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/37/4d3ebe9948686a29f4969120b79632/.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/34/981bbb6fecd40b817ddc7930c036d0/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/981bbb6fecd40b817ddc7930c036d0/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/4d3ebe9948686a29f4969120b79632/.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% @chr1:113682797, elapsed 0.8s, est remaining 15.5s, peak mem 146MB, user 7.2s, sys 0.4s, output queue size 4
progress 10% @chr2:3625914, elapsed 1.6s, est remaining 14.0s, peak mem 146MB, user 14.2s, sys 0.8s, output queue size 5
progress 15% @chr2:178588438, elapsed 2.4s, est remaining 13.3s, peak mem 149MB, user 21.8s, sys 1.3s, output queue size 10
progress 20% @chr3:57489409, elapsed 3.1s, est remaining 12.3s, peak mem 150MB, user 28.7s, sys 1.7s, output queue size 2
progress 25% @chr4:70596899, elapsed 3.9s, est remaining 11.6s, peak mem 150MB, user 36.2s, sys 2.1s, output queue size 4
progress 30% @chr5:135534877, elapsed 4.6s, est remaining 10.8s, peak mem 152MB, user 43.6s, sys 2.6s, output queue size 3
progress 35% @chr6:104849042, elapsed 5.3s, est remaining 9.9s, peak mem 153MB, user 50.2s, sys 3.2s, output queue size 7
progress 40% @chr7:106867451, elapsed 6.1s, est remaining 9.2s, peak mem 153MB, user 57.7s, sys 3.6s, output queue size 23
progress 45% @chr8:143836939, elapsed 6.9s, est remaining 8.4s, peak mem 154MB, user 65.1s, sys 4.0s, output queue size 1
progress 50% @chr10:21514996, elapsed 7.6s, est remaining 7.6s, peak mem 158MB, user 72.3s, sys 4.3s, output queue size 17
progress 55% @chr11:34136542, elapsed 8.3s, est remaining 6.8s, peak mem 159MB, user 79.6s, sys 4.7s, output queue size 5
progress 60% @chr12:12911984, elapsed 9.1s, est remaining 6.0s, peak mem 159MB, user 86.5s, sys 5.2s, output queue size 17
progress 65% @chr13:32149648, elapsed 9.8s, est remaining 5.3s, peak mem 160MB, user 93.7s, sys 5.6s, output queue size 0
progress 70% @chr15:34969439, elapsed 10.6s, est remaining 4.5s, peak mem 161MB, user 100.7s, sys 6.2s, output queue size 7
progress 75% @chr16:28486247, elapsed 11.3s, est remaining 3.8s, peak mem 162MB, user 107.8s, sys 6.6s, output queue size 4
progress 80% @chr17:40032956, elapsed 12.0s, est remaining 3.0s, peak mem 162MB, user 115.2s, sys 7.0s, output queue size 1
progress 85% @chr19:1799847, elapsed 12.8s, est remaining 2.3s, peak mem 162MB, user 122.4s, sys 7.4s, output queue size 15
progress 90% @chr19:54632916, elapsed 13.5s, est remaining 1.5s, peak mem 163MB, user 129.5s, sys 7.7s, output queue size 3
progress 95% @chr22:32043182, elapsed 15.4s, est remaining 0.8s, peak mem 356MB, user 147.7s, sys 8.3s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3933919, elapsed 16.1s, est remaining 0.0s, peak mem 356MB, user 154.3s, sys 8.8s, output queue size 234
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa3203
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 48
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 0.589 user 0.010 sys 0.595 real
"assemble_addRead": 221 calls 0.040 user 0.000 sys 0.011 real
"assemble_buildGraph": 496 calls 0.324 user 0.000 sys 0.260 real
"assemble_computecigar": 329 calls 0.070 user 0.029 sys 0.092 real
"assemble_kg_build_calcsize": 496 calls 0.095 user 0.000 sys 0.121 real
"assemble_kg_build_clear": 650 calls 0.010 user 0.000 sys 0.011 real
"assemble_kg_build_prepare": 992 calls 0.109 user 0.009 sys 0.113 real
"assemble_kg_build_threading": 342 calls 0.229 user 0.000 sys 0.134 real
"assemble_kg_op1": 342 calls 0.087 user 0.000 sys 0.093 real
"assemble_kg_op2": 342 calls 0.010 user 0.000 sys 0.005 real
"assemble_kg_op3": 342 calls 0.000 user 0.000 sys 0.006 real
"assemble_sg_clean": 329 calls 0.010 user 0.000 sys 0.030 real
"assemble_sg_create": 329 calls 0.018 user 0.000 sys 0.046 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.090 user 0.029 sys 0.096 real
advance: 189104 calls 16.275 user 0.307 sys 21.389 real
assemble_region: 221 calls 0.719 user 0.039 sys 0.705 real
build_pileup: 70986 calls 0.493 user 0.013 sys 0.567 real
build_stats: 71711 calls 2.636 user 0.070 sys 3.106 real
build_variants: 178 calls 0.000 user 0.000 sys 0.001 real
calc: 128717 calls 2.916 user 0.054 sys 4.151 real
calc_region: 178 calls 3.183 user 0.013 sys 3.412 real
call_region: 178 calls 0.070 user 0.000 sys 0.069 real
clip_region: 399 calls 0.042 user 0.000 sys 0.050 real
done: 1 calls 0.476 user 0.000 sys 0.479 real
execute: 1 calls 0.002 user 0.010 sys 16.126 real
fetch: 743546 calls 0.839 user 0.074 sys 1.082 real
fetch_ref: 745726 calls 1.317 user 0.431 sys 2.892 real
fetch_region: 221 calls 0.010 user 0.000 sys 0.010 real
fetch_vcf: 189104 calls 46.082 user 1.059 sys 64.502 real
idle: 35 calls 0.006 user 0.001 sys 12.836 real
init: 1 calls 0.049 user 0.010 sys 0.059 real
pairhmm: 837 calls 5.397 user 0.010 sys 5.407 real
realign: 178 calls 0.614 user 0.000 sys 0.687 real
region: 367297 calls 3.923 user 0.098 sys 4.251 real
tracker: 367297 calls 0.448 user 0.040 sys 0.730 real
trim_region: 221 calls 0.000 user 0.000 sys 0.002 real
overall: 374128640 mem 184.400 user 12.538 sys 17.424 real