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/4d/920dc830638321c2f996bdc03493ee/.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/4d/920dc830638321c2f996bdc03493ee/.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% @chr21:14593913, elapsed 0.8s, est remaining 15.9s, peak mem 287MB, user 6.3s, sys 0.2s, output queue size 41
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progress 95% @chr21:46324129, elapsed 24.6s, est remaining 1.3s, peak mem 1958MB, user 192.7s, sys 3.1s, output queue size 15
progress 100% @chr21:46558123, elapsed 25.9s, est remaining 0.0s, peak mem 1958MB, user 200.0s, sys 3.1s, output queue size 19
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 11.046 user 0.194 sys 11.311 real
"assemble_addRead": 405 calls 0.376 user 0.040 sys 0.346 real
"assemble_buildGraph": 944 calls 5.615 user 0.031 sys 5.752 real
"assemble_computecigar": 561 calls 0.303 user 0.046 sys 0.366 real
"assemble_kg_build_calcsize": 944 calls 3.178 user 0.000 sys 3.209 real
"assemble_kg_build_clear": 1284 calls 0.552 user 0.001 sys 0.636 real
"assemble_kg_build_prepare": 1888 calls 3.082 user 0.130 sys 3.260 real
"assemble_kg_build_threading": 604 calls 2.217 user 0.031 sys 2.257 real
"assemble_kg_op1": 604 calls 1.204 user 0.012 sys 1.243 real
"assemble_kg_op2": 604 calls 0.010 user 0.000 sys 0.018 real
"assemble_kg_op3": 604 calls 0.030 user 0.000 sys 0.016 real
"assemble_sg_clean": 561 calls 0.165 user 0.010 sys 0.120 real
"assemble_sg_create": 561 calls 0.100 user 0.000 sys 0.105 real
"checkGraph": 405 calls 0.000 user 0.000 sys 0.003 real
"findHaplotype": 405 calls 0.333 user 0.047 sys 0.409 real
advance: 2074 calls 43.348 user 1.714 sys 45.290 real
assemble_region: 405 calls 11.755 user 0.281 sys 12.078 real
build_pileup: 1976 calls 0.533 user 0.000 sys 0.466 real
build_stats: 2008 calls 9.822 user 0.363 sys 10.181 real
build_variants: 297 calls 0.020 user 0.000 sys 0.006 real
calc: 3928 calls 5.794 user 0.002 sys 5.814 real
calc_region: 297 calls 104.015 user 0.366 sys 105.337 real
call_region: 297 calls 2.060 user 0.040 sys 2.124 real
clip_region: 702 calls 1.242 user 0.020 sys 1.328 real
done: 1 calls 1.842 user 0.001 sys 1.849 real
execute: 1 calls 0.006 user 0.002 sys 25.891 real
fetch: 8147 calls 13.992 user 0.162 sys 14.101 real
fetch_ref: 8606 calls 0.037 user 0.015 sys 0.071 real
fetch_region: 405 calls 0.402 user 0.000 sys 0.492 real
fetch_vcf: 2074 calls 0.786 user 0.030 sys 0.885 real
idle: 48 calls 0.062 user 0.000 sys 25.847 real
init: 1 calls 0.070 user 0.010 sys 0.085 real
pairhmm: 24353 calls 193.151 user 0.461 sys 194.090 real
realign: 297 calls 11.504 user 0.014 sys 12.195 real
region: 4053 calls 116.658 user 0.668 sys 118.479 real
tracker: 4053 calls 0.010 user 0.000 sys 0.029 real
trim_region: 405 calls 0.030 user 0.000 sys 0.009 real
overall: 2053885952 mem 307.840 user 3.539 sys 28.309 real