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/intervals/regression_intervals/scatter/chr21_5117103-5117231.bed.gz
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/5f446e06a09ba37398ded595e6b23d/.command.sh
  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/19/5f446e06a09ba37398ded595e6b23d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr21_5117103-5117231.bed.gz -i HCC1395_BL.recal.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant HCC1395_BL.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14144623, elapsed 0.0s, est remaining 0.8s, peak mem 96MB, user 0.2s, sys 0.1s, output queue size 48
progress 10% @chr21:21410274, elapsed 0.1s, est remaining 0.5s, peak mem 103MB, user 0.4s, sys 0.1s, output queue size 85
progress 15% @chr21:14964716, elapsed 0.1s, est remaining 0.4s, peak mem 106MB, user 0.6s, sys 0.1s, output queue size 172
progress 20% @chr21:29591112, elapsed 0.1s, est remaining 0.4s, peak mem 111MB, user 0.8s, sys 0.1s, output queue size 64
progress 25% @chr21:30881033, elapsed 0.1s, est remaining 0.4s, peak mem 124MB, user 0.9s, sys 0.1s, output queue size 28
progress 30% @chr21:32344570, elapsed 0.1s, est remaining 0.3s, peak mem 124MB, user 1.2s, sys 0.1s, output queue size 21
progress 35% @chr21:32771326, elapsed 0.2s, est remaining 0.3s, peak mem 127MB, user 1.5s, sys 0.1s, output queue size 57
progress 40% @chr21:33567157, elapsed 0.2s, est remaining 0.3s, peak mem 127MB, user 1.6s, sys 0.1s, output queue size 26
progress 45% @chr21:34716321, elapsed 0.2s, est remaining 0.3s, peak mem 133MB, user 1.8s, sys 0.1s, output queue size 101
progress 50% @chr21:33549476, elapsed 0.2s, est remaining 0.2s, peak mem 172MB, user 2.0s, sys 0.1s, output queue size 153
progress 55% @chr21:36756542, elapsed 0.4s, est remaining 0.3s, peak mem 201MB, user 2.6s, sys 0.2s, output queue size 120
progress 60% @chr21:37267238, elapsed 0.4s, est remaining 0.3s, peak mem 201MB, user 2.8s, sys 0.2s, output queue size 16
progress 65% @chr21:39269899, elapsed 0.4s, est remaining 0.2s, peak mem 201MB, user 3.0s, sys 0.2s, output queue size 59
progress 70% @chr21:39451908, elapsed 0.4s, est remaining 0.2s, peak mem 206MB, user 3.2s, sys 0.2s, output queue size 150
progress 75% @chr21:41488133, elapsed 1.1s, est remaining 0.4s, peak mem 345MB, user 6.1s, sys 0.2s, output queue size 4
progress 80% @chr21:41899053, elapsed 1.6s, est remaining 0.4s, peak mem 392MB, user 12.5s, sys 0.3s, output queue size 42
progress 85% @chr21:42416442, elapsed 1.9s, est remaining 0.3s, peak mem 392MB, user 14.7s, sys 0.3s, output queue size 121
progress 91% @chr21:41497133, elapsed 1.9s, est remaining 0.2s, peak mem 392MB, user 16.9s, sys 0.3s, output queue size 168
progress 95% @chr21:43419021, elapsed 1.9s, est remaining 0.1s, peak mem 392MB, user 17.1s, sys 0.4s, output queue size 7
progress 100% @chr21:44120348, elapsed 1.9s, est remaining 0.0s, peak mem 392MB, user 17.3s, sys 0.4s, output queue size 0
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 111697681
output file size: 61481
reads: 1322929
contig: 1576 intervals 300011 bases
"assemble": 223 calls 0.683 user 0.038 sys 0.852 real
"assemble_addRead": 223 calls 0.069 user 0.000 sys 0.045 real
"assemble_buildGraph": 457 calls 0.328 user 0.010 sys 0.440 real
"assemble_computecigar": 365 calls 0.331 user 0.033 sys 0.411 real
"assemble_kg_build_calcsize": 457 calls 0.164 user 0.000 sys 0.249 real
"assemble_kg_build_clear": 526 calls 0.038 user 0.000 sys 0.024 real
"assemble_kg_build_prepare": 914 calls 0.211 user 0.019 sys 0.212 real
"assemble_kg_build_threading": 388 calls 0.154 user 0.010 sys 0.186 real
"assemble_kg_op1": 388 calls 0.024 user 0.009 sys 0.034 real
"assemble_kg_op2": 388 calls 0.000 user 0.000 sys 0.011 real
"assemble_kg_op3": 388 calls 0.020 user 0.000 sys 0.010 real
"assemble_sg_clean": 365 calls 0.008 user 0.000 sys 0.042 real
"assemble_sg_create": 365 calls 0.033 user 0.000 sys 0.041 real
"checkGraph": 223 calls 0.010 user 0.000 sys 0.001 real
"findHaplotype": 223 calls 0.341 user 0.033 sys 0.442 real
active: 3201 calls 0.020 user 0.003 sys 0.016 real
advance: 1625 calls 3.009 user 0.171 sys 3.444 real
annotate: 248 calls 0.029 user 0.000 sys 0.033 real
assemble_region: 223 calls 1.102 user 0.071 sys 1.342 real
build_variants: 219 calls 0.000 user 0.000 sys 0.002 real
calc: 3201 calls 0.316 user 0.000 sys 0.381 real
calc_region: 219 calls 9.354 user 0.061 sys 9.711 real
call_region: 219 calls 0.084 user 0.000 sys 0.088 real
clip_region: 442 calls 0.110 user 0.001 sys 0.087 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.009 sys 1.943 real
fetch: 3201 calls 0.189 user 0.026 sys 0.196 real
fetch_db: 219 calls 0.045 user 0.000 sys 0.054 real
fetch_ref: 3424 calls 0.016 user 0.007 sys 0.017 real
fetch_region: 223 calls 0.039 user 0.001 sys 0.018 real
idle: 39 calls 0.007 user 0.000 sys 12.210 real
init: 1 calls 0.038 user 0.002 sys 0.047 real
pairhmm: 3815 calls 15.192 user 0.027 sys 16.083 real
realign: 797 calls 0.682 user 0.000 sys 0.990 real
region: 3201 calls 13.646 user 0.127 sys 13.863 real
tracker: 3201 calls 0.022 user 0.000 sys 0.013 real
trim_region: 223 calls 0.000 user 0.000 sys 0.005 real
overall: 411381760 mem 22.596 user 0.482 sys 3.119 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory