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/ae/015b79f38c9c047ef4cb379026c936/.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-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.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/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  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/ae/015b79f38c9c047ef4cb379026c936/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> 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 HCC1395_BL.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz HCC1395_BL.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL HCC1395_BL.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_BL.tnseq_tumor_only.segments HCC1395_BL.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14521050, elapsed 0.1s, est remaining 2.0s, peak mem 151MB, user 0.6s, sys 0.0s, output queue size 55
progress 10% @chr21:25607303, elapsed 0.2s, est remaining 1.4s, peak mem 159MB, user 1.3s, sys 0.1s, output queue size 106
progress 15% @chr21:28943567, elapsed 0.2s, est remaining 1.3s, peak mem 166MB, user 2.0s, sys 0.1s, output queue size 36
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progress 95% @chr21:46227452, elapsed 2.4s, est remaining 0.1s, peak mem 381MB, user 21.4s, sys 0.5s, output queue size 34
progress 100% @chr21:46661700, elapsed 2.5s, est remaining 0.0s, peak mem 381MB, user 22.4s, sys 0.5s, output queue size 2
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: 163002590
output file size: 51811
reads: 1955548
contig: 1979 intervals 801713 bases
"assemble": 227 calls 1.064 user 0.030 sys 1.089 real
"assemble_addRead": 227 calls 0.017 user 0.000 sys 0.025 real
"assemble_buildGraph": 511 calls 0.425 user 0.010 sys 0.500 real
"assemble_computecigar": 321 calls 0.131 user 0.029 sys 0.193 real
"assemble_kg_build_calcsize": 511 calls 0.265 user 0.000 sys 0.271 real
"assemble_kg_build_clear": 699 calls 0.037 user 0.000 sys 0.027 real
"assemble_kg_build_prepare": 1022 calls 0.269 user 0.020 sys 0.260 real
"assemble_kg_build_threading": 323 calls 0.140 user 0.010 sys 0.214 real
"assemble_kg_op1": 323 calls 0.156 user 0.000 sys 0.140 real
"assemble_kg_op2": 323 calls 0.018 user 0.000 sys 0.007 real
"assemble_kg_op3": 323 calls 0.000 user 0.000 sys 0.007 real
"assemble_sg_clean": 321 calls 0.037 user 0.000 sys 0.041 real
"assemble_sg_create": 321 calls 0.082 user 0.000 sys 0.059 real
"checkGraph": 227 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.131 user 0.029 sys 0.199 real
advance: 2074 calls 7.429 user 0.254 sys 7.997 real
assemble_region: 227 calls 1.212 user 0.059 sys 1.317 real
build_pileup: 1957 calls 0.061 user 0.000 sys 0.068 real
build_stats: 1979 calls 2.081 user 0.046 sys 2.175 real
build_variants: 179 calls 0.000 user 0.000 sys 0.001 real
calc: 3869 calls 1.231 user 0.009 sys 1.120 real
calc_region: 179 calls 5.247 user 0.022 sys 5.506 real
call_region: 179 calls 0.071 user 0.000 sys 0.097 real
clip_region: 406 calls 0.062 user 0.000 sys 0.076 real
done: 1 calls 0.701 user 0.000 sys 0.708 real
execute: 1 calls 0.006 user 0.001 sys 2.502 real
fetch: 8147 calls 1.432 user 0.001 sys 1.473 real
fetch_ref: 8428 calls 0.066 user 0.008 sys 0.069 real
fetch_region: 227 calls 0.020 user 0.000 sys 0.024 real
fetch_vcf: 2074 calls 0.975 user 0.020 sys 0.945 real
idle: 41 calls 0.069 user 0.000 sys 13.307 real
init: 1 calls 0.060 user 0.020 sys 0.081 real
pairhmm: 1058 calls 10.281 user 0.026 sys 10.357 real
realign: 179 calls 0.648 user 0.010 sys 0.826 real
region: 4053 calls 6.488 user 0.081 sys 6.887 real
tracker: 4053 calls 0.020 user 0.000 sys 0.019 real
trim_region: 227 calls 0.000 user 0.000 sys 0.003 real
overall: 399917056 mem 29.897 user 0.657 sys 3.832 real