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/a1/560470717ee1d02e81f587dcea9a63/.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/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed
  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/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/a1/560470717ee1d02e81f587dcea9a63/.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 (12 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i Sig_18_Blood.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample Sig_18_Blood --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz Sig_18_Blood.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample Sig_18_Blood Sig_18_Blood.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_Blood --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments Sig_18_Blood.tnseq_tumor_only.segments Sig_18_Blood.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14546105, elapsed 0.1s, est remaining 2.2s, peak mem 152MB, user 0.8s, sys 0.1s, output queue size 46
progress 10% @chr21:25709334, elapsed 0.2s, est remaining 1.9s, peak mem 165MB, user 1.6s, sys 0.1s, output queue size 106
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progress 100% @chr21:46334297, elapsed 3.9s, est remaining 0.0s, peak mem 466MB, user 31.1s, sys 0.8s, output queue size 91
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
output file size: 57860
reads: 2481283
contig: 1979 intervals 801713 bases
"assemble": 236 calls 1.536 user 0.042 sys 1.577 real
"assemble_addRead": 236 calls 0.040 user 0.000 sys 0.038 real
"assemble_buildGraph": 545 calls 0.681 user 0.001 sys 0.735 real
"assemble_computecigar": 331 calls 0.166 user 0.000 sys 0.165 real
"assemble_kg_build_calcsize": 545 calls 0.357 user 0.001 sys 0.406 real
"assemble_kg_build_clear": 752 calls 0.045 user 0.000 sys 0.056 real
"assemble_kg_build_prepare": 1090 calls 0.327 user 0.039 sys 0.403 real
"assemble_kg_build_threading": 338 calls 0.307 user 0.000 sys 0.300 real
"assemble_kg_op1": 338 calls 0.266 user 0.001 sys 0.206 real
"assemble_kg_op2": 338 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 338 calls 0.020 user 0.000 sys 0.008 real
"assemble_sg_clean": 331 calls 0.059 user 0.000 sys 0.044 real
"assemble_sg_create": 331 calls 0.055 user 0.000 sys 0.058 real
"checkGraph": 236 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 236 calls 0.176 user 0.000 sys 0.174 real
advance: 2074 calls 9.164 user 0.337 sys 9.738 real
assemble_region: 236 calls 1.752 user 0.042 sys 1.793 real
build_pileup: 1969 calls 0.010 user 0.000 sys 0.090 real
build_stats: 1999 calls 2.571 user 0.156 sys 2.760 real
build_variants: 195 calls 0.000 user 0.000 sys 0.002 real
calc: 3915 calls 1.488 user 0.012 sys 1.384 real
calc_region: 195 calls 10.037 user 0.053 sys 10.313 real
call_region: 195 calls 0.160 user 0.000 sys 0.177 real
clip_region: 431 calls 0.188 user 0.010 sys 0.136 real
done: 1 calls 0.722 user 0.000 sys 0.726 real
execute: 1 calls 0.002 user 0.000 sys 3.877 real
fetch: 8147 calls 2.140 user 0.031 sys 2.055 real
fetch_ref: 8437 calls 0.047 user 0.029 sys 0.064 real
fetch_region: 236 calls 0.035 user 0.000 sys 0.039 real
fetch_vcf: 2074 calls 0.994 user 0.012 sys 0.886 real
idle: 38 calls 0.060 user 0.000 sys 14.058 real
init: 1 calls 0.060 user 0.030 sys 0.081 real
pairhmm: 2129 calls 20.786 user 0.050 sys 20.916 real
realign: 195 calls 1.469 user 0.000 sys 1.642 real
region: 4053 calls 11.898 user 0.105 sys 12.211 real
tracker: 4053 calls 0.030 user 0.000 sys 0.019 real
trim_region: 236 calls 0.000 user 0.000 sys 0.004 real
overall: 489271296 mem 45.305 user 1.020 sys 5.263 real