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/34/c9bd1940495138659c37c221c762b5/.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/34/c9bd1940495138659c37c221c762b5/.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% @chr21:14498442, elapsed 0.1s, est remaining 1.6s, peak mem 108MB, user 0.7s, sys 0.1s, output queue size 1
progress 10% @chr21:21418473, elapsed 0.1s, est remaining 1.1s, peak mem 117MB, user 0.8s, sys 0.1s, output queue size 94
progress 15% @chr21:28882160, elapsed 0.1s, est remaining 0.8s, peak mem 117MB, user 1.0s, sys 0.1s, output queue size 9
progress 20% @chr21:29537798, elapsed 0.2s, est remaining 0.8s, peak mem 132MB, user 1.4s, sys 0.1s, output queue size 13
progress 25% @chr21:31135933, elapsed 0.2s, est remaining 0.7s, peak mem 132MB, user 1.6s, sys 0.1s, output queue size 23
progress 30% @chr21:32349304, elapsed 0.3s, est remaining 0.6s, peak mem 138MB, user 1.9s, sys 0.1s, output queue size 23
progress 35% @chr21:33241923, elapsed 0.3s, est remaining 0.6s, peak mem 138MB, user 2.4s, sys 0.1s, output queue size 50
progress 40% @chr21:33559877, elapsed 0.3s, est remaining 0.5s, peak mem 141MB, user 2.7s, sys 0.1s, output queue size 7
progress 45% @chr21:34521302, elapsed 0.4s, est remaining 0.4s, peak mem 150MB, user 2.9s, sys 0.1s, output queue size 101
progress 50% @chr21:36072446, elapsed 0.7s, est remaining 0.7s, peak mem 228MB, user 5.1s, sys 0.1s, output queue size 36
progress 55% @chr21:36412884, elapsed 0.8s, est remaining 0.6s, peak mem 228MB, user 5.9s, sys 0.1s, output queue size 48
progress 60% @chr21:37472684, elapsed 0.8s, est remaining 0.5s, peak mem 228MB, user 6.1s, sys 0.1s, output queue size 27
progress 65% @chr21:39278743, elapsed 0.8s, est remaining 0.5s, peak mem 243MB, user 6.4s, sys 0.2s, output queue size 59
progress 70% @chr21:41250752, elapsed 0.9s, est remaining 0.4s, peak mem 258MB, user 6.6s, sys 0.2s, output queue size 153
progress 75% @chr21:41488973, elapsed 1.9s, est remaining 0.6s, peak mem 414MB, user 11.8s, sys 0.3s, output queue size 4
progress 80% @chr21:41889124, elapsed 3.9s, est remaining 1.0s, peak mem 549MB, user 25.7s, sys 0.4s, output queue size 46
progress 85% @chr21:42127672, elapsed 4.1s, est remaining 0.7s, peak mem 552MB, user 33.4s, sys 0.4s, output queue size 87
progress 91% @chr21:41501693, elapsed 4.3s, est remaining 0.4s, peak mem 552MB, user 36.4s, sys 0.4s, output queue size 151
progress 95% @chr21:43417543, elapsed 4.3s, est remaining 0.2s, peak mem 552MB, user 36.7s, sys 0.4s, output queue size 6
progress 100% @chr21:44082788, elapsed 4.3s, est remaining 0.0s, peak mem 552MB, user 37.1s, sys 0.5s, 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 1.180 user 0.069 sys 1.420 real
"assemble_addRead": 237 calls 0.037 user 0.000 sys 0.080 real
"assemble_buildGraph": 494 calls 0.600 user 0.017 sys 0.723 real
"assemble_computecigar": 375 calls 0.472 user 0.029 sys 0.556 real
"assemble_kg_build_calcsize": 494 calls 0.318 user 0.003 sys 0.416 real
"assemble_kg_build_clear": 572 calls 0.050 user 0.000 sys 0.044 real
"assemble_kg_build_prepare": 988 calls 0.346 user 0.053 sys 0.409 real
"assemble_kg_build_threading": 416 calls 0.272 user 0.013 sys 0.296 real
"assemble_kg_op1": 416 calls 0.037 user 0.000 sys 0.049 real
"assemble_kg_op2": 416 calls 0.025 user 0.000 sys 0.019 real
"assemble_kg_op3": 416 calls 0.013 user 0.000 sys 0.012 real
"assemble_sg_clean": 375 calls 0.014 user 0.000 sys 0.060 real
"assemble_sg_create": 375 calls 0.025 user 0.000 sys 0.050 real
"checkGraph": 237 calls 0.000 user 0.000 sys 0.002 real
"findHaplotype": 237 calls 0.515 user 0.029 sys 0.614 real
active: 3201 calls 0.010 user 0.000 sys 0.011 real
advance: 1625 calls 4.168 user 0.178 sys 4.755 real
annotate: 279 calls 0.083 user 0.000 sys 0.055 real
assemble_region: 237 calls 1.731 user 0.098 sys 2.119 real
build_variants: 236 calls 0.010 user 0.000 sys 0.003 real
calc: 3201 calls 0.564 user 0.014 sys 0.577 real
calc_region: 236 calls 22.406 user 0.060 sys 22.715 real
call_region: 236 calls 0.224 user 0.000 sys 0.210 real
clip_region: 473 calls 0.136 user 0.000 sys 0.155 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.007 user 0.002 sys 4.328 real
fetch: 3201 calls 0.322 user 0.037 sys 0.354 real
fetch_db: 236 calls 0.010 user 0.000 sys 0.059 real
fetch_ref: 3438 calls 0.020 user 0.012 sys 0.022 real
fetch_region: 237 calls 0.040 user 0.000 sys 0.048 real
idle: 61 calls 0.046 user 0.000 sys 12.766 real
init: 1 calls 0.039 user 0.011 sys 0.056 real
pairhmm: 9053 calls 40.055 user 0.036 sys 40.822 real
realign: 1302 calls 1.253 user 0.022 sys 1.885 real
region: 3201 calls 31.849 user 0.146 sys 32.211 real
tracker: 3201 calls 0.027 user 0.000 sys 0.010 real
trim_region: 237 calls 0.020 user 0.000 sys 0.007 real
overall: 578949120 mem 50.818 user 0.599 sys 5.474 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory