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-rnd-pltf-dev-nextflow-scratch-01/work/53/ceed4bf612d62859d876f95d1d2d6f/HCC1395_BL.recalibrated.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/97/c3b91be88fa4fd3c26d5718f572e73/.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/53/ceed4bf612d62859d876f95d1d2d6f/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/c3b91be88fa4fd3c26d5718f572e73/.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_BL.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_BL --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz negative_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL negative_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_1.tnseq.segments negative_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113698162, elapsed 1.0s, est remaining 19.2s, peak mem 144MB, user 9.6s, sys 0.7s, output queue size 4
progress 10% @chr2:3580705, elapsed 2.0s, est remaining 17.9s, peak mem 145MB, user 18.2s, sys 1.3s, output queue size 7
progress 15% @chr2:178598406, elapsed 3.1s, est remaining 17.7s, peak mem 146MB, user 29.4s, sys 1.8s, output queue size 11
progress 20% @chr3:57489409, elapsed 4.2s, est remaining 16.8s, peak mem 146MB, user 39.9s, sys 2.5s, output queue size 0
progress 25% @chr4:70632551, elapsed 5.3s, est remaining 16.0s, peak mem 147MB, user 51.5s, sys 3.2s, output queue size 9
progress 30% @chr5:135574472, elapsed 6.5s, est remaining 15.1s, peak mem 150MB, user 63.2s, sys 3.9s, output queue size 4
progress 35% @chr6:104843123, elapsed 7.5s, est remaining 14.0s, peak mem 151MB, user 73.5s, sys 4.6s, output queue size 2
progress 40% @chr7:106248199, elapsed 8.7s, est remaining 13.1s, peak mem 151MB, user 84.4s, sys 5.2s, output queue size 19
progress 45% @chr8:143821497, elapsed 9.9s, est remaining 12.1s, peak mem 152MB, user 95.4s, sys 5.8s, output queue size 3
progress 50% @chr10:21514996, elapsed 11.0s, est remaining 11.0s, peak mem 155MB, user 105.8s, sys 6.6s, output queue size 13
progress 55% @chr11:34132025, elapsed 12.1s, est remaining 9.9s, peak mem 155MB, user 115.5s, sys 7.2s, output queue size 4
progress 60% @chr12:12727270, elapsed 13.1s, est remaining 8.8s, peak mem 156MB, user 124.7s, sys 7.9s, output queue size 5
progress 65% @chr13:32078734, elapsed 14.2s, est remaining 7.6s, peak mem 156MB, user 135.2s, sys 8.6s, output queue size 10
progress 70% @chr15:35521993, elapsed 15.2s, est remaining 6.5s, peak mem 156MB, user 145.8s, sys 9.3s, output queue size 7
progress 75% @chr16:28494582, elapsed 16.3s, est remaining 5.4s, peak mem 156MB, user 156.6s, sys 9.8s, output queue size 0
progress 80% @chr17:40076771, elapsed 17.6s, est remaining 4.4s, peak mem 156MB, user 169.4s, sys 10.7s, output queue size 1
progress 85% @chr19:1805788, elapsed 18.8s, est remaining 3.3s, peak mem 157MB, user 181.8s, sys 11.4s, output queue size 2
progress 90% @chr19:54600412, elapsed 20.0s, est remaining 2.2s, peak mem 157MB, user 194.1s, sys 12.0s, output queue size 4
progress 95% @chr22:32067867, elapsed 22.6s, est remaining 1.2s, peak mem 332MB, user 220.6s, sys 12.9s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 23.5s, est remaining 0.0s, peak mem 332MB, user 228.9s, sys 13.5s, output queue size 10
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 48
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 71692764
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.698 user 0.000 sys 0.755 real
"assemble_addRead": 183 calls 0.030 user 0.000 sys 0.014 real
"assemble_buildGraph": 422 calls 0.304 user 0.000 sys 0.330 real
"assemble_computecigar": 264 calls 0.149 user 0.003 sys 0.134 real
"assemble_kg_build_calcsize": 422 calls 0.200 user 0.000 sys 0.157 real
"assemble_kg_build_clear": 573 calls 0.020 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 844 calls 0.119 user 0.000 sys 0.161 real
"assemble_kg_build_threading": 271 calls 0.104 user 0.000 sys 0.165 real
"assemble_kg_op1": 271 calls 0.095 user 0.000 sys 0.090 real
"assemble_kg_op2": 271 calls 0.000 user 0.000 sys 0.006 real
"assemble_kg_op3": 271 calls 0.020 user 0.000 sys 0.007 real
"assemble_sg_clean": 264 calls 0.046 user 0.000 sys 0.038 real
"assemble_sg_create": 264 calls 0.055 user 0.000 sys 0.057 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.149 user 0.003 sys 0.140 real
advance: 189104 calls 23.510 user 0.627 sys 29.710 real
assemble_region: 183 calls 0.877 user 0.003 sys 0.912 real
build_pileup: 70974 calls 0.847 user 0.027 sys 1.033 real
build_stats: 71688 calls 4.684 user 0.099 sys 5.289 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 5.730 user 0.098 sys 7.263 real
calc_region: 142 calls 3.617 user 0.018 sys 3.716 real
call_region: 142 calls 0.090 user 0.000 sys 0.065 real
clip_region: 325 calls 0.050 user 0.000 sys 0.047 real
done: 1 calls 0.652 user 0.000 sys 0.659 real
execute: 1 calls 0.005 user 0.011 sys 23.509 real
fetch: 743546 calls 1.407 user 0.117 sys 1.817 real
fetch_ref: 745688 calls 3.320 user 0.644 sys 5.352 real
fetch_region: 183 calls 0.020 user 0.000 sys 0.012 real
fetch_vcf: 189104 calls 73.509 user 1.682 sys 94.749 real
idle: 35 calls 0.007 user 0.003 sys 13.308 real
init: 1 calls 0.080 user 0.000 sys 0.084 real
pairhmm: 472 calls 5.397 user 0.016 sys 5.536 real
realign: 142 calls 0.466 user 0.000 sys 0.508 real
region: 367297 calls 4.709 user 0.084 sys 4.908 real
tracker: 367297 calls 0.885 user 0.107 sys 1.329 real
trim_region: 183 calls 0.000 user 0.000 sys 0.003 real
overall: 348835840 mem 268.100 user 18.679 sys 24.925 real