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/ea/0dcdcd1374b4e06f2e7b3abbf221f2/.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/ea/0dcdcd1374b4e06f2e7b3abbf221f2/.command.run
  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.bai
  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% @chr21:14500429, elapsed 0.0s, est remaining 0.9s, peak mem 156MB, user 0.3s, sys 0.0s, output queue size 55
progress 10% @chr21:25597202, elapsed 0.1s, est remaining 0.7s, peak mem 164MB, user 0.6s, sys 0.0s, output queue size 28
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progress 90% @chr21:46115772, elapsed 1.4s, est remaining 0.2s, peak mem 485MB, user 10.9s, sys 0.2s, output queue size 611
progress 95% @chr21:46385732, elapsed 1.4s, est remaining 0.1s, peak mem 485MB, user 11.4s, sys 0.2s, output queue size 720
progress 100% @chr21:46334297, elapsed 1.5s, est remaining 0.0s, peak mem 486MB, user 12.7s, sys 0.3s, output queue size 91
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: AuthenticAMD
 signature: 00b00f21
  features: 178bfbff fefa320b
  extended: f1bf07ab 18405f5a
  amd bits: 2fd3fbff 00c001f3
     brand: AMD EPYC 9R05
threads: 12 max 48
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 0.555 user 0.010 sys 0.610 real
"assemble_addRead": 236 calls 0.000 user 0.000 sys 0.016 real
"assemble_buildGraph": 545 calls 0.243 user 0.000 sys 0.283 real
"assemble_computecigar": 331 calls 0.044 user 0.010 sys 0.066 real
"assemble_kg_build_calcsize": 545 calls 0.142 user 0.000 sys 0.172 real
"assemble_kg_build_clear": 752 calls 0.002 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 1090 calls 0.146 user 0.010 sys 0.162 real
"assemble_kg_build_threading": 338 calls 0.099 user 0.000 sys 0.103 real
"assemble_kg_op1": 338 calls 0.079 user 0.000 sys 0.076 real
"assemble_kg_op2": 338 calls 0.010 user 0.000 sys 0.004 real
"assemble_kg_op3": 338 calls 0.000 user 0.000 sys 0.003 real
"assemble_sg_clean": 331 calls 0.010 user 0.000 sys 0.018 real
"assemble_sg_create": 331 calls 0.032 user 0.000 sys 0.023 real
"checkGraph": 236 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 236 calls 0.044 user 0.010 sys 0.069 real
advance: 2074 calls 3.607 user 0.085 sys 4.134 real
assemble_region: 236 calls 0.599 user 0.020 sys 0.696 real
build_pileup: 1969 calls 0.047 user 0.000 sys 0.027 real
build_stats: 1999 calls 0.996 user 0.040 sys 0.969 real
build_variants: 195 calls 0.000 user 0.000 sys 0.001 real
calc: 3915 calls 0.593 user 0.000 sys 0.437 real
calc_region: 195 calls 4.546 user 0.015 sys 4.594 real
call_region: 195 calls 0.083 user 0.000 sys 0.073 real
clip_region: 431 calls 0.026 user 0.000 sys 0.057 real
done: 1 calls 0.322 user 0.001 sys 0.323 real
execute: 1 calls 0.001 user 0.010 sys 1.527 real
fetch: 8147 calls 0.643 user 0.011 sys 0.698 real
fetch_ref: 8437 calls 0.023 user 0.000 sys 0.019 real
fetch_region: 236 calls 0.047 user 0.000 sys 0.014 real
fetch_vcf: 2074 calls 0.349 user 0.008 sys 0.383 real
idle: 37 calls 0.049 user 0.000 sys 12.904 real
init: 1 calls 0.020 user 0.000 sys 0.029 real
pairhmm: 2129 calls 7.243 user 0.020 sys 7.424 real
realign: 195 calls 1.214 user 0.000 sys 1.259 real
region: 4053 calls 5.218 user 0.035 sys 5.330 real
tracker: 4053 calls 0.000 user 0.000 sys 0.006 real
trim_region: 236 calls 0.000 user 0.000 sys 0.002 real
overall: 512147456 mem 17.753 user 0.310 sys 2.641 real