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/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  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/53/d20e768757aeae325fc90a9d215101/.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/d20e768757aeae325fc90a9d215101/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b8328367b22c15bd3300ec483b8d21/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b8328367b22c15bd3300ec483b8d21/Sig_18_Blood.recalibrated.bam
==> 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_Blood.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_Blood --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_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_Blood negative_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_Blood --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_2.tnseq.segments negative_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113703957, elapsed 2.2s, est remaining 41.1s, peak mem 141MB, user 9.0s, sys 1.2s, output queue size 69
progress 10% @chr2:3701412, elapsed 4.3s, est remaining 38.9s, peak mem 141MB, user 17.3s, sys 2.3s, output queue size 419
progress 15% @chr2:178613651, elapsed 6.8s, est remaining 38.6s, peak mem 141MB, user 26.4s, sys 3.3s, output queue size 109
progress 20% @chr3:57366629, elapsed 8.8s, est remaining 35.0s, peak mem 141MB, user 34.9s, sys 4.0s, output queue size 222
progress 25% @chr4:70634208, elapsed 11.1s, est remaining 33.2s, peak mem 141MB, user 44.1s, sys 4.9s, output queue size 417
progress 30% @chr5:135879868, elapsed 13.2s, est remaining 30.8s, peak mem 142MB, user 53.5s, sys 6.0s, output queue size 70
progress 35% @chr6:104850807, elapsed 14.8s, est remaining 27.6s, peak mem 142MB, user 62.0s, sys 6.8s, output queue size 78
progress 40% @chr7:107128112, elapsed 16.6s, est remaining 25.0s, peak mem 142MB, user 71.7s, sys 7.7s, output queue size 115
progress 45% @chr8:143838580, elapsed 18.7s, est remaining 22.9s, peak mem 143MB, user 81.2s, sys 8.5s, output queue size 104
progress 50% @chr10:21673250, elapsed 20.5s, est remaining 20.5s, peak mem 146MB, user 90.5s, sys 9.4s, output queue size 68
progress 55% @chr11:34140300, elapsed 22.5s, est remaining 18.4s, peak mem 146MB, user 99.6s, sys 10.2s, output queue size 205
progress 60% @chr12:12823770, elapsed 24.4s, est remaining 16.3s, peak mem 146MB, user 107.9s, sys 11.0s, output queue size 74
progress 65% @chr13:32182877, elapsed 26.4s, est remaining 14.2s, peak mem 147MB, user 117.1s, sys 11.7s, output queue size 167
progress 70% @chr15:36808224, elapsed 28.1s, est remaining 12.0s, peak mem 147MB, user 126.4s, sys 12.3s, output queue size 129
progress 75% @chr16:28499551, elapsed 29.6s, est remaining 9.9s, peak mem 147MB, user 135.7s, sys 13.1s, output queue size 67
progress 80% @chr17:40083735, elapsed 31.2s, est remaining 7.8s, peak mem 147MB, user 145.5s, sys 14.0s, output queue size 15
progress 85% @chr19:1806528, elapsed 33.0s, est remaining 5.8s, peak mem 147MB, user 155.2s, sys 14.7s, output queue size 28
progress 90% @chr19:54663432, elapsed 34.7s, est remaining 3.9s, peak mem 147MB, user 164.5s, sys 15.5s, output queue size 19
progress 95% @chr22:32084339, elapsed 38.5s, est remaining 2.0s, peak mem 319MB, user 187.6s, sys 16.4s, output queue size 458
progress 100% @chrY:23248663, elapsed 40.3s, est remaining 0.0s, peak mem 319MB, user 195.2s, sys 17.7s, output queue size 1122
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef 40417f5e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 74732894
output file size: 51112
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.825 user 0.001 sys 1.248 real
"assemble_addRead": 189 calls 0.010 user 0.000 sys 0.026 real
"assemble_buildGraph": 446 calls 0.316 user 0.000 sys 0.471 real
"assemble_computecigar": 274 calls 0.082 user 0.010 sys 0.193 real
"assemble_kg_build_calcsize": 446 calls 0.130 user 0.000 sys 0.214 real
"assemble_kg_build_clear": 608 calls 0.040 user 0.000 sys 0.049 real
"assemble_kg_build_prepare": 892 calls 0.158 user 0.000 sys 0.246 real
"assemble_kg_build_threading": 284 calls 0.186 user 0.000 sys 0.248 real
"assemble_kg_op1": 284 calls 0.139 user 0.000 sys 0.220 real
"assemble_kg_op2": 284 calls 0.010 user 0.000 sys 0.016 real
"assemble_kg_op3": 284 calls 0.020 user 0.000 sys 0.007 real
"assemble_sg_clean": 274 calls 0.010 user 0.000 sys 0.058 real
"assemble_sg_create": 274 calls 0.090 user 0.000 sys 0.107 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.082 user 0.010 sys 0.198 real
advance: 189104 calls 18.934 user 0.515 sys 37.994 real
assemble_region: 189 calls 0.916 user 0.010 sys 1.475 real
build_pileup: 70986 calls 0.636 user 0.038 sys 1.405 real
build_stats: 71708 calls 4.624 user 0.079 sys 8.543 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 6.045 user 0.159 sys 11.359 real
calc_region: 158 calls 2.658 user 0.011 sys 4.403 real
call_region: 158 calls 0.120 user 0.000 sys 0.149 real
clip_region: 347 calls 0.071 user 0.000 sys 0.100 real
done: 1 calls 0.893 user 0.009 sys 0.908 real
execute: 1 calls 0.012 user 0.000 sys 40.352 real
fetch: 743546 calls 1.587 user 0.120 sys 2.858 real
fetch_ref: 745694 calls 2.036 user 0.955 sys 5.893 real
fetch_region: 189 calls 0.020 user 0.000 sys 0.023 real
fetch_vcf: 189104 calls 64.012 user 1.402 sys 124.879 real
idle: 35 calls 0.003 user 0.004 sys 13.613 real
init: 1 calls 0.086 user 0.019 sys 0.108 real
pairhmm: 454 calls 4.747 user 0.028 sys 6.806 real
realign: 158 calls 0.511 user 0.000 sys 0.921 real
region: 367297 calls 3.721 user 0.123 sys 6.200 real
tracker: 367297 calls 0.899 user 0.134 sys 1.823 real
trim_region: 189 calls 0.000 user 0.000 sys 0.003 real
overall: 334733312 mem 220.366 user 19.841 sys 42.025 real