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/ad/ded0dc28f0bedef0afd0b3c848896c/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/b8/06e919f7e3f9ee3a0b3a35f50495c7/.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/ad/ded0dc28f0bedef0afd0b3c848896c/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/06e919f7e3f9ee3a0b3a35f50495c7/.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% @chr1:113711646, elapsed 1.1s, est remaining 21.2s, peak mem 144MB, user 11.0s, sys 0.6s, output queue size 4
progress 10% @chr2:3643344, elapsed 2.2s, est remaining 20.0s, peak mem 145MB, user 21.6s, sys 1.4s, output queue size 6
progress 15% @chr2:178609108, elapsed 3.4s, est remaining 19.4s, peak mem 146MB, user 32.8s, sys 1.9s, output queue size 12
progress 20% @chr3:57508282, elapsed 4.5s, est remaining 17.9s, peak mem 147MB, user 42.6s, sys 2.7s, output queue size 1
progress 25% @chr4:70530939, elapsed 5.6s, est remaining 16.8s, peak mem 147MB, user 53.3s, sys 3.2s, output queue size 8
progress 30% @chr5:135850325, elapsed 6.8s, est remaining 16.0s, peak mem 149MB, user 64.8s, sys 3.9s, output queue size 4
progress 35% @chr6:104859467, elapsed 7.9s, est remaining 14.7s, peak mem 150MB, user 75.7s, sys 4.7s, output queue size 2
progress 40% @chr7:106867451, elapsed 9.0s, est remaining 13.5s, peak mem 152MB, user 85.8s, sys 5.4s, output queue size 23
progress 45% @chr8:143821497, elapsed 10.1s, est remaining 12.4s, peak mem 152MB, user 96.9s, sys 6.0s, output queue size 0
progress 50% @chr10:21726144, elapsed 11.2s, est remaining 11.2s, peak mem 154MB, user 106.4s, sys 6.6s, output queue size 1
progress 55% @chr11:34124202, elapsed 12.3s, est remaining 10.1s, peak mem 154MB, user 114.8s, sys 7.1s, output queue size 5
progress 60% @chr12:12908150, elapsed 13.4s, est remaining 8.9s, peak mem 154MB, user 125.9s, sys 7.7s, output queue size 17
progress 65% @chr13:32149648, elapsed 14.5s, est remaining 7.8s, peak mem 154MB, user 136.5s, sys 8.3s, output queue size 0
progress 70% @chr15:35542313, elapsed 15.6s, est remaining 6.7s, peak mem 155MB, user 147.6s, sys 9.0s, output queue size 4
progress 75% @chr16:28488491, elapsed 16.7s, est remaining 5.6s, peak mem 156MB, user 159.1s, sys 9.7s, output queue size 2
progress 80% @chr17:40032956, elapsed 17.9s, est remaining 4.5s, peak mem 156MB, user 171.3s, sys 10.4s, output queue size 2
progress 85% @chr19:1805788, elapsed 19.1s, est remaining 3.4s, peak mem 156MB, user 182.4s, sys 10.9s, output queue size 15
progress 90% @chr19:54662811, elapsed 20.2s, est remaining 2.2s, peak mem 156MB, user 193.2s, sys 11.5s, output queue size 6
progress 95% @chr22:32043182, elapsed 22.7s, est remaining 1.2s, peak mem 328MB, user 217.9s, sys 12.5s, output queue size 5
progress 100% @chr6_GL000251v2_alt:3935549, elapsed 23.6s, est remaining 0.0s, peak mem 329MB, user 227.5s, sys 13.1s, output queue size 405
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 71692760
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.824 user 0.001 sys 0.704 real
"assemble_addRead": 183 calls 0.000 user 0.010 sys 0.013 real
"assemble_buildGraph": 422 calls 0.292 user 0.000 sys 0.307 real
"assemble_computecigar": 264 calls 0.110 user 0.000 sys 0.119 real
"assemble_kg_build_calcsize": 422 calls 0.160 user 0.000 sys 0.146 real
"assemble_kg_build_clear": 573 calls 0.010 user 0.000 sys 0.013 real
"assemble_kg_build_prepare": 844 calls 0.252 user 0.001 sys 0.150 real
"assemble_kg_build_threading": 271 calls 0.112 user 0.000 sys 0.153 real
"assemble_kg_op1": 271 calls 0.091 user 0.000 sys 0.084 real
"assemble_kg_op2": 271 calls 0.010 user 0.000 sys 0.007 real
"assemble_kg_op3": 271 calls 0.010 user 0.000 sys 0.007 real
"assemble_sg_clean": 264 calls 0.040 user 0.000 sys 0.036 real
"assemble_sg_create": 264 calls 0.100 user 0.000 sys 0.054 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.110 user 0.000 sys 0.125 real
advance: 189104 calls 23.405 user 0.505 sys 29.758 real
assemble_region: 183 calls 0.935 user 0.010 sys 0.844 real
build_pileup: 70974 calls 0.979 user 0.029 sys 1.035 real
build_stats: 71688 calls 4.613 user 0.105 sys 5.279 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 5.909 user 0.151 sys 7.340 real
calc_region: 142 calls 2.911 user 0.011 sys 3.037 real
call_region: 142 calls 0.030 user 0.000 sys 0.058 real
clip_region: 325 calls 0.010 user 0.000 sys 0.044 real
done: 1 calls 0.754 user 0.000 sys 0.754 real
execute: 1 calls 0.006 user 0.002 sys 23.664 real
fetch: 743546 calls 1.361 user 0.160 sys 1.800 real
fetch_ref: 745688 calls 3.309 user 0.758 sys 5.360 real
fetch_region: 183 calls 0.000 user 0.000 sys 0.011 real
fetch_vcf: 189104 calls 74.229 user 1.487 sys 95.588 real
idle: 35 calls 0.002 user 0.007 sys 13.329 real
init: 1 calls 0.060 user 0.020 sys 0.085 real
pairhmm: 472 calls 5.423 user 0.020 sys 5.479 real
realign: 142 calls 0.401 user 0.000 sys 0.456 real
region: 367297 calls 4.040 user 0.102 sys 4.160 real
tracker: 367297 calls 1.047 user 0.104 sys 1.352 real
trim_region: 183 calls 0.000 user 0.000 sys 0.003 real
overall: 345100288 mem 270.124 user 18.327 sys 25.076 real