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/86/52d4bf326834ba2e8db8661a564b11/.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-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/52d4bf326834ba2e8db8661a564b11/.command.run
  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.recalibrated.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 81MB, user 0.2s, sys 0.1s, output queue size 46
progress 10% @chr21:21418473, elapsed 0.1s, est remaining 0.6s, peak mem 90MB, user 0.4s, sys 0.1s, output queue size 85
progress 15% @chr21:14964716, elapsed 0.1s, est remaining 0.5s, peak mem 93MB, user 0.6s, sys 0.1s, output queue size 177
progress 20% @chr21:26844225, elapsed 0.1s, est remaining 0.4s, peak mem 99MB, user 0.8s, sys 0.1s, output queue size 103
progress 25% @chr21:30371686, elapsed 0.1s, est remaining 0.4s, peak mem 108MB, user 1.0s, sys 0.1s, output queue size 27
progress 30% @chr21:32344570, elapsed 0.2s, est remaining 0.4s, peak mem 117MB, user 1.3s, sys 0.1s, output queue size 20
progress 35% @chr21:32771326, elapsed 0.2s, est remaining 0.3s, peak mem 117MB, user 1.5s, sys 0.1s, output queue size 56
progress 40% @chr21:33579350, elapsed 0.2s, est remaining 0.3s, peak mem 120MB, user 1.8s, sys 0.1s, output queue size 26
progress 45% @chr21:34716321, elapsed 0.2s, est remaining 0.3s, peak mem 123MB, user 1.9s, sys 0.1s, output queue size 100
progress 50% @chr21:36230450, elapsed 0.3s, est remaining 0.3s, peak mem 159MB, user 2.2s, sys 0.1s, output queue size 48
progress 55% @chr21:36896860, elapsed 0.4s, est remaining 0.3s, peak mem 189MB, user 3.0s, sys 0.1s, output queue size 121
progress 60% @chr21:37267238, elapsed 0.4s, est remaining 0.3s, peak mem 189MB, user 3.3s, sys 0.2s, output queue size 16
progress 65% @chr21:39270283, elapsed 0.4s, est remaining 0.2s, peak mem 195MB, user 3.4s, sys 0.2s, output queue size 59
progress 70% @chr21:41245962, elapsed 0.4s, est remaining 0.2s, peak mem 207MB, user 3.6s, sys 0.2s, output queue size 150
progress 75% @chr21:41464388, elapsed 0.9s, est remaining 0.3s, peak mem 300MB, user 6.7s, sys 0.3s, output queue size 15
progress 80% @chr21:41871494, elapsed 1.4s, est remaining 0.3s, peak mem 387MB, user 11.1s, sys 0.3s, output queue size 41
progress 85% @chr21:42285880, elapsed 1.6s, est remaining 0.3s, peak mem 389MB, user 13.3s, sys 0.4s, output queue size 88
progress 90% @chr21:42854562, elapsed 1.7s, est remaining 0.2s, peak mem 389MB, user 14.4s, sys 0.4s, output queue size 192
progress 95% @chr21:43419021, elapsed 1.8s, est remaining 0.1s, peak mem 389MB, user 15.3s, sys 0.5s, output queue size 36
progress 100% @chr21:44120348, elapsed 1.8s, est remaining 0.0s, peak mem 389MB, user 15.6s, sys 0.5s, output queue size 0
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: 163002590
output file size: 61539
reads: 1955548
contig: 1576 intervals 300011 bases
"assemble": 223 calls 0.608 user 0.043 sys 0.879 real
"assemble_addRead": 223 calls 0.072 user 0.010 sys 0.055 real
"assemble_buildGraph": 457 calls 0.328 user 0.004 sys 0.449 real
"assemble_computecigar": 366 calls 0.348 user 0.014 sys 0.423 real
"assemble_kg_build_calcsize": 457 calls 0.172 user 0.000 sys 0.252 real
"assemble_kg_build_clear": 525 calls 0.001 user 0.000 sys 0.026 real
"assemble_kg_build_prepare": 914 calls 0.137 user 0.043 sys 0.229 real
"assemble_kg_build_threading": 389 calls 0.156 user 0.000 sys 0.192 real
"assemble_kg_op1": 389 calls 0.015 user 0.000 sys 0.034 real
"assemble_kg_op2": 389 calls 0.033 user 0.000 sys 0.011 real
"assemble_kg_op3": 389 calls 0.004 user 0.000 sys 0.010 real
"assemble_sg_clean": 366 calls 0.011 user 0.000 sys 0.041 real
"assemble_sg_create": 366 calls 0.053 user 0.000 sys 0.042 real
"checkGraph": 223 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 223 calls 0.371 user 0.014 sys 0.453 real
active: 3201 calls 0.000 user 0.000 sys 0.009 real
advance: 1625 calls 3.365 user 0.253 sys 3.910 real
annotate: 248 calls 0.016 user 0.000 sys 0.034 real
assemble_region: 223 calls 1.050 user 0.067 sys 1.391 real
build_variants: 219 calls 0.000 user 0.000 sys 0.002 real
calc: 3201 calls 0.315 user 0.002 sys 0.418 real
calc_region: 219 calls 7.624 user 0.118 sys 7.996 real
call_region: 219 calls 0.046 user 0.000 sys 0.088 real
clip_region: 442 calls 0.063 user 0.000 sys 0.091 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.009 user 0.000 sys 1.782 real
fetch: 3201 calls 0.245 user 0.005 sys 0.257 real
fetch_db: 219 calls 0.013 user 0.001 sys 0.054 real
fetch_ref: 3424 calls 0.011 user 0.016 sys 0.016 real
fetch_region: 223 calls 0.040 user 0.000 sys 0.025 real
idle: 39 calls 0.054 user 0.001 sys 12.452 real
init: 1 calls 0.030 user 0.010 sys 0.043 real
pairhmm: 3494 calls 12.752 user 0.177 sys 13.596 real
realign: 789 calls 0.764 user 0.003 sys 0.920 real
region: 3201 calls 11.430 user 0.200 sys 11.687 real
tracker: 3201 calls 0.010 user 0.000 sys 0.009 real
trim_region: 223 calls 0.010 user 0.000 sys 0.005 real
overall: 411963392 mem 20.498 user 0.647 sys 2.899 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory