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-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_5BE-N1-BDNA-1_A237CFYLT3_1/1136_5BE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/f619691a5f9e8cb1e7f1ca6501ed13/.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_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_5BE-N1-BDNA-1_A237CFYLT3_1/1136_5BE-N1-BDNA-1_A237CFYLT3_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/02/f619691a5f9e8cb1e7f1ca6501ed13/.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 1136_5BE-N1-BDNA-1_A237CFYLT3_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 1136_5BE-N1-BDNA-1_A237CFYLT3_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 1136_5BE-N1-BDNA-1_A237CFYLT3_1 1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 1136_5BE-N1-BDNA-1_A237CFYLT3_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.segments 1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113704566, elapsed 12.7s, est remaining 242.2s, peak mem 735MB, user 120.1s, sys 1.9s, output queue size 29
progress 10% @chr2:3695617, elapsed 27.5s, est remaining 247.7s, peak mem 952MB, user 250.6s, sys 3.3s, output queue size 50
progress 15% @chr2:178598406, elapsed 46.2s, est remaining 261.9s, peak mem 998MB, user 400.8s, sys 4.7s, output queue size 12
progress 20% @chr3:57457621, elapsed 63.9s, est remaining 255.7s, peak mem 1019MB, user 559.4s, sys 5.9s, output queue size 53
progress 25% @chr4:70666327, elapsed 83.6s, est remaining 250.8s, peak mem 1083MB, user 718.8s, sys 7.3s, output queue size 46
progress 30% @chr5:135028679, elapsed 96.1s, est remaining 224.2s, peak mem 1083MB, user 827.5s, sys 8.8s, output queue size 277
progress 35% @chr6:105376025, elapsed 120.9s, est remaining 224.4s, peak mem 1083MB, user 1054.7s, sys 10.1s, output queue size 560
progress 40% @chr7:107683102, elapsed 147.9s, est remaining 221.9s, peak mem 1118MB, user 1253.4s, sys 11.6s, output queue size 589
progress 45% @chr8:143840606, elapsed 169.8s, est remaining 207.5s, peak mem 1167MB, user 1460.1s, sys 13.3s, output queue size 24
progress 50% @chr10:21739930, elapsed 192.0s, est remaining 192.0s, peak mem 1173MB, user 1642.1s, sys 15.0s, output queue size 30
progress 55% @chr11:34152287, elapsed 211.7s, est remaining 173.2s, peak mem 1190MB, user 1798.5s, sys 16.5s, output queue size 36
progress 60% @chr12:14788851, elapsed 233.2s, est remaining 155.5s, peak mem 1223MB, user 1978.8s, sys 17.9s, output queue size 198
progress 65% @chr13:32194043, elapsed 251.2s, est remaining 135.3s, peak mem 1237MB, user 2136.4s, sys 19.4s, output queue size 195
progress 70% @chr15:37966525, elapsed 267.2s, est remaining 114.5s, peak mem 1237MB, user 2277.3s, sys 20.8s, output queue size 299
progress 75% @chr16:28499551, elapsed 290.2s, est remaining 96.7s, peak mem 1286MB, user 2489.6s, sys 22.6s, output queue size 139
progress 80% @chr17:40094835, elapsed 310.9s, est remaining 77.7s, peak mem 1308MB, user 2673.7s, sys 24.1s, output queue size 153
progress 85% @chr19:1818382, elapsed 331.4s, est remaining 58.5s, peak mem 1308MB, user 2863.6s, sys 25.9s, output queue size 35
progress 90% @chr19:54665715, elapsed 356.4s, est remaining 39.6s, peak mem 1327MB, user 3073.5s, sys 27.6s, output queue size 18
progress 95% @chr22:32099083, elapsed 376.3s, est remaining 19.8s, peak mem 1340MB, user 3258.3s, sys 29.6s, output queue size 67
progress 100% @chrX:156009716, elapsed 398.6s, est remaining 0.0s, peak mem 1340MB, user 3457.3s, sys 31.4s, 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: 24372509455
output file size: 3862184
reads: 344921621
contig: 178193 intervals 76355618 bases
"assemble": 27148 calls 180.068 user 0.385 sys 183.941 real
"assemble_addRead": 27148 calls 5.344 user 0.001 sys 5.275 real
"assemble_buildGraph": 58818 calls 88.046 user 0.103 sys 90.187 real
"assemble_computecigar": 40925 calls 10.791 user 0.052 sys 10.932 real
"assemble_kg_build_calcsize": 58818 calls 43.180 user 0.015 sys 43.945 real
"assemble_kg_build_clear": 75672 calls 6.573 user 0.020 sys 6.511 real
"assemble_kg_build_prepare": 117636 calls 44.205 user 0.084 sys 45.457 real
"assemble_kg_build_threading": 41964 calls 42.414 user 0.046 sys 43.660 real
"assemble_kg_op1": 41964 calls 23.218 user 0.023 sys 23.828 real
"assemble_kg_op2": 41964 calls 0.650 user 0.000 sys 0.780 real
"assemble_kg_op3": 41964 calls 0.834 user 0.000 sys 0.873 real
"assemble_sg_clean": 40925 calls 3.994 user 0.002 sys 3.817 real
"assemble_sg_create": 40925 calls 5.827 user 0.013 sys 5.877 real
"checkGraph": 27148 calls 0.105 user 0.010 sys 0.091 real
"findHaplotype": 27148 calls 11.565 user 0.052 sys 11.846 real
advance: 189104 calls 1003.995 user 13.326 sys 1013.640 real
assemble_region: 27148 calls 197.389 user 0.480 sys 201.475 real
build_pileup: 186651 calls 8.852 user 0.056 sys 9.091 real
build_stats: 187403 calls 286.035 user 1.094 sys 299.876 real
build_variants: 22538 calls 0.089 user 0.000 sys 0.164 real
calc: 364153 calls 137.763 user 0.133 sys 148.330 real
calc_region: 22538 calls 1124.063 user 0.696 sys 1155.261 real
call_region: 22538 calls 23.134 user 0.029 sys 23.638 real
clip_region: 49686 calls 21.142 user 0.027 sys 21.778 real
done: 1 calls 31.784 user 0.128 sys 31.920 real
execute: 1 calls 0.004 user 0.001 sys 398.572 real
fetch: 743546 calls 282.772 user 0.477 sys 293.152 real
fetch_ref: 772653 calls 25.820 user 1.458 sys 6.464 real
fetch_region: 27148 calls 7.008 user 0.001 sys 7.236 real
fetch_vcf: 189104 calls 55.239 user 1.324 sys 60.011 real
idle: 420 calls 0.057 user 0.001 sys 396.788 real
init: 1 calls 0.047 user 0.010 sys 0.060 real
pairhmm: 301397 calls 2080.731 user 0.499 sys 2093.144 real
realign: 22538 calls 198.105 user 0.021 sys 222.306 real
region: 367297 calls 1338.136 user 1.308 sys 1374.203 real
tracker: 367297 calls 1.378 user 0.071 sys 1.483 real
trim_region: 27148 calls 0.322 user 0.040 sys 0.379 real
overall: 1641652224 mem 4750.301 user 34.834 sys 432.090 real