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/90/0b54fe50afe94e030665fb5e8c4d9b/.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/3c/c4ab70cd0462681d725647f4082e13/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/c4ab70cd0462681d725647f4082e13/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/0b54fe50afe94e030665fb5e8c4d9b/.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% @chr1:113705733, elapsed 0.9s, est remaining 17.4s, peak mem 145MB, user 8.7s, sys 0.8s, output queue size 4
progress 10% @chr2:3613211, elapsed 1.7s, est remaining 15.7s, peak mem 146MB, user 16.8s, sys 1.5s, output queue size 6
progress 15% @chr2:178610893, elapsed 2.6s, est remaining 14.9s, peak mem 147MB, user 25.8s, sys 2.2s, output queue size 12
progress 20% @chr3:57483276, elapsed 3.5s, est remaining 13.9s, peak mem 149MB, user 34.3s, sys 2.8s, output queue size 0
progress 25% @chr4:70602524, elapsed 4.4s, est remaining 13.1s, peak mem 149MB, user 43.2s, sys 3.5s, output queue size 8
progress 30% @chr5:135834748, elapsed 5.3s, est remaining 12.4s, peak mem 152MB, user 52.4s, sys 4.1s, output queue size 4
progress 35% @chr6:104791404, elapsed 6.2s, est remaining 11.4s, peak mem 154MB, user 60.5s, sys 4.8s, output queue size 6
progress 40% @chr7:106248199, elapsed 7.1s, est remaining 10.6s, peak mem 155MB, user 69.1s, sys 5.5s, output queue size 16
progress 45% @chr8:143824213, elapsed 8.0s, est remaining 9.7s, peak mem 155MB, user 78.0s, sys 6.1s, output queue size 4
progress 50% @chr10:21726144, elapsed 8.8s, est remaining 8.8s, peak mem 158MB, user 86.9s, sys 6.7s, output queue size 2
progress 55% @chr11:34132025, elapsed 9.7s, est remaining 8.0s, peak mem 158MB, user 95.9s, sys 7.4s, output queue size 1
progress 60% @chr12:12821108, elapsed 10.5s, est remaining 7.0s, peak mem 158MB, user 103.8s, sys 8.0s, output queue size 3
progress 65% @chr13:32078734, elapsed 11.4s, est remaining 6.1s, peak mem 158MB, user 112.4s, sys 8.8s, output queue size 10
progress 70% @chr15:35521993, elapsed 12.2s, est remaining 5.2s, peak mem 158MB, user 120.8s, sys 9.3s, output queue size 7
progress 75% @chr16:28488491, elapsed 13.1s, est remaining 4.4s, peak mem 158MB, user 129.1s, sys 10.0s, output queue size 2
progress 80% @chr17:40035622, elapsed 13.9s, est remaining 3.5s, peak mem 158MB, user 138.3s, sys 10.6s, output queue size 2
progress 85% @chr19:1809543, elapsed 14.8s, est remaining 2.6s, peak mem 158MB, user 147.1s, sys 11.1s, output queue size 16
progress 90% @chr19:54663432, elapsed 15.6s, est remaining 1.7s, peak mem 159MB, user 155.5s, sys 11.7s, output queue size 3
progress 95% @chr22:32067867, elapsed 17.8s, est remaining 0.9s, peak mem 355MB, user 177.0s, sys 12.6s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3935549, elapsed 18.6s, est remaining 0.0s, peak mem 355MB, user 184.6s, sys 13.2s, output queue size 421
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
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 0.711 user 0.011 sys 0.711 real
"assemble_addRead": 221 calls 0.000 user 0.000 sys 0.014 real
"assemble_buildGraph": 496 calls 0.331 user 0.011 sys 0.309 real
"assemble_computecigar": 329 calls 0.040 user 0.010 sys 0.109 real
"assemble_kg_build_calcsize": 496 calls 0.127 user 0.000 sys 0.143 real
"assemble_kg_build_clear": 650 calls 0.020 user 0.000 sys 0.014 real
"assemble_kg_build_prepare": 992 calls 0.128 user 0.000 sys 0.132 real
"assemble_kg_build_threading": 342 calls 0.204 user 0.011 sys 0.160 real
"assemble_kg_op1": 342 calls 0.081 user 0.000 sys 0.109 real
"assemble_kg_op2": 342 calls 0.010 user 0.000 sys 0.006 real
"assemble_kg_op3": 342 calls 0.004 user 0.000 sys 0.007 real
"assemble_sg_clean": 329 calls 0.050 user 0.000 sys 0.038 real
"assemble_sg_create": 329 calls 0.054 user 0.000 sys 0.055 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.045 user 0.010 sys 0.114 real
advance: 189104 calls 18.313 user 0.470 sys 23.990 real
assemble_region: 221 calls 0.757 user 0.021 sys 0.842 real
build_pileup: 70986 calls 0.456 user 0.010 sys 0.716 real
build_stats: 71711 calls 3.677 user 0.124 sys 3.967 real
build_variants: 178 calls 0.000 user 0.000 sys 0.001 real
calc: 128717 calls 4.389 user 0.115 sys 5.381 real
calc_region: 178 calls 3.703 user 0.021 sys 3.795 real
call_region: 178 calls 0.053 user 0.000 sys 0.084 real
clip_region: 399 calls 0.040 user 0.000 sys 0.057 real
done: 1 calls 0.473 user 0.000 sys 0.476 real
execute: 1 calls 0.008 user 0.001 sys 18.621 real
fetch: 743546 calls 0.975 user 0.124 sys 1.334 real
fetch_ref: 745726 calls 1.872 user 0.727 sys 3.236 real
fetch_region: 221 calls 0.000 user 0.000 sys 0.012 real
fetch_vcf: 189104 calls 55.026 user 1.311 sys 73.349 real
idle: 35 calls 0.023 user 0.021 sys 12.855 real
init: 1 calls 0.050 user 0.000 sys 0.058 real
pairhmm: 837 calls 6.320 user 0.018 sys 6.300 real
realign: 178 calls 0.788 user 0.000 sys 0.761 real
region: 367297 calls 4.525 user 0.127 sys 4.797 real
tracker: 367297 calls 0.543 user 0.122 sys 0.902 real
trim_region: 221 calls 0.000 user 0.000 sys 0.002 real
overall: 372817920 mem 210.417 user 17.690 sys 19.921 real