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-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_padded_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21_padded100bp.bed
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-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/PON/pon_tnseq_42_curated_v4.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-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/fff6a050b906a2ee56f0d408649c25/.command.sh
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_tumor/HCC1395_tumor.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz.tbi
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.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/fff6a050b906a2ee56f0d408649c25/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (14 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i HCC1395_BL.recalibrated.bam -i HCC1395_tumor.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21_padded100bp.bed --algo TNhaplotyper2 --tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_tumor HCC1395_tumor_vs_HCC1395_BL.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_tumor_vs_HCC1395_BL.tnseq.segments HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14382995, elapsed 0.5s, est remaining 10.4s, peak mem 219MB, user 2.9s, sys 0.2s, output queue size 56
progress 10% @chr21:25592712, elapsed 0.7s, est remaining 6.5s, peak mem 237MB, user 4.8s, sys 0.2s, output queue size 28
progress 15% @chr21:29037176, elapsed 0.9s, est remaining 5.0s, peak mem 247MB, user 6.5s, sys 0.2s, output queue size 39
progress 20% @chr21:30812929, elapsed 1.0s, est remaining 4.1s, peak mem 255MB, user 8.1s, sys 0.2s, output queue size 10
progress 25% @chr21:32357437, elapsed 1.2s, est remaining 3.6s, peak mem 255MB, user 10.1s, sys 0.3s, output queue size 5
progress 30% @chr21:33070147, elapsed 1.4s, est remaining 3.2s, peak mem 261MB, user 12.0s, sys 0.3s, output queue size 24
progress 35% @chr21:34379405, elapsed 1.6s, est remaining 3.0s, peak mem 274MB, user 13.9s, sys 0.3s, output queue size 74
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progress 70% @chr21:43418921, elapsed 5.8s, est remaining 2.5s, peak mem 915MB, user 46.5s, sys 1.1s, output queue size 227
progress 75% @chr21:44126800, elapsed 6.0s, est remaining 2.0s, peak mem 923MB, user 49.1s, sys 1.1s, output queue size 327
progress 80% @chr21:44426560, elapsed 6.3s, est remaining 1.6s, peak mem 944MB, user 51.9s, sys 1.1s, output queue size 431
progress 85% @chr21:45180230, elapsed 6.8s, est remaining 1.2s, peak mem 945MB, user 55.3s, sys 1.2s, output queue size 506
progress 90% @chr21:45990673, elapsed 7.0s, est remaining 0.8s, peak mem 945MB, user 60.2s, sys 1.3s, output queue size 27
progress 95% @chr21:46315374, elapsed 7.4s, est remaining 0.4s, peak mem 945MB, user 64.2s, sys 1.4s, output queue size 15
progress 100% @chr21:46558123, elapsed 7.8s, est remaining 0.0s, peak mem 945MB, user 67.6s, sys 1.5s, output queue size 19
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 333302564
output file size: 71258
reads: 7311657
contig: 1979 intervals 801713 bases
"assemble": 288 calls 3.468 user 0.063 sys 3.549 real
"assemble_addRead": 288 calls 0.134 user 0.000 sys 0.095 real
"assemble_buildGraph": 670 calls 1.566 user 0.013 sys 1.756 real
"assemble_computecigar": 418 calls 0.190 user 0.020 sys 0.192 real
"assemble_kg_build_calcsize": 670 calls 0.983 user 0.010 sys 1.015 real
"assemble_kg_build_clear": 902 calls 0.210 user 0.000 sys 0.152 real
"assemble_kg_build_prepare": 1340 calls 1.033 user 0.040 sys 0.998 real
"assemble_kg_build_threading": 438 calls 0.494 user 0.004 sys 0.669 real
"assemble_kg_op1": 438 calls 0.423 user 0.000 sys 0.399 real
"assemble_kg_op2": 438 calls 0.000 user 0.010 sys 0.009 real
"assemble_kg_op3": 438 calls 0.000 user 0.000 sys 0.010 real
"assemble_sg_clean": 418 calls 0.081 user 0.000 sys 0.055 real
"assemble_sg_create": 418 calls 0.112 user 0.000 sys 0.072 real
"checkGraph": 288 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 288 calls 0.190 user 0.020 sys 0.204 real
advance: 2074 calls 23.693 user 0.817 sys 24.856 real
assemble_region: 288 calls 3.803 user 0.083 sys 3.854 real
build_pileup: 1963 calls 0.249 user 0.000 sys 0.205 real
build_stats: 1987 calls 3.668 user 0.108 sys 3.819 real
build_variants: 215 calls 0.010 user 0.000 sys 0.002 real
calc: 3888 calls 2.652 user 0.011 sys 2.906 real
calc_region: 215 calls 22.569 user 0.108 sys 23.368 real
call_region: 215 calls 0.420 user 0.010 sys 0.450 real
clip_region: 503 calls 0.335 user 0.000 sys 0.315 real
done: 1 calls 1.025 user 0.000 sys 1.028 real
execute: 1 calls 0.003 user 0.001 sys 7.818 real
fetch: 8147 calls 5.794 user 0.072 sys 5.697 real
fetch_ref: 8489 calls 0.060 user 0.011 sys 0.067 real
fetch_region: 288 calls 0.154 user 0.000 sys 0.124 real
fetch_vcf: 2074 calls 0.908 user 0.037 sys 0.892 real
idle: 49 calls 0.070 user 0.000 sys 25.517 real
init: 1 calls 0.083 user 0.001 sys 0.085 real
pairhmm: 4281 calls 41.632 user 0.134 sys 41.817 real
realign: 215 calls 2.779 user 0.030 sys 3.138 real
region: 4053 calls 26.719 user 0.191 sys 27.487 real
tracker: 4053 calls 0.005 user 0.000 sys 0.021 real
trim_region: 288 calls 0.010 user 0.000 sys 0.004 real
overall: 991014912 mem 92.558 user 1.599 sys 10.173 real