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/34/3c4d8e89441e84db2a4dff39bdef0c/.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/f6/bfa67d0b98a4e5b82b2b677c7e210c/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/bfa67d0b98a4e5b82b2b677c7e210c/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/3c4d8e89441e84db2a4dff39bdef0c/.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% @chr1:113700694, elapsed 1.0s, est remaining 19.4s, peak mem 145MB, user 8.2s, sys 1.0s, output queue size 3
progress 10% @chr2:3643344, elapsed 2.0s, est remaining 17.6s, peak mem 146MB, user 16.0s, sys 2.1s, output queue size 6
progress 15% @chr2:178604608, elapsed 3.0s, est remaining 17.1s, peak mem 147MB, user 25.1s, sys 3.0s, output queue size 12
progress 20% @chr3:57483276, elapsed 4.0s, est remaining 15.9s, peak mem 148MB, user 33.2s, sys 4.0s, output queue size 0
progress 25% @chr4:70602524, elapsed 5.0s, est remaining 14.9s, peak mem 148MB, user 41.7s, sys 5.0s, output queue size 9
progress 30% @chr5:135873921, elapsed 6.0s, est remaining 14.0s, peak mem 151MB, user 50.4s, sys 5.8s, output queue size 4
progress 35% @chr6:104791404, elapsed 6.9s, est remaining 12.8s, peak mem 152MB, user 57.6s, sys 6.7s, output queue size 7
progress 40% @chr7:106284249, elapsed 7.9s, est remaining 11.8s, peak mem 154MB, user 66.1s, sys 7.5s, output queue size 5
progress 45% @chr8:143820566, elapsed 8.8s, est remaining 10.8s, peak mem 155MB, user 74.5s, sys 8.6s, output queue size 2
progress 50% @chr10:21514996, elapsed 9.8s, est remaining 9.8s, peak mem 156MB, user 83.0s, sys 9.4s, output queue size 12
progress 55% @chr11:34135075, elapsed 10.8s, est remaining 8.8s, peak mem 157MB, user 91.1s, sys 10.2s, output queue size 1
progress 60% @chr12:12718707, elapsed 11.7s, est remaining 7.8s, peak mem 157MB, user 98.8s, sys 11.1s, output queue size 15
progress 65% @chr13:32078734, elapsed 12.7s, est remaining 6.8s, peak mem 158MB, user 107.5s, sys 11.8s, output queue size 10
progress 70% @chr15:35521993, elapsed 13.6s, est remaining 5.8s, peak mem 158MB, user 115.7s, sys 12.6s, output queue size 0
progress 75% @chr16:28488491, elapsed 14.6s, est remaining 4.9s, peak mem 158MB, user 124.2s, sys 13.6s, output queue size 4
progress 80% @chr17:40032956, elapsed 15.6s, est remaining 3.9s, peak mem 159MB, user 133.7s, sys 14.3s, output queue size 2
progress 85% @chr19:1805788, elapsed 16.6s, est remaining 2.9s, peak mem 160MB, user 142.3s, sys 15.2s, output queue size 2
progress 90% @chr19:54632916, elapsed 17.5s, est remaining 1.9s, peak mem 161MB, user 150.7s, sys 15.8s, output queue size 2
progress 95% @chr22:32043182, elapsed 20.1s, est remaining 1.1s, peak mem 358MB, user 175.1s, sys 17.0s, output queue size 203
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 21.0s, est remaining 0.0s, peak mem 359MB, user 182.7s, sys 17.8s, output queue size 12
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 93219163
output file size: 53232
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.891 user 0.014 sys 0.875 real
"assemble_addRead": 221 calls 0.040 user 0.000 sys 0.019 real
"assemble_buildGraph": 496 calls 0.420 user 0.012 sys 0.378 real
"assemble_computecigar": 329 calls 0.130 user 0.010 sys 0.130 real
"assemble_kg_build_calcsize": 496 calls 0.190 user 0.000 sys 0.165 real
"assemble_kg_build_clear": 650 calls 0.010 user 0.000 sys 0.018 real
"assemble_kg_build_prepare": 992 calls 0.121 user 0.000 sys 0.169 real
"assemble_kg_build_threading": 342 calls 0.231 user 0.009 sys 0.204 real
"assemble_kg_op1": 342 calls 0.104 user 0.000 sys 0.130 real
"assemble_kg_op2": 342 calls 0.010 user 0.000 sys 0.007 real
"assemble_kg_op3": 342 calls 0.000 user 0.000 sys 0.008 real
"assemble_sg_clean": 329 calls 0.070 user 0.000 sys 0.044 real
"assemble_sg_create": 329 calls 0.095 user 0.003 sys 0.067 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.130 user 0.010 sys 0.137 real
advance: 189104 calls 19.142 user 0.852 sys 26.252 real
assemble_region: 221 calls 1.061 user 0.024 sys 1.034 real
build_pileup: 70986 calls 0.560 user 0.024 sys 0.909 real
build_stats: 71711 calls 4.578 user 0.092 sys 5.170 real
build_variants: 178 calls 0.000 user 0.000 sys 0.002 real
calc: 128717 calls 4.948 user 0.125 sys 6.692 real
calc_region: 178 calls 4.556 user 0.026 sys 4.743 real
call_region: 178 calls 0.123 user 0.000 sys 0.102 real
clip_region: 399 calls 0.070 user 0.000 sys 0.075 real
done: 1 calls 0.898 user 0.000 sys 0.905 real
execute: 1 calls 0.012 user 0.000 sys 21.045 real
fetch: 743546 calls 1.152 user 0.203 sys 1.795 real
fetch_ref: 745726 calls 1.693 user 0.710 sys 3.880 real
fetch_region: 221 calls 0.010 user 0.000 sys 0.016 real
fetch_vcf: 189104 calls 51.876 user 2.004 sys 77.874 real
idle: 35 calls 0.006 user 0.003 sys 13.507 real
init: 1 calls 0.080 user 0.010 sys 0.094 real
pairhmm: 837 calls 7.290 user 0.020 sys 7.347 real
realign: 178 calls 0.758 user 0.000 sys 0.864 real
region: 367297 calls 5.667 user 0.128 sys 5.971 real
tracker: 367297 calls 0.679 user 0.078 sys 1.105 real
trim_region: 221 calls 0.000 user 0.000 sys 0.003 real
overall: 376479744 mem 231.225 user 26.426 sys 22.548 real