10.949 user 0.087 sys 11.162 real
done: 1 calls 17.383 user 0.095 sys 17.481 real
execute: 1 calls 0.000 user 0.006 sys 256.303 real
fetch: 743546 calls 191.016 user 0.990 sys 200.435 real
fetch_ref: 765167 calls 26.136 user 1.361 sys 6.132 real
fetch_region: 19662 calls 3.746 user 0.022 sys 3.593 real
fetch_vcf: 189104 calls 55.168 user 1.485 sys 61.390 real
idle: 239 calls 0.020 user 0.000 sys 217.060 real
init: 1 calls 0.042 user 0.018 sys 0.061 real
pairhmm: 138593 calls 1042.752 user 2.330 sys 1052.584 real
realign: 15929 calls 107.715 user 0.328 sys 123.157 real
region: 367297 calls 729.491 user 2.316 sys 756.419 real
tracker: 367297 calls 1.196 user 0.074 sys 1.369 real
trim_region: 19662 calls 0.209 user 0.000 sys 0.253 real
overall: 1053466624 mem 3041.455 user 37.364 sys 274.681 real