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/77/af1377d933589826e521e86a718ee3/.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-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_HUS-N1-BDNA-1_A23FG3YLT4_1/869_HUS-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_HUS-N1-BDNA-1_A23FG3YLT4_1/869_HUS-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
  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-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/77/af1377d933589826e521e86a718ee3/.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_HUS-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_HUS-N1-BDNA-1_A23FG3YLT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 869_HUS-N1-BDNA-1_A23FG3YLT4_1 869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 869_HUS-N1-BDNA-1_A23FG3YLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments 869_HUS-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 9.7s, est remaining 184.8s, peak mem 629MB, user 95.2s, sys 1.6s, output queue size 28
progress 10% @chr2:3847054, elapsed 20.9s, est remaining 188.5s, peak mem 743MB, user 199.0s, sys 2.9s, output queue size 451
progress 15% @chr2:178598406, elapsed 33.7s, est remaining 190.7s, peak mem 750MB, user 311.0s, sys 4.5s, output queue size 12
progress 20% @chr3:57501221, elapsed 45.1s, est remaining 180.3s, peak mem 754MB, user 423.6s, sys 6.1s, output queue size 53
progress 25% @chr4:70704837, elapsed 57.5s, est remaining 172.5s, peak mem 803MB, user 535.4s, sys 7.6s, output queue size 298
progress 30% @chr5:135880673, elapsed 66.3s, est remaining 154.7s, peak mem 803MB, user 619.6s, sys 9.3s, output queue size 277
progress 35% @chr6:87254550, elapsed 92.5s, est remaining 171.8s, peak mem 833MB, user 855.4s, sys 11.4s, output queue size 541
progress 40% @chr7:107195734, elapsed 108.0s, est remaining 162.0s, peak mem 849MB, user 984.3s, sys 13.4s, output queue size 550
progress 45% @chr8:143812717, elapsed 124.1s, est remaining 151.6s, peak mem 867MB, user 1128.7s, sys 15.7s, output queue size 22
progress 50% @chr10:21732799, elapsed 139.6s, est remaining 139.6s, peak mem 880MB, user 1264.6s, sys 17.1s, output queue size 28
progress 55% @chr11:34143345, elapsed 153.5s, est remaining 125.6s, peak mem 889MB, user 1385.0s, sys 18.5s, output queue size 186
progress 60% @chr12:14480903, elapsed 167.6s, est remaining 111.7s, peak mem 899MB, user 1516.0s, sys 20.1s, output queue size 157
progress 65% @chr13:32231079, elapsed 179.5s, est remaining 96.6s, peak mem 899MB, user 1629.2s, sys 21.7s, output queue size 195
progress 70% @chr15:37947556, elapsed 189.1s, est remaining 81.1s, peak mem 906MB, user 1723.9s, sys 23.2s, output queue size 302
progress 75% @chr16:28062976, elapsed 204.9s, est remaining 68.3s, peak mem 926MB, user 1873.4s, sys 24.8s, output queue size 139
progress 80% @chr17:40126104, elapsed 217.9s, est remaining 54.5s, peak mem 926MB, user 1997.7s, sys 26.5s, output queue size 153
progress 85% @chr19:1652201, elapsed 230.2s, est remaining 40.6s, peak mem 926MB, user 2118.7s, sys 28.1s, output queue size 35
progress 90% @chr19:54665715, elapsed 245.6s, est remaining 27.3s, peak mem 933MB, user 2253.2s, sys 29.9s, output queue size 20
progress 95% @chr22:32152462, elapsed 260.2s, est remaining 13.7s, peak mem 942MB, user 2398.8s, sys 32.0s, output queue size 67
progress 100% @chrY:25622343, elapsed 271.6s, est remaining 0.0s, peak mem 942MB, user 2515.6s, sys 34.1s, output queue size 30
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: 19739590996
output file size: 2985219
reads: 250527529
contig: 178193 intervals 76355618 bases
"assemble": 20120 calls 122.289 user 0.726 sys 125.049 real
"assemble_addRead": 20120 calls 2.860 user 0.004 sys 3.169 real
"assemble_buildGraph": 44684 calls 55.689 user 0.293 sys 57.374 real
"assemble_computecigar": 29059 calls 8.338 user 0.047 sys 8.450 real
"assemble_kg_build_calcsize": 44684 calls 29.882 user 0.096 sys 30.991 real
"assemble_kg_build_clear": 59702 calls 4.383 user 0.026 sys 4.712 real
"assemble_kg_build_prepare": 89368 calls 32.276 user 0.219 sys 33.347 real
"assemble_kg_build_threading": 29666 calls 23.845 user 0.120 sys 24.221 real
"assemble_kg_op1": 29666 calls 16.035 user 0.093 sys 15.903 real
"assemble_kg_op2": 29666 calls 0.422 user 0.007 sys 0.511 real
"assemble_kg_op3": 29666 calls 0.618 user 0.000 sys 0.609 real
"assemble_sg_clean": 29059 calls 2.766 user 0.008 sys 2.701 real
"assemble_sg_create": 29059 calls 4.124 user 0.016 sys 4.187 real
"checkGraph": 20120 calls 0.059 user 0.001 sys 0.065 real
"findHaplotype": 20120 calls 9.001 user 0.047 sys 9.148 real
advance: 189104 calls 819.798 user 13.692 sys 833.853 real
assemble_region: 20120 calls 134.453 user 0.788 sys 137.668 real
build_pileup: 186587 calls 6.423 user 0.034 sys 6.968 real
build_stats: 187515 calls 229.062 user 1.383 sys 239.935 real
build_variants: 16402 calls 0.133 user 0.000 sys 0.123 real
calc: 364324 calls 121.594 user 0.525 sys 131.524 real
calc_region: 16402 calls 649.313 user 1.722 sys 673.465 real
call_region: 16402 calls 13.064 user 0.078 sys 13.533 real
clip_region: 36522 calls 11.750 user 0.069 sys 12.222 real
done: 1 calls 23.911 user 0.101 sys 24.020 real
execute: 1 calls 0.006 user 0.000 sys 271.650 real
fetch: 743546 calls 203.594 user 0.933 sys 214.894 real
fetch_ref: 765625 calls 27.276 user 1.439 sys 6.295 real
fetch_region: 20120 calls 3.849 user 0.014 sys 3.926 real
fetch_vcf: 189104 calls 55.677 user 1.542 sys 61.049 real
idle: 323 calls 0.052 user 0.005 sys 301.305 real
init: 1 calls 0.054 user 0.009 sys 0.069 real
pairhmm: 155387 calls 1145.359 user 2.691 sys 1156.318 real
realign: 16402 calls 116.133 user 0.236 sys 133.062 real
region: 367297 calls 792.765 user 2.609 sys 820.792 real
tracker: 367297 calls 1.177 user 0.057 sys 1.376 real
trim_region: 20120 calls 0.190 user 0.001 sys 0.273 real
overall: 1098711040 mem 3231.279 user 38.976 sys 297.247 real