Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/379f588e0d26cfb992218518ae6664/.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/55/379f588e0d26cfb992218518ae6664/.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/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.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 HCC1395_BL.recal.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 123MB, user 0.5s, sys 0.0s, output queue size 53
progress 10% @chr21:14964616, elapsed 0.1s, est remaining 1.0s, peak mem 138MB, user 1.0s, sys 0.1s, output queue size 105
progress 15% @chr21:29034737, elapsed 0.2s, est remaining 0.9s, peak mem 144MB, user 1.4s, sys 0.1s, output queue size 11
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progress 95% @chr21:46296062, elapsed 1.7s, est remaining 0.1s, peak mem 374MB, user 16.3s, sys 0.5s, output queue size 26
progress 100% @chr21:46661700, elapsed 1.8s, est remaining 0.0s, peak mem 374MB, user 17.0s, sys 0.5s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000a06d1
features: bfebfbff 7ffefbff
extended: f3bfb7ef fb417ffe
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: 111697681
output file size: 58752
reads: 1322929
contig: 1979 intervals 801713 bases
"assemble": 392 calls 1.037 user 0.035 sys 1.123 real
"assemble_addRead": 392 calls 0.033 user 0.000 sys 0.024 real
"assemble_buildGraph": 837 calls 0.470 user 0.002 sys 0.519 real
"assemble_computecigar": 610 calls 0.127 user 0.010 sys 0.108 real
"assemble_kg_build_calcsize": 837 calls 0.291 user 0.000 sys 0.279 real
"assemble_kg_build_clear": 1061 calls 0.033 user 0.000 sys 0.027 real
"assemble_kg_build_prepare": 1674 calls 0.215 user 0.011 sys 0.243 real
"assemble_kg_build_threading": 613 calls 0.162 user 0.002 sys 0.228 real
"assemble_kg_op1": 613 calls 0.122 user 0.012 sys 0.139 real
"assemble_kg_op2": 613 calls 0.000 user 0.000 sys 0.006 real
"assemble_kg_op3": 613 calls 0.010 user 0.000 sys 0.009 real
"assemble_sg_clean": 610 calls 0.040 user 0.000 sys 0.045 real
"assemble_sg_create": 610 calls 0.104 user 0.010 sys 0.077 real
"checkGraph": 392 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 392 calls 0.127 user 0.010 sys 0.113 real
advance: 2074 calls 5.644 user 0.202 sys 5.937 real
assemble_region: 392 calls 1.197 user 0.045 sys 1.264 real
build_pileup: 1955 calls 0.050 user 0.000 sys 0.048 real
build_stats: 1978 calls 1.428 user 0.034 sys 1.436 real
build_variants: 232 calls 0.000 user 0.000 sys 0.001 real
calc: 3859 calls 0.647 user 0.013 sys 0.705 real
calc_region: 232 calls 4.205 user 0.047 sys 4.341 real
call_region: 232 calls 0.079 user 0.000 sys 0.080 real
clip_region: 624 calls 0.083 user 0.000 sys 0.078 real
done: 1 calls 0.535 user 0.001 sys 0.541 real
execute: 1 calls 0.004 user 0.001 sys 1.823 real
fetch: 8147 calls 1.200 user 0.015 sys 1.065 real
fetch_ref: 8593 calls 0.036 user 0.000 sys 0.039 real
fetch_region: 392 calls 0.014 user 0.009 sys 0.023 real
fetch_vcf: 2074 calls 0.608 user 0.027 sys 0.765 real
idle: 37 calls 0.072 user 0.001 sys 12.873 real
init: 1 calls 0.050 user 0.010 sys 0.059 real
pairhmm: 1073 calls 6.839 user 0.055 sys 7.039 real
realign: 232 calls 0.754 user 0.000 sys 0.779 real
region: 4053 calls 5.482 user 0.101 sys 5.671 real
tracker: 4053 calls 0.000 user 0.001 sys 0.014 real
trim_region: 392 calls 0.000 user 0.000 sys 0.003 real
overall: 392536064 mem 21.854 user 0.630 sys 3.098 real