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/ac/95f87abad1129bcd32385bf2a66486/.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-outputs/cgp_runs/nextflow/daq/20260225_LH00527_0055_B23KYWJLT4__5d8e7d70--20260227-170008/alignments/recalibrated/NA12878_c_0002_gDNA_0005_B23KYWJLT4_1/NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.recalibrated.bam
  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-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/ac/95f87abad1129bcd32385bf2a66486/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260225_LH00527_0055_B23KYWJLT4__5d8e7d70--20260227-170008/alignments/recalibrated/NA12878_c_0002_gDNA_0005_B23KYWJLT4_1/NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.recalibrated.bam.bai
  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 NA12878_c_0002_gDNA_0005_B23KYWJLT4_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 NA12878_c_0002_gDNA_0005_B23KYWJLT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample NA12878_c_0002_gDNA_0005_B23KYWJLT4_1 NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample NA12878_c_0002_gDNA_0005_B23KYWJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq_tumor_only.segments NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113711646, elapsed 15.2s, est remaining 288.4s, peak mem 884MB, user 143.9s, sys 3.3s, output queue size 320
progress 10% @chr2:6849750, elapsed 32.3s, est remaining 290.6s, peak mem 956MB, user 290.5s, sys 5.1s, output queue size 454
progress 15% @chr2:178529860, elapsed 55.5s, est remaining 314.3s, peak mem 1183MB, user 487.8s, sys 7.7s, output queue size 145
progress 20% @chr3:57489409, elapsed 78.8s, est remaining 315.0s, peak mem 1183MB, user 693.8s, sys 10.3s, output queue size 53
progress 25% @chr4:70764375, elapsed 100.9s, est remaining 302.8s, peak mem 1183MB, user 877.8s, sys 12.2s, output queue size 298
progress 30% @chr5:135852463, elapsed 115.4s, est remaining 269.3s, peak mem 1183MB, user 1009.2s, sys 14.3s, output queue size 275
progress 35% @chr6:105377286, elapsed 157.0s, est remaining 291.6s, peak mem 1243MB, user 1362.9s, sys 16.8s, output queue size 560
progress 40% @chr7:107773820, elapsed 189.6s, est remaining 284.4s, peak mem 1243MB, user 1611.5s, sys 19.1s, output queue size 611
progress 45% @chr8:143838580, elapsed 219.5s, est remaining 268.3s, peak mem 1304MB, user 1899.0s, sys 21.4s, output queue size 740
progress 50% @chr10:20868564, elapsed 244.7s, est remaining 244.7s, peak mem 1355MB, user 2113.8s, sys 23.7s, output queue size 34
progress 55% @chr11:34154165, elapsed 265.6s, est remaining 217.3s, peak mem 1355MB, user 2289.2s, sys 25.7s, output queue size 187
progress 60% @chr12:11826019, elapsed 290.2s, est remaining 193.5s, peak mem 1355MB, user 2497.7s, sys 27.5s, output queue size 212
progress 65% @chr13:32231079, elapsed 309.4s, est remaining 166.6s, peak mem 1355MB, user 2683.1s, sys 29.5s, output queue size 195
progress 70% @chr15:38247737, elapsed 356.9s, est remaining 153.0s, peak mem 1399MB, user 3062.8s, sys 31.6s, output queue size 942
progress 75% @chr16:28591490, elapsed 379.6s, est remaining 126.5s, peak mem 1418MB, user 3315.3s, sys 33.6s, output queue size 140
progress 80% @chr17:40096343, elapsed 401.6s, est remaining 100.4s, peak mem 1442MB, user 3514.6s, sys 35.8s, output queue size 153
progress 85% @chr19:1820164, elapsed 425.8s, est remaining 75.1s, peak mem 1447MB, user 3726.7s, sys 38.0s, output queue size 83
progress 90% @chr19:54666594, elapsed 452.2s, est remaining 50.2s, peak mem 1476MB, user 3945.3s, sys 40.0s, output queue size 28
progress 95% @chr22:32202233, elapsed 476.5s, est remaining 25.1s, peak mem 1557MB, user 4162.6s, sys 42.3s, output queue size 67
progress 100% @chrX:156009716, elapsed 499.1s, est remaining 0.0s, peak mem 1557MB, user 4364.6s, sys 44.8s, output queue size 497
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 128
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 22577664247
output file size: 3095840
reads: 349291619
contig: 178193 intervals 76355618 bases
"assemble": 21510 calls 210.087 user 0.603 sys 212.852 real
"assemble_addRead": 21510 calls 6.408 user 0.020 sys 6.513 real
"assemble_buildGraph": 47668 calls 98.314 user 0.205 sys 99.552 real
"assemble_computecigar": 31548 calls 14.432 user 0.042 sys 14.316 real
"assemble_kg_build_calcsize": 47668 calls 50.779 user 0.060 sys 52.308 real
"assemble_kg_build_clear": 63019 calls 12.454 user 0.021 sys 11.883 real
"assemble_kg_build_prepare": 95336 calls 56.686 user 0.157 sys 57.640 real
"assemble_kg_build_threading": 32317 calls 42.066 user 0.066 sys 41.966 real
"assemble_kg_op1": 32317 calls 22.864 user 0.035 sys 23.530 real
"assemble_kg_op2": 32317 calls 0.741 user 0.028 sys 0.731 real
"assemble_kg_op3": 32317 calls 0.722 user 0.010 sys 0.846 real
"assemble_sg_clean": 31548 calls 4.059 user 0.020 sys 4.159 real
"assemble_sg_create": 31548 calls 6.266 user 0.029 sys 6.397 real
"checkGraph": 21510 calls 0.089 user 0.000 sys 0.098 real
"findHaplotype": 21510 calls 15.815 user 0.062 sys 15.736 real
advance: 189104 calls 1185.722 user 20.012 sys 1205.871 real
assemble_region: 21510 calls 232.731 user 0.695 sys 235.541 real
build_pileup: 186804 calls 14.302 user 0.055 sys 14.401 real
build_stats: 187521 calls 347.562 user 1.653 sys 363.053 real
build_variants: 17058 calls 0.160 user 0.000 sys 0.184 real
calc: 364308 calls 196.077 user 0.307 sys 207.136 real
calc_region: 17058 calls 1454.785 user 1.003 sys 1485.545 real
call_region: 17058 calls 29.185 user 0.041 sys 29.895 real
clip_region: 38568 calls 24.469 user 0.075 sys 25.114 real
done: 1 calls 21.910 user 0.218 sys 22.137 real
execute: 1 calls 0.005 user 0.001 sys 499.156 real
fetch: 743546 calls 415.914 user 0.951 sys 425.126 real
fetch_ref: 767015 calls 26.690 user 1.887 sys 6.830 real
fetch_region: 21510 calls 9.825 user 0.028 sys 10.116 real
fetch_vcf: 189104 calls 66.116 user 1.898 sys 71.785 real
idle: 314 calls 0.090 user 0.003 sys 277.572 real
init: 1 calls 0.049 user 0.010 sys 0.063 real
pairhmm: 279851 calls 2676.089 user 0.671 sys 2685.234 real
realign: 17058 calls 210.873 user 0.071 sys 229.010 real
region: 367297 calls 1709.118 user 1.890 sys 1743.571 real
tracker: 367297 calls 1.708 user 0.074 sys 1.974 real
trim_region: 21510 calls 0.438 user 0.000 sys 0.427 real
overall: 1688764416 mem 5933.520 user 49.248 sys 522.761 real