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/09/cd42a442d1adb2b58ee18c96241d00/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/1ba39fc6c614f2be29cd8d31b84675/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/cd42a442d1adb2b58ee18c96241d00/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/2b/1ba39fc6c614f2be29cd8d31b84675/.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% @chr1:113682797, elapsed 0.7s, est remaining 13.2s, peak mem 144MB, user 6.8s, sys 0.5s, output queue size 3
progress 10% @chr2:3643344, elapsed 1.4s, est remaining 12.4s, peak mem 144MB, user 13.5s, sys 1.1s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.6s, peak mem 145MB, user 20.3s, sys 1.6s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.7s, est remaining 10.6s, peak mem 145MB, user 26.5s, sys 2.1s, output queue size 0
progress 25% @chr4:70631570, elapsed 3.4s, est remaining 10.1s, peak mem 146MB, user 33.4s, sys 2.4s, output queue size 3
progress 30% @chr5:135571753, elapsed 4.1s, est remaining 9.5s, peak mem 148MB, user 40.4s, sys 2.8s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.7s, est remaining 8.7s, peak mem 148MB, user 46.8s, sys 3.3s, output queue size 2
progress 40% @chr7:106879419, elapsed 5.4s, est remaining 8.0s, peak mem 149MB, user 53.6s, sys 3.7s, output queue size 2
progress 45% @chr8:143821497, elapsed 6.0s, est remaining 7.4s, peak mem 150MB, user 60.7s, sys 4.1s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.7s, est remaining 6.7s, peak mem 152MB, user 67.2s, sys 4.5s, output queue size 1
progress 55% @chr11:34132025, elapsed 7.4s, est remaining 6.0s, peak mem 152MB, user 73.7s, sys 4.9s, output queue size 1
progress 60% @chr12:12911984, elapsed 8.0s, est remaining 5.3s, peak mem 153MB, user 79.9s, sys 5.5s, output queue size 17
progress 65% @chr13:32147739, elapsed 8.7s, est remaining 4.7s, peak mem 153MB, user 86.5s, sys 5.9s, output queue size 10
progress 70% @chr15:34969439, elapsed 9.3s, est remaining 4.0s, peak mem 154MB, user 93.0s, sys 6.3s, output queue size 6
progress 75% @chr16:28499551, elapsed 9.9s, est remaining 3.3s, peak mem 155MB, user 99.4s, sys 6.8s, output queue size 4
progress 80% @chr17:40032956, elapsed 10.6s, est remaining 2.7s, peak mem 156MB, user 106.7s, sys 7.2s, output queue size 4
progress 85% @chr19:1806528, elapsed 11.3s, est remaining 2.0s, peak mem 156MB, user 113.5s, sys 7.6s, output queue size 3
progress 90% @chr19:54630974, elapsed 11.9s, est remaining 1.3s, peak mem 156MB, user 120.3s, sys 7.9s, output queue size 5
progress 95% @chr22:32066835, elapsed 13.5s, est remaining 0.7s, peak mem 331MB, user 135.4s, sys 8.4s, output queue size 1
progress 100% @chrY:13359667, elapsed 14.1s, est remaining 0.0s, peak mem 331MB, user 141.5s, sys 8.8s, output queue size 406
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 81484552
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.507 user 0.006 sys 0.427 real
"assemble_addRead": 207 calls 0.010 user 0.000 sys 0.007 real
"assemble_buildGraph": 465 calls 0.265 user 0.005 sys 0.182 real
"assemble_computecigar": 304 calls 0.059 user 0.000 sys 0.092 real
"assemble_kg_build_calcsize": 465 calls 0.133 user 0.000 sys 0.089 real
"assemble_kg_build_clear": 618 calls 0.010 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 930 calls 0.056 user 0.000 sys 0.082 real
"assemble_kg_build_threading": 312 calls 0.122 user 0.005 sys 0.090 real
"assemble_kg_op1": 312 calls 0.051 user 0.000 sys 0.061 real
"assemble_kg_op2": 312 calls 0.000 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 0.002 user 0.000 sys 0.023 real
"assemble_sg_create": 304 calls 0.046 user 0.000 sys 0.037 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 207 calls 0.059 user 0.000 sys 0.096 real
advance: 189104 calls 15.170 user 0.412 sys 19.306 real
assemble_region: 207 calls 0.576 user 0.006 sys 0.532 real
build_pileup: 70976 calls 0.304 user 0.034 sys 0.473 real
build_stats: 71686 calls 2.054 user 0.036 sys 2.365 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.168 user 0.037 sys 3.078 real
calc_region: 162 calls 1.755 user 0.021 sys 1.824 real
call_region: 162 calls 0.014 user 0.000 sys 0.040 real
clip_region: 369 calls 0.020 user 0.000 sys 0.029 real
done: 1 calls 0.446 user 0.003 sys 0.453 real
execute: 1 calls 0.003 user 0.010 sys 14.083 real
fetch: 743546 calls 0.602 user 0.109 sys 0.872 real
fetch_ref: 745712 calls 1.682 user 0.415 sys 2.789 real
fetch_region: 207 calls 0.020 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 42.815 user 1.013 sys 56.948 real
idle: 35 calls 0.003 user 0.019 sys 12.894 real
init: 1 calls 0.049 user 0.011 sys 0.059 real
pairhmm: 466 calls 3.091 user 0.050 sys 3.064 real
realign: 162 calls 0.267 user 0.000 sys 0.344 real
region: 367297 calls 2.367 user 0.070 sys 2.465 real
tracker: 367297 calls 0.371 user 0.048 sys 0.580 real
trim_region: 207 calls 0.010 user 0.000 sys 0.002 real
overall: 347697152 mem 158.839 user 12.141 sys 15.402 real