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/e4/3bcd1705aeeb238b6d1a0292be9aeb/.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/11/3addc8f0c39978145d931d25ba2ce6/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/3addc8f0c39978145d931d25ba2ce6/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/3bcd1705aeeb238b6d1a0292be9aeb/.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 Sig_18_tissue.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_tissue --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_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_tissue positive_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_2.tnseq.segments positive_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113682797, elapsed 0.7s, est remaining 12.6s, peak mem 145MB, user 6.3s, sys 0.3s, output queue size 3
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.7s, peak mem 146MB, user 12.2s, sys 0.8s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.1s, peak mem 146MB, user 18.5s, sys 1.2s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.3s, peak mem 146MB, user 24.3s, sys 1.5s, output queue size 0
progress 25% @chr4:70530939, elapsed 3.2s, est remaining 9.7s, peak mem 146MB, user 30.3s, sys 2.0s, output queue size 9
progress 30% @chr5:135571753, elapsed 3.9s, est remaining 9.1s, peak mem 148MB, user 36.4s, sys 2.4s, output queue size 4
progress 35% @chr6:104832942, elapsed 4.5s, est remaining 8.4s, peak mem 148MB, user 41.8s, sys 2.8s, output queue size 3
progress 40% @chr7:106872437, elapsed 5.2s, est remaining 7.8s, peak mem 148MB, user 47.9s, sys 3.1s, output queue size 2
progress 45% @chr8:143821497, elapsed 5.8s, est remaining 7.1s, peak mem 149MB, user 54.0s, sys 3.6s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.5s, est remaining 6.5s, peak mem 152MB, user 59.8s, sys 4.0s, output queue size 1
progress 55% @chr11:34132025, elapsed 7.1s, est remaining 5.8s, peak mem 152MB, user 65.6s, sys 4.5s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.7s, est remaining 5.1s, peak mem 152MB, user 71.2s, sys 4.9s, output queue size 9
progress 65% @chr13:32149648, elapsed 8.4s, est remaining 4.5s, peak mem 152MB, user 76.9s, sys 5.6s, output queue size 10
progress 70% @chr15:35521993, elapsed 9.0s, est remaining 3.9s, peak mem 152MB, user 82.7s, sys 6.0s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.7s, est remaining 3.2s, peak mem 152MB, user 88.4s, sys 6.5s, output queue size 2
progress 80% @chr17:40034816, elapsed 10.3s, est remaining 2.6s, peak mem 152MB, user 95.1s, sys 7.0s, output queue size 1
progress 85% @chr19:1805788, elapsed 11.0s, est remaining 1.9s, peak mem 153MB, user 101.4s, sys 7.3s, output queue size 2
progress 90% @chr19:54630974, elapsed 11.7s, est remaining 1.3s, peak mem 153MB, user 107.5s, sys 7.7s, output queue size 4
progress 95% @chr22:31897382, elapsed 13.3s, est remaining 0.7s, peak mem 342MB, user 123.0s, sys 8.4s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 13.9s, est remaining 0.0s, peak mem 342MB, user 128.4s, sys 8.8s, output queue size 199
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa3203
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 93248829
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.426 user 0.020 sys 0.499 real
"assemble_addRead": 221 calls 0.000 user 0.000 sys 0.008 real
"assemble_buildGraph": 496 calls 0.189 user 0.000 sys 0.214 real
"assemble_computecigar": 329 calls 0.051 user 0.009 sys 0.079 real
"assemble_kg_build_calcsize": 496 calls 0.110 user 0.000 sys 0.103 real
"assemble_kg_build_clear": 650 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_build_prepare": 992 calls 0.150 user 0.020 sys 0.096 real
"assemble_kg_build_threading": 342 calls 0.079 user 0.000 sys 0.107 real
"assemble_kg_op1": 342 calls 0.045 user 0.000 sys 0.079 real
"assemble_kg_op2": 342 calls 0.010 user 0.000 sys 0.005 real
"assemble_kg_op3": 342 calls 0.000 user 0.000 sys 0.006 real
"assemble_sg_clean": 329 calls 0.010 user 0.000 sys 0.026 real
"assemble_sg_create": 329 calls 0.010 user 0.000 sys 0.039 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.061 user 0.009 sys 0.082 real
advance: 189104 calls 13.542 user 0.479 sys 18.905 real
assemble_region: 221 calls 0.487 user 0.030 sys 0.592 real
build_pileup: 70986 calls 0.358 user 0.000 sys 0.454 real
build_stats: 71711 calls 2.301 user 0.083 sys 2.337 real
build_variants: 178 calls 0.000 user 0.000 sys 0.001 real
calc: 128717 calls 2.217 user 0.035 sys 2.911 real
calc_region: 178 calls 2.951 user 0.031 sys 2.979 real
call_region: 178 calls 0.064 user 0.000 sys 0.058 real
clip_region: 399 calls 0.035 user 0.000 sys 0.042 real
done: 1 calls 0.474 user 0.006 sys 0.483 real
execute: 1 calls 0.000 user 0.006 sys 13.959 real
fetch: 743546 calls 0.524 user 0.092 sys 0.877 real
fetch_ref: 745726 calls 1.435 user 0.557 sys 2.908 real
fetch_region: 221 calls 0.000 user 0.000 sys 0.008 real
fetch_vcf: 189104 calls 37.992 user 1.109 sys 55.669 real
idle: 35 calls 0.001 user 0.000 sys 12.858 real
init: 1 calls 0.055 user 0.000 sys 0.059 real
pairhmm: 837 calls 4.853 user 0.039 sys 4.807 real
realign: 178 calls 0.594 user 0.000 sys 0.621 real
region: 367297 calls 3.449 user 0.102 sys 3.684 real
tracker: 367297 calls 0.292 user 0.041 sys 0.554 real
trim_region: 221 calls 0.000 user 0.000 sys 0.002 real
overall: 359211008 mem 158.167 user 13.183 sys 15.292 real