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/90/c6c19583d7f45f82f68ed89ca3a1ff/.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/90/c6c19583d7f45f82f68ed89ca3a1ff/.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% @chr21:14373617, elapsed 0.1s, est remaining 1.1s, peak mem 69MB, user 0.3s, sys 0.1s, output queue size 47
progress 10% @chr21:21418473, elapsed 0.1s, est remaining 0.8s, peak mem 72MB, user 0.5s, sys 0.1s, output queue size 85
progress 15% @chr21:28882160, elapsed 0.1s, est remaining 0.6s, peak mem 72MB, user 0.8s, sys 0.2s, output queue size 12
progress 20% @chr21:29561624, elapsed 0.1s, est remaining 0.5s, peak mem 75MB, user 1.0s, sys 0.2s, output queue size 65
progress 25% @chr21:31146895, elapsed 0.2s, est remaining 0.5s, peak mem 78MB, user 1.2s, sys 0.2s, output queue size 30
progress 30% @chr21:32344570, elapsed 0.2s, est remaining 0.5s, peak mem 81MB, user 1.5s, sys 0.2s, output queue size 86
progress 35% @chr21:32771326, elapsed 0.2s, est remaining 0.4s, peak mem 81MB, user 1.8s, sys 0.3s, output queue size 57
progress 40% @chr21:33509783, elapsed 0.3s, est remaining 0.4s, peak mem 81MB, user 2.1s, sys 0.3s, output queue size 26
progress 45% @chr21:34834409, elapsed 0.3s, est remaining 0.4s, peak mem 84MB, user 2.3s, sys 0.4s, output queue size 101
progress 50% @chr21:36230450, elapsed 0.4s, est remaining 0.4s, peak mem 114MB, user 2.8s, sys 0.4s, output queue size 56
progress 55% @chr21:36966444, elapsed 0.4s, est remaining 0.3s, peak mem 129MB, user 3.0s, sys 0.4s, output queue size 123
progress 60% @chr21:37714211, elapsed 0.5s, est remaining 0.4s, peak mem 159MB, user 3.3s, sys 0.4s, output queue size 221
progress 65% @chr21:38380028, elapsed 0.6s, est remaining 0.3s, peak mem 159MB, user 4.2s, sys 0.5s, output queue size 284
progress 70% @chr21:40189042, elapsed 0.6s, est remaining 0.3s, peak mem 159MB, user 4.7s, sys 0.5s, output queue size 52
progress 75% @chr21:41495093, elapsed 1.2s, est remaining 0.4s, peak mem 240MB, user 6.5s, sys 0.6s, output queue size 4
progress 80% @chr21:41899053, elapsed 1.7s, est remaining 0.4s, peak mem 303MB, user 12.7s, sys 0.8s, output queue size 43
progress 85% @chr21:41990895, elapsed 1.9s, est remaining 0.3s, peak mem 303MB, user 14.8s, sys 0.8s, output queue size 107
progress 92% @chr21:41501693, elapsed 2.0s, est remaining 0.2s, peak mem 303MB, user 17.2s, sys 0.9s, output queue size 178
progress 95% @chr21:43419021, elapsed 2.0s, est remaining 0.1s, peak mem 303MB, user 17.4s, sys 0.9s, output queue size 10
progress 100% @chr21:44120348, elapsed 2.1s, est remaining 0.0s, peak mem 303MB, user 17.6s, sys 0.9s, 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 0.790 user 0.065 sys 1.083 real
"assemble_addRead": 223 calls 0.163 user 0.000 sys 0.080 real
"assemble_buildGraph": 457 calls 0.346 user 0.015 sys 0.536 real
"assemble_computecigar": 366 calls 0.399 user 0.062 sys 0.516 real
"assemble_kg_build_calcsize": 457 calls 0.196 user 0.011 sys 0.298 real
"assemble_kg_build_clear": 525 calls 0.021 user 0.001 sys 0.033 real
"assemble_kg_build_prepare": 914 calls 0.253 user 0.035 sys 0.297 real
"assemble_kg_build_threading": 389 calls 0.145 user 0.004 sys 0.230 real
"assemble_kg_op1": 389 calls 0.036 user 0.006 sys 0.044 real
"assemble_kg_op2": 389 calls 0.010 user 0.000 sys 0.012 real
"assemble_kg_op3": 389 calls 0.010 user 0.001 sys 0.012 real
"assemble_sg_clean": 366 calls 0.022 user 0.003 sys 0.049 real
"assemble_sg_create": 366 calls 0.043 user 0.002 sys 0.052 real
"checkGraph": 223 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 223 calls 0.411 user 0.064 sys 0.551 real
active: 3201 calls 0.021 user 0.001 sys 0.014 real
advance: 1625 calls 3.668 user 0.342 sys 4.562 real
annotate: 248 calls 0.025 user 0.010 sys 0.053 real
assemble_region: 223 calls 1.365 user 0.128 sys 1.719 real
build_variants: 219 calls 0.001 user 0.007 sys 0.004 real
calc: 3201 calls 0.458 user 0.014 sys 0.569 real
calc_region: 219 calls 8.452 user 0.159 sys 8.870 real
call_region: 219 calls 0.065 user 0.010 sys 0.119 real
clip_region: 442 calls 0.080 user 0.004 sys 0.133 real
done: 1 calls 0.002 user 0.000 sys 0.003 real
execute: 1 calls 0.002 user 0.000 sys 2.066 real
fetch: 3201 calls 0.496 user 0.055 sys 0.434 real
fetch_db: 219 calls 0.018 user 0.003 sys 0.069 real
fetch_ref: 3424 calls 0.025 user 0.003 sys 0.022 real
fetch_region: 223 calls 0.021 user 0.000 sys 0.033 real
idle: 38 calls 0.042 user 0.000 sys 12.543 real
init: 1 calls 0.049 user 0.000 sys 0.049 real
pairhmm: 3494 calls 14.050 user 0.112 sys 14.900 real
realign: 789 calls 0.949 user 0.002 sys 1.010 real
region: 3201 calls 12.738 user 0.311 sys 13.280 real
tracker: 3201 calls 0.026 user 0.001 sys 0.016 real
trim_region: 223 calls 0.026 user 0.000 sys 0.006 real
overall: 317857792 mem 23.040 user 1.048 sys 3.224 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory