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/72/a239d5555367ac7ea4c0befde6f0a7/.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/72/a239d5555367ac7ea4c0befde6f0a7/.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% @chr21:14500429, elapsed 0.2s, est remaining 4.7s, peak mem 152MB, user 0.9s, sys 0.1s, output queue size 57
progress 10% @chr21:25702070, elapsed 0.4s, est remaining 3.4s, peak mem 161MB, user 2.0s, sys 0.1s, output queue size 107
progress 15% @chr21:29040509, elapsed 0.5s, est remaining 2.8s, peak mem 169MB, user 2.9s, sys 0.1s, output queue size 39
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progress 75% @chr21:44122077, elapsed 5.2s, est remaining 1.7s, peak mem 471MB, user 27.4s, sys 0.7s, output queue size 327
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progress 95% @chr21:46348912, elapsed 6.0s, est remaining 0.3s, peak mem 483MB, user 33.2s, sys 0.7s, output queue size 720
progress 100% @chr21:41501593, elapsed 6.9s, est remaining 0.0s, peak mem 483MB, user 36.7s, sys 0.8s, output queue size 804
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef 40417f5e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
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 1.910 user 0.021 sys 2.669 real
"assemble_addRead": 236 calls 0.091 user 0.000 sys 0.093 real
"assemble_buildGraph": 545 calls 0.810 user 0.001 sys 1.170 real
"assemble_computecigar": 331 calls 0.180 user 0.010 sys 0.302 real
"assemble_kg_build_calcsize": 545 calls 0.476 user 0.000 sys 0.684 real
"assemble_kg_build_clear": 752 calls 0.030 user 0.000 sys 0.064 real
"assemble_kg_build_prepare": 1090 calls 0.504 user 0.020 sys 0.680 real
"assemble_kg_build_threading": 338 calls 0.314 user 0.001 sys 0.453 real
"assemble_kg_op1": 338 calls 0.306 user 0.000 sys 0.384 real
"assemble_kg_op2": 338 calls 0.010 user 0.000 sys 0.020 real
"assemble_kg_op3": 338 calls 0.020 user 0.000 sys 0.018 real
"assemble_sg_clean": 331 calls 0.122 user 0.000 sys 0.149 real
"assemble_sg_create": 331 calls 0.041 user 0.000 sys 0.077 real
"checkGraph": 236 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 236 calls 0.191 user 0.010 sys 0.312 real
advance: 2074 calls 10.267 user 0.318 sys 15.506 real
assemble_region: 236 calls 2.192 user 0.031 sys 3.078 real
build_pileup: 1969 calls 0.140 user 0.000 sys 0.221 real
build_stats: 1999 calls 3.216 user 0.095 sys 4.978 real
build_variants: 195 calls 0.000 user 0.000 sys 0.002 real
calc: 3915 calls 1.795 user 0.020 sys 2.940 real
calc_region: 195 calls 10.972 user 0.019 sys 16.264 real
call_region: 195 calls 0.193 user 0.000 sys 0.324 real
clip_region: 431 calls 0.202 user 0.001 sys 0.260 real
done: 1 calls 1.063 user 0.000 sys 1.088 real
execute: 1 calls 0.009 user 0.001 sys 7.080 real
fetch: 8147 calls 2.780 user 0.040 sys 3.950 real
fetch_ref: 8437 calls 0.059 user 0.020 sys 0.108 real
fetch_region: 236 calls 0.040 user 0.000 sys 0.076 real
fetch_vcf: 2074 calls 1.075 user 0.061 sys 1.365 real
idle: 76 calls 0.189 user 0.011 sys 31.764 real
init: 1 calls 0.094 user 0.010 sys 0.132 real
pairhmm: 2129 calls 23.093 user 0.022 sys 33.387 real
realign: 195 calls 1.890 user 0.000 sys 2.743 real
region: 4053 calls 13.237 user 0.050 sys 19.517 real
tracker: 4053 calls 0.051 user 0.000 sys 0.043 real
trim_region: 236 calls 0.000 user 0.000 sys 0.005 real
overall: 507392000 mem 53.783 user 0.897 sys 9.465 real