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/5c/81a0bbd77c18e74eacd36ee2826f96/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4ad81cda182851fcb18a2054095a66/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/81a0bbd77c18e74eacd36ee2826f96/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/7b/4ad81cda182851fcb18a2054095a66/.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% @chr1:113710154, elapsed 1.3s, est remaining 25.0s, peak mem 141MB, user 12.1s, sys 1.7s, output queue size 6
progress 10% @chr2:3643344, elapsed 2.7s, est remaining 24.2s, peak mem 142MB, user 24.2s, sys 3.2s, output queue size 6
progress 15% @chr2:178609108, elapsed 4.2s, est remaining 23.7s, peak mem 142MB, user 37.4s, sys 4.8s, output queue size 12
progress 20% @chr3:57498400, elapsed 5.5s, est remaining 22.1s, peak mem 142MB, user 49.4s, sys 6.3s, output queue size 0
progress 25% @chr4:70602524, elapsed 7.0s, est remaining 20.9s, peak mem 142MB, user 62.1s, sys 8.1s, output queue size 7
progress 30% @chr5:135850325, elapsed 8.4s, est remaining 19.7s, peak mem 144MB, user 75.3s, sys 9.7s, output queue size 4
progress 35% @chr6:104791404, elapsed 9.7s, est remaining 18.1s, peak mem 145MB, user 87.1s, sys 11.0s, output queue size 6
progress 40% @chr7:106248199, elapsed 11.1s, est remaining 16.7s, peak mem 145MB, user 100.0s, sys 12.6s, output queue size 20
progress 45% @chr8:143820566, elapsed 12.5s, est remaining 15.3s, peak mem 147MB, user 113.1s, sys 14.1s, output queue size 1
progress 50% @chr10:21514996, elapsed 13.9s, est remaining 13.9s, peak mem 148MB, user 126.0s, sys 15.5s, output queue size 12
progress 55% @chr11:34135075, elapsed 15.2s, est remaining 12.5s, peak mem 149MB, user 138.6s, sys 17.0s, output queue size 1
progress 60% @chr12:12718707, elapsed 16.5s, est remaining 11.0s, peak mem 149MB, user 150.6s, sys 18.3s, output queue size 12
progress 65% @chr13:32155391, elapsed 17.9s, est remaining 9.6s, peak mem 150MB, user 163.4s, sys 19.9s, output queue size 6
progress 70% @chr15:35538174, elapsed 19.2s, est remaining 8.2s, peak mem 150MB, user 175.5s, sys 21.4s, output queue size 2
progress 75% @chr16:28491382, elapsed 20.5s, est remaining 6.8s, peak mem 151MB, user 188.1s, sys 22.5s, output queue size 7
progress 80% @chr17:40053198, elapsed 22.0s, est remaining 5.5s, peak mem 151MB, user 201.5s, sys 24.0s, output queue size 3
progress 85% @chr19:1799847, elapsed 23.3s, est remaining 4.1s, peak mem 151MB, user 214.2s, sys 25.6s, output queue size 9
progress 90% @chr19:54632916, elapsed 24.6s, est remaining 2.7s, peak mem 152MB, user 226.6s, sys 26.9s, output queue size 3
progress 95% @chr22:32068396, elapsed 27.7s, est remaining 1.5s, peak mem 326MB, user 256.0s, sys 29.0s, output queue size 10
progress 100% @chrY:23159853, elapsed 29.0s, est remaining 0.0s, peak mem 327MB, user 267.8s, sys 30.4s, output queue size 333
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 81484548
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.966 user 0.039 sys 0.927 real
"assemble_addRead": 207 calls 0.000 user 0.000 sys 0.014 real
"assemble_buildGraph": 465 calls 0.476 user 0.009 sys 0.421 real
"assemble_computecigar": 304 calls 0.189 user 0.000 sys 0.210 real
"assemble_kg_build_calcsize": 465 calls 0.223 user 0.000 sys 0.201 real
"assemble_kg_build_clear": 618 calls 0.010 user 0.000 sys 0.017 real
"assemble_kg_build_prepare": 930 calls 0.158 user 0.011 sys 0.180 real
"assemble_kg_build_threading": 312 calls 0.243 user 0.009 sys 0.212 real
"assemble_kg_op1": 312 calls 0.154 user 0.010 sys 0.110 real
"assemble_kg_op2": 312 calls 0.020 user 0.000 sys 0.008 real
"assemble_kg_op3": 312 calls 0.009 user 0.000 sys 0.009 real
"assemble_sg_clean": 304 calls 0.031 user 0.009 sys 0.049 real
"assemble_sg_create": 304 calls 0.071 user 0.000 sys 0.076 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.189 user 0.000 sys 0.218 real
advance: 189104 calls 20.487 user 0.963 sys 33.111 real
assemble_region: 207 calls 1.154 user 0.039 sys 1.163 real
build_pileup: 70976 calls 0.636 user 0.048 sys 1.217 real
build_stats: 71686 calls 5.013 user 0.361 sys 6.929 real
build_variants: 162 calls 0.000 user 0.000 sys 0.002 real
calc: 128670 calls 4.362 user 0.128 sys 6.950 real
calc_region: 162 calls 3.312 user 0.036 sys 3.528 real
call_region: 162 calls 0.072 user 0.000 sys 0.080 real
clip_region: 369 calls 0.076 user 0.000 sys 0.059 real
done: 1 calls 1.248 user 0.001 sys 1.249 real
execute: 1 calls 0.001 user 0.010 sys 29.080 real
fetch: 743546 calls 1.465 user 0.213 sys 2.175 real
fetch_ref: 745712 calls 1.866 user 0.941 sys 5.093 real
fetch_region: 207 calls 0.010 user 0.000 sys 0.016 real
fetch_vcf: 189104 calls 57.512 user 2.999 sys 105.708 real
idle: 47 calls 0.035 user 0.007 sys 25.865 real
init: 1 calls 0.080 user 0.030 sys 0.111 real
pairhmm: 466 calls 5.619 user 0.041 sys 5.809 real
realign: 162 calls 0.567 user 0.001 sys 0.574 real
region: 367297 calls 4.576 user 0.132 sys 4.988 real
tracker: 367297 calls 0.652 user 0.104 sys 1.467 real
trim_region: 207 calls 0.010 user 0.000 sys 0.005 real
overall: 342900736 mem 298.986 user 43.581 sys 31.674 real