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/de/b0a4002342a30599908379d4072c3d/.command.sh
  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/83/278f819846ff96c6923bdd66ccea66/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/278f819846ff96c6923bdd66ccea66/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/b0a4002342a30599908379d4072c3d/.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 Sig_18_tissue.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 Sig_18_tissue --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_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_tissue positive_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_2.tnseq.segments positive_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113711646, elapsed 1.4s, est remaining 26.5s, peak mem 143MB, user 11.3s, sys 1.8s, output queue size 3
progress 10% @chr2:3643344, elapsed 2.7s, est remaining 24.6s, peak mem 145MB, user 22.7s, sys 3.5s, output queue size 8
progress 15% @chr2:178609108, elapsed 4.2s, est remaining 23.6s, peak mem 146MB, user 35.7s, sys 4.9s, output queue size 12
progress 20% @chr3:57508282, elapsed 5.5s, est remaining 22.2s, peak mem 147MB, user 47.9s, sys 6.3s, output queue size 2
progress 25% @chr4:70602524, elapsed 7.0s, est remaining 21.0s, peak mem 147MB, user 60.6s, sys 7.8s, output queue size 3
progress 30% @chr5:135873921, elapsed 8.4s, est remaining 19.6s, peak mem 149MB, user 73.5s, sys 9.3s, output queue size 4
progress 35% @chr6:104859467, elapsed 9.7s, est remaining 18.0s, peak mem 150MB, user 85.2s, sys 10.8s, output queue size 1
progress 40% @chr7:106867451, elapsed 11.0s, est remaining 16.5s, peak mem 151MB, user 97.7s, sys 12.2s, output queue size 2
progress 45% @chr8:143821497, elapsed 12.4s, est remaining 15.1s, peak mem 151MB, user 110.5s, sys 13.5s, output queue size 1
progress 50% @chr10:21727756, elapsed 13.7s, est remaining 13.7s, peak mem 154MB, user 122.9s, sys 14.9s, output queue size 2
progress 55% @chr11:34132025, elapsed 15.0s, est remaining 12.3s, peak mem 155MB, user 135.5s, sys 16.1s, output queue size 1
progress 60% @chr12:12718707, elapsed 16.2s, est remaining 10.8s, peak mem 156MB, user 147.2s, sys 17.4s, output queue size 13
progress 65% @chr13:32178744, elapsed 17.5s, est remaining 9.4s, peak mem 157MB, user 159.7s, sys 18.6s, output queue size 17
progress 70% @chr15:35538174, elapsed 18.8s, est remaining 8.1s, peak mem 157MB, user 172.1s, sys 19.8s, output queue size 4
progress 75% @chr16:28488491, elapsed 20.1s, est remaining 6.7s, peak mem 158MB, user 183.9s, sys 21.4s, output queue size 4
progress 80% @chr17:40032956, elapsed 21.5s, est remaining 5.4s, peak mem 159MB, user 197.4s, sys 22.8s, output queue size 1
progress 85% @chr19:1805788, elapsed 22.8s, est remaining 4.0s, peak mem 160MB, user 210.1s, sys 24.2s, output queue size 2
progress 90% @chr19:54630974, elapsed 24.1s, est remaining 2.7s, peak mem 160MB, user 222.6s, sys 25.3s, output queue size 3
progress 95% @chr22:32049843, elapsed 27.5s, est remaining 1.4s, peak mem 357MB, user 254.2s, sys 27.3s, output queue size 19
progress 100% @chrY:23169898, elapsed 28.7s, est remaining 0.0s, peak mem 357MB, user 265.6s, sys 28.6s, output queue size 115
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 93248820
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 1.049 user 0.046 sys 1.117 real
"assemble_addRead": 221 calls 0.010 user 0.000 sys 0.018 real
"assemble_buildGraph": 496 calls 0.477 user 0.020 sys 0.512 real
"assemble_computecigar": 329 calls 0.160 user 0.010 sys 0.182 real
"assemble_kg_build_calcsize": 496 calls 0.269 user 0.000 sys 0.250 real
"assemble_kg_build_clear": 650 calls 0.020 user 0.000 sys 0.022 real
"assemble_kg_build_prepare": 992 calls 0.192 user 0.036 sys 0.222 real
"assemble_kg_build_threading": 342 calls 0.198 user 0.010 sys 0.252 real
"assemble_kg_op1": 342 calls 0.118 user 0.000 sys 0.140 real
"assemble_kg_op2": 342 calls 0.000 user 0.000 sys 0.009 real
"assemble_kg_op3": 342 calls 0.010 user 0.000 sys 0.011 real
"assemble_sg_clean": 329 calls 0.090 user 0.000 sys 0.055 real
"assemble_sg_create": 329 calls 0.074 user 0.000 sys 0.083 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.160 user 0.010 sys 0.191 real
advance: 189104 calls 19.947 user 0.929 sys 32.661 real
assemble_region: 221 calls 1.219 user 0.056 sys 1.330 real
build_pileup: 70986 calls 0.729 user 0.054 sys 1.177 real
build_stats: 71711 calls 5.377 user 0.260 sys 6.948 real
build_variants: 178 calls 0.000 user 0.000 sys 0.002 real
calc: 128717 calls 4.445 user 0.185 sys 6.913 real
calc_region: 178 calls 4.849 user 0.048 sys 5.103 real
call_region: 178 calls 0.161 user 0.000 sys 0.123 real
clip_region: 399 calls 0.120 user 0.000 sys 0.087 real
done: 1 calls 1.331 user 0.009 sys 1.341 real
execute: 1 calls 0.000 user 0.012 sys 28.738 real
fetch: 743546 calls 1.528 user 0.207 sys 2.170 real
fetch_ref: 745726 calls 1.602 user 0.804 sys 4.916 real
fetch_region: 221 calls 0.050 user 0.000 sys 0.019 real
fetch_vcf: 189104 calls 58.537 user 2.772 sys 104.074 real
idle: 47 calls 0.029 user 0.011 sys 25.976 real
init: 1 calls 0.080 user 0.030 sys 0.118 real
pairhmm: 837 calls 8.977 user 0.053 sys 9.156 real
realign: 178 calls 0.898 user 0.000 sys 1.025 real
region: 367297 calls 6.184 user 0.210 sys 6.739 real
tracker: 367297 calls 0.686 user 0.127 sys 1.420 real
trim_region: 221 calls 0.010 user 0.000 sys 0.005 real
overall: 374611968 mem 298.862 user 40.836 sys 31.373 real