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/35/f31f6ad0a7f55deae9d327e5baf98c/.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/35/f31f6ad0a7f55deae9d327e5baf98c/.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% @chr21:14373517, elapsed 0.1s, est remaining 2.5s, peak mem 155MB, user 0.9s, sys 0.1s, output queue size 56
progress 10% @chr21:25588735, elapsed 0.3s, est remaining 2.3s, peak mem 164MB, user 2.0s, sys 0.2s, output queue size 44
progress 15% @chr21:29037176, elapsed 0.4s, est remaining 2.1s, peak mem 169MB, user 3.1s, sys 0.2s, output queue size 39
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progress 95% @chr21:46385732, elapsed 3.7s, est remaining 0.2s, peak mem 462MB, user 28.5s, sys 0.7s, output queue size 720
progress 100% @chr21:46334297, elapsed 3.9s, est remaining 0.0s, peak mem 463MB, user 31.4s, sys 0.7s, 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 1.551 user 0.032 sys 1.592 real
"assemble_addRead": 236 calls 0.040 user 0.000 sys 0.037 real
"assemble_buildGraph": 545 calls 0.761 user 0.010 sys 0.747 real
"assemble_computecigar": 331 calls 0.152 user 0.020 sys 0.161 real
"assemble_kg_build_calcsize": 545 calls 0.458 user 0.000 sys 0.407 real
"assemble_kg_build_clear": 752 calls 0.038 user 0.000 sys 0.052 real
"assemble_kg_build_prepare": 1090 calls 0.383 user 0.011 sys 0.405 real
"assemble_kg_build_threading": 338 calls 0.285 user 0.010 sys 0.311 real
"assemble_kg_op1": 338 calls 0.213 user 0.011 sys 0.206 real
"assemble_kg_op2": 338 calls 0.014 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 0.054 user 0.000 sys 0.045 real
"assemble_sg_create": 331 calls 0.050 user 0.000 sys 0.060 real
"checkGraph": 236 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 236 calls 0.192 user 0.020 sys 0.170 real
advance: 2074 calls 9.687 user 0.235 sys 9.920 real
assemble_region: 236 calls 1.793 user 0.051 sys 1.803 real
build_pileup: 1969 calls 0.050 user 0.000 sys 0.087 real
build_stats: 1999 calls 2.378 user 0.127 sys 2.827 real
build_variants: 195 calls 0.000 user 0.000 sys 0.002 real
calc: 3915 calls 1.308 user 0.011 sys 1.450 real
calc_region: 195 calls 10.193 user 0.024 sys 10.550 real
call_region: 195 calls 0.204 user 0.000 sys 0.177 real
clip_region: 431 calls 0.131 user 0.000 sys 0.132 real
done: 1 calls 0.715 user 0.000 sys 0.723 real
execute: 1 calls 0.002 user 0.001 sys 3.893 real
fetch: 8147 calls 1.818 user 0.021 sys 2.043 real
fetch_ref: 8437 calls 0.067 user 0.021 sys 0.065 real
fetch_region: 236 calls 0.043 user 0.000 sys 0.038 real
fetch_vcf: 2074 calls 0.918 user 0.011 sys 0.928 real
idle: 39 calls 0.067 user 0.000 sys 13.579 real
init: 1 calls 0.070 user 0.010 sys 0.081 real
pairhmm: 2129 calls 20.782 user 0.046 sys 20.937 real
realign: 195 calls 1.334 user 0.000 sys 1.563 real
region: 4053 calls 12.049 user 0.075 sys 12.455 real
tracker: 4053 calls 0.017 user 0.000 sys 0.020 real
trim_region: 236 calls 0.000 user 0.000 sys 0.004 real
overall: 487436288 mem 45.571 user 0.861 sys 5.212 real