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/58/52929cba19d9b064778c257f6733b9/.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/f0/f8e7931c441b58d5eba8c2dd0f8018/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/f8e7931c441b58d5eba8c2dd0f8018/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/52929cba19d9b064778c257f6733b9/.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% @chr1:113710154, elapsed 0.7s, est remaining 12.5s, peak mem 142MB, user 6.5s, sys 0.4s, output queue size 4
progress 10% @chr2:3671058, elapsed 1.3s, est remaining 11.6s, peak mem 142MB, user 12.6s, sys 0.7s, output queue size 5
progress 15% @chr2:178606921, elapsed 1.9s, est remaining 11.0s, peak mem 143MB, user 18.9s, sys 1.2s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.2s, peak mem 144MB, user 24.7s, sys 1.6s, output queue size 0
progress 25% @chr4:70532355, elapsed 3.2s, est remaining 9.7s, peak mem 144MB, user 31.1s, sys 2.1s, output queue size 7
progress 30% @chr5:135850325, elapsed 3.9s, est remaining 9.1s, peak mem 146MB, user 37.4s, sys 2.5s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.5s, est remaining 8.4s, peak mem 146MB, user 43.1s, sys 2.9s, output queue size 3
progress 40% @chr7:106248199, elapsed 5.2s, est remaining 7.7s, peak mem 147MB, user 49.3s, sys 3.4s, output queue size 14
progress 45% @chr8:143820566, elapsed 5.8s, est remaining 7.1s, peak mem 148MB, user 55.4s, sys 4.0s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.5s, est remaining 6.5s, peak mem 149MB, user 61.5s, sys 4.4s, output queue size 1
progress 55% @chr11:34132025, elapsed 7.1s, est remaining 5.8s, peak mem 149MB, user 67.4s, sys 4.9s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.7s, est remaining 5.1s, peak mem 149MB, user 73.2s, sys 5.3s, output queue size 9
progress 65% @chr13:32149648, elapsed 8.4s, est remaining 4.5s, peak mem 150MB, user 79.4s, sys 5.7s, output queue size 6
progress 70% @chr15:35521993, elapsed 9.0s, est remaining 3.9s, peak mem 150MB, user 85.1s, sys 6.2s, output queue size 3
progress 75% @chr16:28494582, elapsed 9.6s, est remaining 3.2s, peak mem 151MB, user 91.0s, sys 6.6s, output queue size 0
progress 80% @chr17:40034816, elapsed 10.3s, est remaining 2.6s, peak mem 151MB, user 97.7s, sys 7.1s, output queue size 2
progress 85% @chr19:1805788, elapsed 11.0s, est remaining 1.9s, peak mem 151MB, user 104.0s, sys 7.6s, output queue size 2
progress 90% @chr19:54630974, elapsed 11.6s, est remaining 1.3s, peak mem 151MB, user 110.2s, sys 8.0s, output queue size 3
progress 95% @chr22:31897382, elapsed 13.3s, est remaining 0.7s, peak mem 340MB, user 126.1s, sys 8.7s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3946851, elapsed 13.9s, est remaining 0.0s, peak mem 340MB, user 131.7s, sys 9.1s, output queue size 357
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 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 93248824
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.485 user 0.015 sys 0.502 real
"assemble_addRead": 221 calls 0.000 user 0.000 sys 0.008 real
"assemble_buildGraph": 496 calls 0.181 user 0.009 sys 0.214 real
"assemble_computecigar": 329 calls 0.080 user 0.010 sys 0.079 real
"assemble_kg_build_calcsize": 496 calls 0.100 user 0.000 sys 0.103 real
"assemble_kg_build_clear": 650 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_build_prepare": 992 calls 0.157 user 0.001 sys 0.096 real
"assemble_kg_build_threading": 342 calls 0.081 user 0.009 sys 0.107 real
"assemble_kg_op1": 342 calls 0.077 user 0.000 sys 0.080 real
"assemble_kg_op2": 342 calls 0.000 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 0.020 user 0.000 sys 0.026 real
"assemble_sg_create": 329 calls 0.034 user 0.000 sys 0.039 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.084 user 0.010 sys 0.083 real
advance: 189104 calls 13.718 user 0.401 sys 18.831 real
assemble_region: 221 calls 0.579 user 0.025 sys 0.595 real
build_pileup: 70986 calls 0.315 user 0.031 sys 0.453 real
build_stats: 71711 calls 2.446 user 0.097 sys 2.324 real
build_variants: 178 calls 0.000 user 0.000 sys 0.001 real
calc: 128717 calls 2.102 user 0.059 sys 2.886 real
calc_region: 178 calls 2.957 user 0.001 sys 3.025 real
call_region: 178 calls 0.069 user 0.000 sys 0.059 real
clip_region: 399 calls 0.055 user 0.000 sys 0.042 real
done: 1 calls 0.463 user 0.009 sys 0.477 real
execute: 1 calls 0.005 user 0.001 sys 13.915 real
fetch: 743546 calls 0.896 user 0.048 sys 0.882 real
fetch_ref: 745726 calls 1.521 user 0.461 sys 2.892 real
fetch_region: 221 calls 0.015 user 0.000 sys 0.009 real
fetch_vcf: 189104 calls 37.574 user 1.072 sys 55.513 real
idle: 35 calls 0.005 user 0.001 sys 12.855 real
init: 1 calls 0.050 user 0.010 sys 0.059 real
pairhmm: 837 calls 4.711 user 0.010 sys 4.801 real
realign: 178 calls 0.614 user 0.000 sys 0.620 real
region: 367297 calls 3.590 user 0.067 sys 3.733 real
tracker: 367297 calls 0.413 user 0.024 sys 0.548 real
trim_region: 221 calls 0.000 user 0.000 sys 0.002 real
overall: 357343232 mem 157.359 user 13.467 sys 15.240 real