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/intervals/regression_padded_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21_padded100bp.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/PON/pon_tnseq_42_curated_v4.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-rnd-pltf-dev-nextflow-scratch-01/work/12/3ef8e729502d74ba9fecfdd38cd140/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.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-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/3ef8e729502d74ba9fecfdd38cd140/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
  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-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (14 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i Sig_18_Blood.recalibrated.bam -i Sig_18_tissue.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21_padded100bp.bed --algo TNhaplotyper2 --tumor_sample Sig_18_tissue --normal_sample Sig_18_Blood --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz custom_Sig_18_tumor_normal.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_tissue custom_Sig_18_tumor_normal.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample Sig_18_Blood --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments custom_Sig_18_tumor_normal.tnseq.segments custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14226759, elapsed 0.9s, est remaining 16.2s, peak mem 285MB, user 6.3s, sys 0.2s, output queue size 39
progress 10% @chr21:25592712, elapsed 1.5s, est remaining 13.6s, peak mem 344MB, user 11.1s, sys 0.3s, output queue size 18
progress 15% @chr21:28984592, elapsed 2.1s, est remaining 12.2s, peak mem 375MB, user 16.4s, sys 0.4s, output queue size 11
progress 20% @chr21:31038152, elapsed 2.6s, est remaining 10.3s, peak mem 406MB, user 20.2s, sys 0.5s, output queue size 16
progress 25% @chr21:32375298, elapsed 3.6s, est remaining 10.8s, peak mem 415MB, user 25.7s, sys 0.6s, output queue size 65
progress 30% @chr21:33352658, elapsed 4.1s, est remaining 9.5s, peak mem 420MB, user 30.2s, sys 0.7s, output queue size 24
progress 35% @chr21:33888052, elapsed 4.5s, est remaining 8.3s, peak mem 436MB, user 34.0s, sys 0.7s, output queue size 74
progress 40% @chr21:36244948, elapsed 9.2s, est remaining 13.8s, peak mem 795MB, user 47.2s, sys 0.8s, output queue size 63
progress 45% @chr21:37124519, elapsed 10.1s, est remaining 12.4s, peak mem 795MB, user 66.0s, sys 1.0s, output queue size 133
progress 50% @chr21:39232077, elapsed 10.6s, est remaining 10.6s, peak mem 853MB, user 75.5s, sys 1.1s, output queue size 46
progress 55% @chr21:41345586, elapsed 11.7s, est remaining 9.5s, peak mem 949MB, user 81.2s, sys 1.1s, output queue size 149
progress 60% @chr21:41490073, elapsed 19.0s, est remaining 12.7s, peak mem 1785MB, user 118.6s, sys 2.0s, output queue size 20
progress 65% @chr21:42375616, elapsed 20.7s, est remaining 11.2s, peak mem 1877MB, user 140.7s, sys 2.3s, output queue size 102
progress 70% @chr21:43092857, elapsed 21.6s, est remaining 9.3s, peak mem 1877MB, user 152.2s, sys 2.4s, output queue size 216
progress 75% @chr21:44122077, elapsed 21.9s, est remaining 7.3s, peak mem 1877MB, user 155.8s, sys 2.4s, output queue size 327
progress 80% @chr21:44233457, elapsed 22.5s, est remaining 5.6s, peak mem 1877MB, user 160.8s, sys 2.5s, output queue size 432
progress 85% @chr21:45267351, elapsed 23.6s, est remaining 4.2s, peak mem 1877MB, user 169.0s, sys 2.5s, output queue size 516
progress 90% @chr21:46111377, elapsed 24.3s, est remaining 2.7s, peak mem 1877MB, user 176.5s, sys 2.6s, output queue size 611
progress 95% @chr21:41501593, elapsed 25.0s, est remaining 1.3s, peak mem 1877MB, user 190.8s, sys 2.7s, output queue size 706
progress 100% @chr21:46661700, elapsed 26.2s, est remaining 0.0s, peak mem 1877MB, user 199.2s, sys 2.8s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 12 max 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 208827488 728301144
output file size: 95376
reads: 14812996
contig: 1979 intervals 801713 bases
"assemble": 405 calls 11.051 user 0.171 sys 11.290 real
"assemble_addRead": 405 calls 0.298 user 0.020 sys 0.358 real
"assemble_buildGraph": 944 calls 5.621 user 0.035 sys 5.753 real
"assemble_computecigar": 561 calls 0.305 user 0.010 sys 0.365 real
"assemble_kg_build_calcsize": 944 calls 3.145 user 0.010 sys 3.229 real
"assemble_kg_build_clear": 1284 calls 0.617 user 0.003 sys 0.611 real
"assemble_kg_build_prepare": 1888 calls 3.273 user 0.111 sys 3.245 real
"assemble_kg_build_threading": 604 calls 2.182 user 0.024 sys 2.253 real
"assemble_kg_op1": 604 calls 1.224 user 0.002 sys 1.250 real
"assemble_kg_op2": 604 calls 0.020 user 0.000 sys 0.018 real
"assemble_kg_op3": 604 calls 0.010 user 0.000 sys 0.016 real
"assemble_sg_clean": 561 calls 0.120 user 0.000 sys 0.119 real
"assemble_sg_create": 561 calls 0.120 user 0.000 sys 0.106 real
"checkGraph": 405 calls 0.000 user 0.000 sys 0.003 real
"findHaplotype": 405 calls 0.385 user 0.010 sys 0.403 real
advance: 2074 calls 43.821 user 1.582 sys 45.972 real
assemble_region: 405 calls 11.760 user 0.215 sys 12.062 real
build_pileup: 1976 calls 0.457 user 0.000 sys 0.467 real
build_stats: 2008 calls 10.178 user 0.239 sys 10.310 real
build_variants: 297 calls 0.010 user 0.000 sys 0.006 real
calc: 3928 calls 5.690 user 0.024 sys 5.970 real
calc_region: 297 calls 102.188 user 0.326 sys 103.326 real
call_region: 297 calls 2.011 user 0.020 sys 2.115 real
clip_region: 702 calls 1.460 user 0.010 sys 1.318 real
done: 1 calls 1.765 user 0.000 sys 1.773 real
execute: 1 calls 0.008 user 0.001 sys 26.188 real
fetch: 8147 calls 14.214 user 0.118 sys 14.023 real
fetch_ref: 8606 calls 0.085 user 0.022 sys 0.072 real
fetch_region: 405 calls 0.417 user 0.000 sys 0.491 real
fetch_vcf: 2074 calls 0.868 user 0.037 sys 0.902 real
idle: 56 calls 0.105 user 0.010 sys 26.014 real
init: 1 calls 0.070 user 0.010 sys 0.084 real
pairhmm: 24353 calls 195.236 user 0.662 sys 196.329 real
realign: 297 calls 11.606 user 0.042 sys 12.331 real
region: 4053 calls 114.862 user 0.541 sys 116.450 real
tracker: 4053 calls 0.010 user 0.000 sys 0.030 real
trim_region: 405 calls 0.010 user 0.000 sys 0.009 real
overall: 1968832512 mem 311.166 user 3.380 sys 28.549 real