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-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/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/2f427d74d0fc84d70df9edef62914b/.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/23/2f427d74d0fc84d70df9edef62914b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.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 Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant Sig_18_Blood.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14375652, elapsed 0.1s, est remaining 1.6s, peak mem 114MB, user 0.7s, sys 0.0s, output queue size 27
progress 10% @chr21:21484455, elapsed 0.1s, est remaining 1.1s, peak mem 126MB, user 0.9s, sys 0.0s, output queue size 94
progress 15% @chr21:28878192, elapsed 0.1s, est remaining 0.8s, peak mem 126MB, user 1.2s, sys 0.0s, output queue size 8
progress 20% @chr21:29321281, elapsed 0.2s, est remaining 0.8s, peak mem 132MB, user 1.7s, sys 0.1s, output queue size 3
progress 25% @chr21:31127065, elapsed 0.2s, est remaining 0.7s, peak mem 135MB, user 1.9s, sys 0.1s, output queue size 23
progress 30% @chr21:32349304, elapsed 0.3s, est remaining 0.6s, peak mem 138MB, user 2.2s, sys 0.1s, output queue size 23
progress 35% @chr21:32771326, elapsed 0.3s, est remaining 0.6s, peak mem 141MB, user 2.7s, sys 0.1s, output queue size 48
progress 40% @chr21:33559587, elapsed 0.3s, est remaining 0.5s, peak mem 144MB, user 2.9s, sys 0.1s, output queue size 6
progress 45% @chr21:34782802, elapsed 0.4s, est remaining 0.4s, peak mem 153MB, user 3.1s, sys 0.1s, output queue size 100
progress 50% @chr21:36200331, elapsed 0.7s, est remaining 0.7s, peak mem 234MB, user 4.4s, sys 0.1s, output queue size 38
progress 56% @chr21:34787802, elapsed 0.8s, est remaining 0.6s, peak mem 234MB, user 5.5s, sys 0.2s, output queue size 113
progress 60% @chr21:37472684, elapsed 0.8s, est remaining 0.5s, peak mem 234MB, user 5.7s, sys 0.2s, output queue size 27
progress 65% @chr21:39278743, elapsed 0.8s, est remaining 0.5s, peak mem 249MB, user 5.9s, sys 0.2s, output queue size 59
progress 70% @chr21:39660560, elapsed 0.9s, est remaining 0.4s, peak mem 267MB, user 6.2s, sys 0.2s, output queue size 154
progress 75% @chr21:41488133, elapsed 2.3s, est remaining 0.8s, peak mem 495MB, user 11.8s, sys 0.3s, output queue size 4
progress 80% @chr21:41740838, elapsed 4.0s, est remaining 1.0s, peak mem 504MB, user 27.0s, sys 0.5s, output queue size 41
progress 85% @chr21:42287889, elapsed 4.2s, est remaining 0.7s, peak mem 504MB, user 34.1s, sys 0.6s, output queue size 88
progress 90% @chr21:41501693, elapsed 4.3s, est remaining 0.5s, peak mem 504MB, user 37.2s, sys 0.6s, output queue size 147
progress 95% @chr21:43565239, elapsed 4.3s, est remaining 0.2s, peak mem 504MB, user 37.6s, sys 0.6s, output queue size 48
progress 100% @chr21:44082788, elapsed 4.4s, est remaining 0.0s, peak mem 504MB, user 38.0s, sys 0.6s, output queue size 20
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 208827488
output file size: 65321
reads: 2481283
contig: 1576 intervals 300011 bases
"assemble": 237 calls 1.236 user 0.208 sys 1.543 real
"assemble_addRead": 237 calls 0.112 user 0.000 sys 0.099 real
"assemble_buildGraph": 494 calls 0.652 user 0.011 sys 0.749 real
"assemble_computecigar": 375 calls 0.429 user 0.010 sys 0.569 real
"assemble_kg_build_calcsize": 494 calls 0.401 user 0.000 sys 0.424 real
"assemble_kg_build_clear": 572 calls 0.060 user 0.000 sys 0.048 real
"assemble_kg_build_prepare": 988 calls 0.323 user 0.197 sys 0.494 real
"assemble_kg_build_threading": 416 calls 0.250 user 0.010 sys 0.313 real
"assemble_kg_op1": 416 calls 0.035 user 0.000 sys 0.052 real
"assemble_kg_op2": 416 calls 0.012 user 0.000 sys 0.019 real
"assemble_kg_op3": 416 calls 0.004 user 0.000 sys 0.012 real
"assemble_sg_clean": 375 calls 0.030 user 0.000 sys 0.062 real
"assemble_sg_create": 375 calls 0.080 user 0.000 sys 0.051 real
"checkGraph": 237 calls 0.010 user 0.000 sys 0.002 real
"findHaplotype": 237 calls 0.482 user 0.010 sys 0.630 real
active: 3201 calls 0.010 user 0.000 sys 0.012 real
advance: 1625 calls 4.439 user 0.223 sys 4.803 real
annotate: 279 calls 0.086 user 0.000 sys 0.063 real
assemble_region: 237 calls 1.849 user 0.218 sys 2.277 real
build_variants: 236 calls 0.000 user 0.000 sys 0.004 real
calc: 3201 calls 0.479 user 0.008 sys 0.584 real
calc_region: 236 calls 23.238 user 0.116 sys 23.693 real
call_region: 236 calls 0.208 user 0.000 sys 0.232 real
clip_region: 473 calls 0.072 user 0.010 sys 0.162 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.003 sys 4.381 real
fetch: 3201 calls 0.423 user 0.023 sys 0.366 real
fetch_db: 236 calls 0.012 user 0.000 sys 0.061 real
fetch_ref: 3438 calls 0.028 user 0.001 sys 0.017 real
fetch_region: 237 calls 0.051 user 0.000 sys 0.039 real
idle: 61 calls 0.041 user 0.000 sys 12.595 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
pairhmm: 9053 calls 39.896 user 0.062 sys 41.103 real
realign: 1302 calls 1.546 user 0.030 sys 1.911 real
region: 3201 calls 32.504 user 0.338 sys 33.130 real
tracker: 3201 calls 0.010 user 0.000 sys 0.010 real
trim_region: 237 calls 0.000 user 0.000 sys 0.007 real
overall: 528646144 mem 51.274 user 0.720 sys 5.508 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory