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/17/ff6eaa758c6f025b001c9e7a9f6eb5/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/a06e530ba91e8e382fc1a1479bc41a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ff6eaa758c6f025b001c9e7a9f6eb5/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/60/a06e530ba91e8e382fc1a1479bc41a/.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 0.7s, est remaining 12.9s, peak mem 145MB, user 7.0s, sys 0.3s, output queue size 5
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 12.0s, peak mem 145MB, user 13.5s, sys 0.7s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.3s, peak mem 146MB, user 20.4s, sys 1.1s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.4s, peak mem 146MB, user 26.7s, sys 1.5s, output queue size 0
progress 25% @chr4:70603777, elapsed 3.3s, est remaining 9.8s, peak mem 146MB, user 33.5s, sys 1.9s, output queue size 3
progress 30% @chr5:135873921, elapsed 3.9s, est remaining 9.2s, peak mem 147MB, user 40.3s, sys 2.3s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.5s, est remaining 8.4s, peak mem 150MB, user 46.5s, sys 2.7s, output queue size 3
progress 40% @chr7:106872437, elapsed 5.2s, est remaining 7.8s, peak mem 151MB, user 53.1s, sys 3.1s, output queue size 2
progress 45% @chr8:143820566, elapsed 5.8s, est remaining 7.1s, peak mem 151MB, user 59.9s, sys 3.4s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.5s, est remaining 6.5s, peak mem 153MB, user 66.3s, sys 3.9s, output queue size 1
progress 55% @chr11:34132926, elapsed 7.1s, est remaining 5.8s, peak mem 153MB, user 72.8s, sys 4.3s, output queue size 5
progress 60% @chr12:12718707, elapsed 7.7s, est remaining 5.1s, peak mem 153MB, user 79.0s, sys 4.7s, output queue size 10
progress 65% @chr13:32149648, elapsed 8.3s, est remaining 4.5s, peak mem 153MB, user 85.6s, sys 5.1s, output queue size 0
progress 70% @chr15:35521993, elapsed 9.0s, est remaining 3.8s, peak mem 154MB, user 92.0s, sys 5.5s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.6s, est remaining 3.2s, peak mem 155MB, user 98.4s, sys 5.8s, output queue size 0
progress 80% @chr17:40035622, elapsed 10.3s, est remaining 2.6s, peak mem 155MB, user 105.5s, sys 6.3s, output queue size 1
progress 85% @chr19:1806528, elapsed 10.9s, est remaining 1.9s, peak mem 155MB, user 112.2s, sys 6.7s, output queue size 3
progress 90% @chr19:54630974, elapsed 11.6s, est remaining 1.3s, peak mem 155MB, user 118.9s, sys 7.0s, output queue size 2
progress 95% @chr22:31897382, elapsed 13.1s, est remaining 0.7s, peak mem 341MB, user 133.6s, sys 7.5s, output queue size 10
progress 100% @chrY:20589384, elapsed 13.7s, est remaining 0.0s, peak mem 342MB, user 139.7s, sys 7.9s, output queue size 408
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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 81484549
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.289 user 0.000 sys 0.412 real
"assemble_addRead": 207 calls 0.000 user 0.000 sys 0.007 real
"assemble_buildGraph": 465 calls 0.091 user 0.000 sys 0.176 real
"assemble_computecigar": 304 calls 0.074 user 0.029 sys 0.089 real
"assemble_kg_build_calcsize": 465 calls 0.025 user 0.000 sys 0.085 real
"assemble_kg_build_clear": 618 calls 0.000 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 930 calls 0.046 user 0.000 sys 0.080 real
"assemble_kg_build_threading": 312 calls 0.066 user 0.000 sys 0.087 real
"assemble_kg_op1": 312 calls 0.070 user 0.000 sys 0.058 real
"assemble_kg_op2": 312 calls 0.004 user 0.000 sys 0.004 real
"assemble_kg_op3": 312 calls 0.010 user 0.000 sys 0.005 real
"assemble_sg_clean": 304 calls 0.010 user 0.000 sys 0.022 real
"assemble_sg_create": 304 calls 0.028 user 0.000 sys 0.036 real
"checkGraph": 207 calls 0.010 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.074 user 0.029 sys 0.093 real
advance: 189104 calls 15.864 user 0.294 sys 18.899 real
assemble_region: 207 calls 0.383 user 0.029 sys 0.513 real
build_pileup: 70976 calls 0.418 user 0.012 sys 0.454 real
build_stats: 71686 calls 1.814 user 0.067 sys 2.204 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.260 user 0.047 sys 2.906 real
calc_region: 162 calls 1.784 user 0.001 sys 1.754 real
call_region: 162 calls 0.007 user 0.000 sys 0.038 real
clip_region: 369 calls 0.020 user 0.000 sys 0.029 real
done: 1 calls 0.421 user 0.009 sys 0.439 real
execute: 1 calls 0.003 user 0.010 sys 13.660 real
fetch: 743546 calls 0.605 user 0.057 sys 0.858 real
fetch_ref: 745712 calls 1.710 user 0.459 sys 2.707 real
fetch_region: 207 calls 0.014 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 42.842 user 0.807 sys 55.735 real
idle: 35 calls 0.005 user 0.009 sys 12.863 real
init: 1 calls 0.060 user 0.000 sys 0.058 real
pairhmm: 466 calls 3.109 user 0.005 sys 2.994 real
realign: 162 calls 0.339 user 0.000 sys 0.338 real
region: 367297 calls 2.181 user 0.087 sys 2.372 real
tracker: 367297 calls 0.334 user 0.023 sys 0.547 real
trim_region: 207 calls 0.000 user 0.000 sys 0.002 real
overall: 359026688 mem 155.559 user 10.719 sys 14.950 real