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/c6/78b3d887097e57890636e1c876e7ec/.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/c6/78b3d887097e57890636e1c876e7ec/.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 1.3s, peak mem 141MB, user 0.4s, sys 0.0s, output queue size 56
progress 10% @chr21:25698577, elapsed 0.1s, est remaining 1.0s, peak mem 147MB, user 0.8s, sys 0.1s, output queue size 106
progress 15% @chr21:28992664, elapsed 0.1s, est remaining 0.8s, peak mem 150MB, user 1.2s, sys 0.1s, output queue size 22
progress 20% @chr21:30746851, elapsed 0.2s, est remaining 0.7s, peak mem 150MB, user 1.5s, sys 0.1s, output queue size 16
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progress 90% @chr21:45986844, elapsed 1.2s, est remaining 0.1s, peak mem 370MB, user 11.1s, sys 0.3s, output queue size 67
progress 95% @chr21:46315374, elapsed 1.3s, est remaining 0.1s, peak mem 370MB, user 11.8s, sys 0.4s, output queue size 26
progress 100% @chr21:46661700, elapsed 1.4s, est remaining 0.0s, peak mem 370MB, user 12.5s, sys 0.4s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
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 0.498 user 0.003 sys 0.583 real
"assemble_addRead": 227 calls 0.018 user 0.000 sys 0.012 real
"assemble_buildGraph": 511 calls 0.229 user 0.000 sys 0.265 real
"assemble_computecigar": 321 calls 0.042 user 0.039 sys 0.095 real
"assemble_kg_build_calcsize": 511 calls 0.120 user 0.000 sys 0.156 real
"assemble_kg_build_clear": 699 calls 0.009 user 0.000 sys 0.013 real
"assemble_kg_build_prepare": 1022 calls 0.086 user 0.001 sys 0.140 real
"assemble_kg_build_threading": 323 calls 0.109 user 0.000 sys 0.103 real
"assemble_kg_op1": 323 calls 0.069 user 0.000 sys 0.073 real
"assemble_kg_op2": 323 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 323 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 321 calls 0.020 user 0.000 sys 0.023 real
"assemble_sg_create": 321 calls 0.037 user 0.000 sys 0.032 real
"checkGraph": 227 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.042 user 0.039 sys 0.099 real
advance: 2074 calls 4.553 user 0.097 sys 5.051 real
assemble_region: 227 calls 0.559 user 0.043 sys 0.697 real
build_pileup: 1957 calls 0.040 user 0.000 sys 0.030 real
build_stats: 1979 calls 1.124 user 0.059 sys 1.016 real
build_variants: 179 calls 0.000 user 0.000 sys 0.001 real
calc: 3869 calls 0.460 user 0.003 sys 0.485 real
calc_region: 179 calls 2.901 user 0.021 sys 2.959 real
call_region: 179 calls 0.052 user 0.000 sys 0.052 real
clip_region: 406 calls 0.051 user 0.000 sys 0.046 real
done: 1 calls 0.307 user 0.002 sys 0.314 real
execute: 1 calls 0.002 user 0.001 sys 1.380 real
fetch: 8147 calls 0.814 user 0.011 sys 0.754 real
fetch_ref: 8428 calls 0.028 user 0.019 sys 0.033 real
fetch_region: 227 calls 0.020 user 0.000 sys 0.014 real
fetch_vcf: 2074 calls 0.466 user 0.004 sys 0.599 real
idle: 40 calls 0.053 user 0.000 sys 12.773 real
init: 1 calls 0.031 user 0.019 sys 0.050 real
pairhmm: 1058 calls 5.149 user 0.019 sys 5.168 real
realign: 179 calls 0.578 user 0.000 sys 0.579 real
region: 4053 calls 3.519 user 0.071 sys 3.692 real
tracker: 4053 calls 0.010 user 0.006 sys 0.010 real
trim_region: 227 calls 0.000 user 0.000 sys 0.002 real
overall: 388952064 mem 16.460 user 0.429 sys 2.602 real