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/ee/84e5716c7233b8da48eee617ec08e7/.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/ee/84e5716c7233b8da48eee617ec08e7/.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% @chr21:14381103, elapsed 0.1s, est remaining 2.0s, peak mem 148MB, user 0.6s, sys 0.0s, output queue size 56
progress 10% @chr21:25698577, elapsed 0.2s, est remaining 1.5s, peak mem 159MB, user 1.3s, sys 0.0s, output queue size 106
progress 15% @chr21:28992664, elapsed 0.2s, est remaining 1.2s, peak mem 166MB, user 2.0s, sys 0.1s, output queue size 22
progress 20% @chr21:30746851, elapsed 0.3s, est remaining 1.0s, peak mem 169MB, user 2.5s, sys 0.1s, output queue size 16
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progress 35% @chr21:34379405, elapsed 0.4s, est remaining 0.8s, peak mem 177MB, user 4.4s, sys 0.1s, output queue size 74
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progress 70% @chr21:43417443, elapsed 1.8s, est remaining 0.8s, peak mem 364MB, user 14.9s, sys 0.4s, output queue size 227
progress 75% @chr21:44143105, elapsed 1.9s, est remaining 0.6s, peak mem 367MB, user 15.6s, sys 0.4s, output queue size 336
progress 80% @chr21:44426560, elapsed 2.0s, est remaining 0.5s, peak mem 370MB, user 17.1s, sys 0.4s, output queue size 429
progress 85% @chr21:45220736, elapsed 2.1s, est remaining 0.4s, peak mem 372MB, user 18.0s, sys 0.5s, output queue size 505
progress 90% @chr21:45990673, elapsed 2.2s, est remaining 0.2s, peak mem 372MB, user 19.7s, sys 0.5s, output queue size 37
progress 95% @chr21:46227452, elapsed 2.3s, est remaining 0.1s, peak mem 372MB, user 20.8s, sys 0.5s, output queue size 33
progress 100% @chr21:46661700, elapsed 2.4s, est remaining 0.0s, peak mem 372MB, user 21.8s, sys 0.5s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M 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 1.024 user 0.038 sys 1.034 real
"assemble_addRead": 227 calls 0.010 user 0.000 sys 0.024 real
"assemble_buildGraph": 511 calls 0.459 user 0.000 sys 0.476 real
"assemble_computecigar": 321 calls 0.109 user 0.020 sys 0.161 real
"assemble_kg_build_calcsize": 511 calls 0.267 user 0.000 sys 0.257 real
"assemble_kg_build_clear": 699 calls 0.030 user 0.000 sys 0.028 real
"assemble_kg_build_prepare": 1022 calls 0.278 user 0.023 sys 0.252 real
"assemble_kg_build_threading": 323 calls 0.162 user 0.000 sys 0.204 real
"assemble_kg_op1": 323 calls 0.122 user 0.010 sys 0.122 real
"assemble_kg_op2": 323 calls 0.000 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 0.057 user 0.000 sys 0.040 real
"assemble_sg_create": 321 calls 0.050 user 0.004 sys 0.056 real
"checkGraph": 227 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.119 user 0.020 sys 0.168 real
advance: 2074 calls 7.248 user 0.224 sys 7.606 real
assemble_region: 227 calls 1.154 user 0.058 sys 1.230 real
build_pileup: 1957 calls 0.110 user 0.000 sys 0.068 real
build_stats: 1979 calls 1.849 user 0.091 sys 2.015 real
build_variants: 179 calls 0.000 user 0.000 sys 0.001 real
calc: 3869 calls 0.800 user 0.000 sys 0.992 real
calc_region: 179 calls 5.571 user 0.004 sys 5.689 real
call_region: 179 calls 0.130 user 0.000 sys 0.100 real
clip_region: 406 calls 0.060 user 0.000 sys 0.079 real
done: 1 calls 0.768 user 0.001 sys 0.773 real
execute: 1 calls 0.001 user 0.010 sys 2.432 real
fetch: 8147 calls 1.478 user 0.027 sys 1.488 real
fetch_ref: 8428 calls 0.097 user 0.010 sys 0.062 real
fetch_region: 227 calls 0.014 user 0.000 sys 0.026 real
fetch_vcf: 2074 calls 0.860 user 0.010 sys 0.877 real
idle: 40 calls 0.083 user 0.000 sys 13.375 real
init: 1 calls 0.079 user 0.001 sys 0.081 real
pairhmm: 1058 calls 10.333 user 0.000 sys 10.455 real
realign: 179 calls 0.744 user 0.000 sys 0.884 real
region: 4053 calls 6.789 user 0.062 sys 6.986 real
tracker: 4053 calls 0.012 user 0.000 sys 0.018 real
trim_region: 227 calls 0.000 user 0.000 sys 0.003 real
overall: 390565888 mem 29.250 user 0.592 sys 3.764 real