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/98/1e048d94bbc98f44884bc9c94b54e4/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/ad4f869899ea21e5080a0c9f341540/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/1e048d94bbc98f44884bc9c94b54e4/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/aa/ad4f869899ea21e5080a0c9f341540/.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% @chr1:113713179, elapsed 1.2s, est remaining 23.3s, peak mem 145MB, user 12.0s, sys 0.6s, output queue size 4
progress 10% @chr2:3643344, elapsed 2.3s, est remaining 21.1s, peak mem 145MB, user 22.1s, sys 1.2s, output queue size 9
progress 15% @chr2:178588438, elapsed 3.6s, est remaining 20.3s, peak mem 147MB, user 33.3s, sys 2.0s, output queue size 9
progress 20% @chr3:57472446, elapsed 4.7s, est remaining 18.8s, peak mem 148MB, user 43.3s, sys 2.6s, output queue size 1
progress 25% @chr4:70602524, elapsed 5.9s, est remaining 17.6s, peak mem 148MB, user 54.1s, sys 3.4s, output queue size 4
progress 30% @chr5:135834748, elapsed 7.1s, est remaining 16.6s, peak mem 149MB, user 65.3s, sys 4.1s, output queue size 4
progress 35% @chr6:104843123, elapsed 8.1s, est remaining 15.1s, peak mem 150MB, user 76.0s, sys 4.8s, output queue size 2
progress 40% @chr7:106248199, elapsed 9.4s, est remaining 14.1s, peak mem 151MB, user 88.7s, sys 5.3s, output queue size 18
progress 45% @chr8:143821497, elapsed 10.6s, est remaining 13.0s, peak mem 151MB, user 100.8s, sys 6.1s, output queue size 1
progress 50% @chr10:21514996, elapsed 11.8s, est remaining 11.8s, peak mem 155MB, user 112.7s, sys 6.8s, output queue size 14
progress 55% @chr11:34140300, elapsed 12.9s, est remaining 10.6s, peak mem 155MB, user 123.6s, sys 7.5s, output queue size 0
progress 60% @chr12:12718707, elapsed 14.0s, est remaining 9.3s, peak mem 157MB, user 134.6s, sys 8.3s, output queue size 17
progress 65% @chr13:32149648, elapsed 15.1s, est remaining 8.1s, peak mem 157MB, user 146.4s, sys 9.1s, output queue size 0
progress 70% @chr15:34981259, elapsed 16.2s, est remaining 6.9s, peak mem 158MB, user 157.2s, sys 9.7s, output queue size 6
progress 75% @chr16:28486247, elapsed 17.3s, est remaining 5.8s, peak mem 160MB, user 166.4s, sys 10.4s, output queue size 3
progress 80% @chr17:40036016, elapsed 18.4s, est remaining 4.6s, peak mem 160MB, user 177.8s, sys 10.9s, output queue size 1
progress 85% @chr19:1808122, elapsed 19.6s, est remaining 3.5s, peak mem 160MB, user 188.0s, sys 11.6s, output queue size 5
progress 90% @chr19:54630974, elapsed 20.7s, est remaining 2.3s, peak mem 161MB, user 199.5s, sys 12.1s, output queue size 6
progress 95% @chr22:32081766, elapsed 23.3s, est remaining 1.2s, peak mem 335MB, user 225.8s, sys 12.8s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 24.2s, est remaining 0.0s, peak mem 336MB, user 234.6s, sys 13.4s, output queue size 87
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 81484545
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.812 user 0.010 sys 0.766 real
"assemble_addRead": 207 calls 0.000 user 0.000 sys 0.014 real
"assemble_buildGraph": 465 calls 0.364 user 0.000 sys 0.341 real
"assemble_computecigar": 304 calls 0.160 user 0.010 sys 0.168 real
"assemble_kg_build_calcsize": 465 calls 0.150 user 0.000 sys 0.153 real
"assemble_kg_build_clear": 618 calls 0.010 user 0.000 sys 0.014 real
"assemble_kg_build_prepare": 930 calls 0.194 user 0.010 sys 0.145 real
"assemble_kg_build_threading": 312 calls 0.204 user 0.000 sys 0.181 real
"assemble_kg_op1": 312 calls 0.090 user 0.000 sys 0.094 real
"assemble_kg_op2": 312 calls 0.000 user 0.000 sys 0.007 real
"assemble_kg_op3": 312 calls 0.010 user 0.000 sys 0.008 real
"assemble_sg_clean": 304 calls 0.030 user 0.000 sys 0.042 real
"assemble_sg_create": 304 calls 0.085 user 0.000 sys 0.065 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.160 user 0.010 sys 0.175 real
advance: 189104 calls 24.950 user 0.421 sys 30.766 real
assemble_region: 207 calls 0.972 user 0.020 sys 0.958 real
build_pileup: 70976 calls 0.727 user 0.013 sys 1.068 real
build_stats: 71686 calls 4.838 user 0.093 sys 5.429 real
build_variants: 162 calls 0.000 user 0.000 sys 0.002 real
calc: 128670 calls 5.823 user 0.127 sys 7.641 real
calc_region: 162 calls 2.864 user 0.012 sys 2.985 real
call_region: 162 calls 0.050 user 0.000 sys 0.063 real
clip_region: 369 calls 0.020 user 0.000 sys 0.048 real
done: 1 calls 0.610 user 0.010 sys 0.625 real
execute: 1 calls 0.003 user 0.010 sys 24.233 real
fetch: 743546 calls 1.514 user 0.158 sys 1.851 real
fetch_ref: 745712 calls 3.514 user 0.706 sys 5.391 real
fetch_region: 207 calls 0.010 user 0.000 sys 0.013 real
fetch_vcf: 189104 calls 75.095 user 1.494 sys 97.923 real
idle: 35 calls 0.006 user 0.006 sys 13.352 real
init: 1 calls 0.090 user 0.000 sys 0.087 real
pairhmm: 466 calls 5.084 user 0.019 sys 5.098 real
realign: 162 calls 0.480 user 0.000 sys 0.488 real
region: 367297 calls 3.983 user 0.104 sys 4.231 real
tracker: 367297 calls 1.060 user 0.049 sys 1.394 real
trim_region: 207 calls 0.000 user 0.000 sys 0.003 real
overall: 352653312 mem 276.888 user 18.386 sys 25.662 real