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/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.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/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam.bai
  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/intervals/altera_padded_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/1c68b115c3db929beceec10d9f3ac7/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/67a0334683d3285fa56d6227dc8158/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/1c68b115c3db929beceec10d9f3ac7/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-rnd-pltf-dev-nextflow-scratch-01/work/4c/67a0334683d3285fa56d6227dc8158/.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 reference-NA12878-downsampled-500k.bam -i HCC1395_tumor.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample HCC1395_tumor --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz positive_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_tumor positive_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_tumor --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_1.tnseq.segments positive_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113682797, elapsed 1.7s, est remaining 31.5s, peak mem 141MB, user 13.2s, sys 1.8s, output queue size 2
progress 10% @chr2:3643344, elapsed 3.2s, est remaining 28.4s, peak mem 142MB, user 25.8s, sys 3.3s, output queue size 6
progress 15% @chr2:178606921, elapsed 4.7s, est remaining 26.7s, peak mem 144MB, user 39.1s, sys 4.8s, output queue size 12
progress 20% @chr3:57489409, elapsed 6.1s, est remaining 24.3s, peak mem 145MB, user 51.5s, sys 5.9s, output queue size 16
progress 25% @chr4:70603160, elapsed 7.5s, est remaining 22.5s, peak mem 145MB, user 64.5s, sys 7.4s, output queue size 9
progress 30% @chr5:135571753, elapsed 8.9s, est remaining 20.7s, peak mem 147MB, user 77.6s, sys 9.1s, output queue size 4
progress 35% @chr6:104957999, elapsed 10.2s, est remaining 19.0s, peak mem 147MB, user 89.6s, sys 10.4s, output queue size 3
progress 40% @chr7:106248199, elapsed 11.6s, est remaining 17.4s, peak mem 147MB, user 102.4s, sys 12.0s, output queue size 19
progress 45% @chr8:143812717, elapsed 13.0s, est remaining 15.8s, peak mem 148MB, user 115.2s, sys 13.5s, output queue size 1
progress 50% @chr10:21726144, elapsed 14.3s, est remaining 14.3s, peak mem 151MB, user 128.0s, sys 14.8s, output queue size 1
progress 55% @chr11:34131281, elapsed 15.6s, est remaining 12.8s, peak mem 151MB, user 140.1s, sys 16.3s, output queue size 2
progress 60% @chr12:12718707, elapsed 16.8s, est remaining 11.2s, peak mem 152MB, user 151.7s, sys 17.5s, output queue size 7
progress 65% @chr13:32078734, elapsed 18.1s, est remaining 9.8s, peak mem 152MB, user 164.1s, sys 19.0s, output queue size 10
progress 70% @chr15:35538174, elapsed 19.4s, est remaining 8.3s, peak mem 153MB, user 176.0s, sys 20.5s, output queue size 3
progress 75% @chr16:28494582, elapsed 20.7s, est remaining 6.9s, peak mem 156MB, user 188.3s, sys 21.5s, output queue size 0
progress 80% @chr17:40034816, elapsed 22.1s, est remaining 5.5s, peak mem 156MB, user 201.7s, sys 22.9s, output queue size 0
progress 85% @chr19:1806528, elapsed 23.4s, est remaining 4.1s, peak mem 157MB, user 214.4s, sys 24.3s, output queue size 2
progress 90% @chr19:54630974, elapsed 24.7s, est remaining 2.7s, peak mem 157MB, user 227.2s, sys 25.4s, output queue size 4
progress 95% @chr22:32043182, elapsed 27.6s, est remaining 1.5s, peak mem 327MB, user 255.8s, sys 27.1s, output queue size 10
progress 100% @chrY:23181104, elapsed 28.7s, est remaining 0.0s, peak mem 327MB, user 266.0s, sys 28.5s, output queue size 105
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: AuthenticAMD
 signature: 00800f12
  features: 178bfbff fed83203
  extended: 209c01a9 00000000
  amd bits: 2fd3fbff 00c001f3
     brand: AMD EPYC 7571
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 81484552
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.784 user 0.029 sys 0.869 real
"assemble_addRead": 207 calls 0.010 user 0.000 sys 0.013 real
"assemble_buildGraph": 465 calls 0.346 user 0.009 sys 0.392 real
"assemble_computecigar": 304 calls 0.141 user 0.029 sys 0.198 real
"assemble_kg_build_calcsize": 465 calls 0.166 user 0.000 sys 0.190 real
"assemble_kg_build_clear": 618 calls 0.010 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 930 calls 0.180 user 0.010 sys 0.169 real
"assemble_kg_build_threading": 312 calls 0.181 user 0.009 sys 0.194 real
"assemble_kg_op1": 312 calls 0.109 user 0.000 sys 0.102 real
"assemble_kg_op2": 312 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 312 calls 0.000 user 0.000 sys 0.009 real
"assemble_sg_clean": 304 calls 0.030 user 0.000 sys 0.047 real
"assemble_sg_create": 304 calls 0.050 user 0.000 sys 0.073 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.151 user 0.029 sys 0.206 real
advance: 189104 calls 21.083 user 0.817 sys 32.612 real
assemble_region: 207 calls 0.945 user 0.058 sys 1.092 real
build_pileup: 70976 calls 0.722 user 0.030 sys 1.205 real
build_stats: 71686 calls 4.962 user 0.236 sys 6.746 real
build_variants: 162 calls 0.000 user 0.000 sys 0.002 real
calc: 128670 calls 4.091 user 0.205 sys 6.857 real
calc_region: 162 calls 3.173 user 0.036 sys 3.369 real
call_region: 162 calls 0.050 user 0.000 sys 0.075 real
clip_region: 369 calls 0.044 user 0.000 sys 0.054 real
done: 1 calls 1.237 user 0.010 sys 1.247 real
execute: 1 calls 0.011 user 0.000 sys 28.762 real
fetch: 743546 calls 1.383 user 0.228 sys 2.075 real
fetch_ref: 745712 calls 1.991 user 0.991 sys 5.066 real
fetch_region: 207 calls 0.010 user 0.000 sys 0.015 real
fetch_vcf: 189104 calls 60.301 user 2.946 sys 105.837 real
idle: 47 calls 0.001 user 0.001 sys 25.884 real
init: 1 calls 0.090 user 0.030 sys 0.111 real
pairhmm: 466 calls 5.662 user 0.030 sys 5.574 real
realign: 162 calls 0.405 user 0.000 sys 0.558 real
region: 367297 calls 4.204 user 0.186 sys 4.759 real
tracker: 367297 calls 0.653 user 0.184 sys 1.466 real
trim_region: 207 calls 0.000 user 0.000 sys 0.004 real
overall: 342913024 mem 298.755 user 41.193 sys 31.430 real