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/35/01d5c182234ad7341d3a91529de2c3/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/scatter/chr21_44120631-44120778.bed.gz
  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/35/01d5c182234ad7341d3a91529de2c3/.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_44120631-44120778.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant Sig_18_Blood.haplotyper.chr21_44120631-44120778.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:44240804, elapsed 0.0s, est remaining 0.4s, peak mem 78MB, user 0.1s, sys 0.0s, output queue size 6
progress 10% @chr21:44316432, elapsed 0.0s, est remaining 0.3s, peak mem 87MB, user 0.2s, sys 0.0s, output queue size 39
progress 15% @chr21:44401681, elapsed 0.1s, est remaining 0.4s, peak mem 111MB, user 0.3s, sys 0.0s, output queue size 71
progress 20% @chr21:44456645, elapsed 0.1s, est remaining 0.3s, peak mem 117MB, user 0.4s, sys 0.1s, output queue size 98
progress 25% @chr21:44612101, elapsed 0.1s, est remaining 0.4s, peak mem 195MB, user 0.7s, sys 0.1s, output queue size 108
progress 30% @chr21:44591387, elapsed 0.4s, est remaining 0.9s, peak mem 207MB, user 1.8s, sys 0.1s, output queue size 115
progress 35% @chr21:44627172, elapsed 0.5s, est remaining 0.8s, peak mem 222MB, user 3.2s, sys 0.1s, output queue size 136
progress 44% @chr21:44224713, elapsed 0.5s, est remaining 0.6s, peak mem 222MB, user 4.1s, sys 0.1s, output queue size 147
progress 45% @chr21:44973197, elapsed 0.5s, est remaining 0.6s, peak mem 222MB, user 4.2s, sys 0.1s, output queue size 47
progress 50% @chr21:45267451, elapsed 0.5s, est remaining 0.5s, peak mem 222MB, user 5.0s, sys 0.1s, output queue size 11
progress 55% @chr21:45455531, elapsed 0.5s, est remaining 0.4s, peak mem 222MB, user 5.1s, sys 0.1s, output queue size 23
progress 60% @chr21:45913951, elapsed 0.5s, est remaining 0.3s, peak mem 222MB, user 5.2s, sys 0.1s, output queue size 23
progress 65% @chr21:46121556, elapsed 0.5s, est remaining 0.3s, peak mem 222MB, user 5.5s, sys 0.1s, output queue size 11
progress 70% @chr21:46191104, elapsed 0.6s, est remaining 0.2s, peak mem 225MB, user 5.7s, sys 0.1s, output queue size 21
progress 75% @chr21:46256789, elapsed 0.6s, est remaining 0.2s, peak mem 225MB, user 5.9s, sys 0.2s, output queue size 14
progress 80% @chr21:46315474, elapsed 0.6s, est remaining 0.2s, peak mem 225MB, user 6.1s, sys 0.2s, output queue size 10
progress 85% @chr21:46411189, elapsed 0.7s, est remaining 0.1s, peak mem 225MB, user 6.1s, sys 0.2s, output queue size 35
progress 90% @chr21:46440855, elapsed 0.7s, est remaining 0.1s, peak mem 228MB, user 6.2s, sys 0.2s, output queue size 34
progress 95% @chr21:46443810, elapsed 0.7s, est remaining 0.0s, peak mem 231MB, user 6.7s, sys 0.2s, output queue size 27
progress 100% @chr21:46660833, elapsed 0.7s, est remaining 0.0s, peak mem 231MB, user 6.8s, sys 0.2s, output queue size 3
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: 38078
reads: 2481283
contig: 516 intervals 92221 bases
"assemble": 89 calls 0.267 user 0.015 sys 0.316 real
"assemble_addRead": 89 calls 0.020 user 0.000 sys 0.014 real
"assemble_buildGraph": 199 calls 0.117 user 0.010 sys 0.161 real
"assemble_computecigar": 129 calls 0.163 user 0.015 sys 0.203 real
"assemble_kg_build_calcsize": 199 calls 0.092 user 0.000 sys 0.099 real
"assemble_kg_build_clear": 260 calls 0.009 user 0.000 sys 0.008 real
"assemble_kg_build_prepare": 398 calls 0.066 user 0.005 sys 0.082 real
"assemble_kg_build_threading": 138 calls 0.025 user 0.008 sys 0.058 real
"assemble_kg_op1": 138 calls 0.021 user 0.000 sys 0.014 real
"assemble_kg_op2": 138 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_op3": 138 calls 0.000 user 0.000 sys 0.004 real
"assemble_sg_clean": 129 calls 0.012 user 0.000 sys 0.013 real
"assemble_sg_create": 129 calls 0.011 user 0.000 sys 0.015 real
"checkGraph": 89 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 89 calls 0.163 user 0.015 sys 0.211 real
active: 1044 calls 0.010 user 0.000 sys 0.003 real
advance: 528 calls 1.446 user 0.069 sys 1.792 real
annotate: 116 calls 0.009 user 0.000 sys 0.013 real
assemble_region: 89 calls 0.450 user 0.030 sys 0.541 real
build_variants: 88 calls 0.000 user 0.000 sys 0.001 real
calc: 1044 calls 0.095 user 0.000 sys 0.156 real
calc_region: 88 calls 3.499 user 0.029 sys 3.590 real
call_region: 88 calls 0.012 user 0.000 sys 0.024 real
clip_region: 177 calls 0.046 user 0.000 sys 0.025 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.006 sys 0.729 real
fetch: 1044 calls 0.083 user 0.000 sys 0.074 real
fetch_db: 88 calls 0.015 user 0.002 sys 0.027 real
fetch_ref: 1133 calls 0.015 user 0.004 sys 0.005 real
fetch_region: 89 calls 0.000 user 0.000 sys 0.005 real
idle: 41 calls 0.044 user 0.000 sys 12.500 real
init: 1 calls 0.019 user 0.021 sys 0.043 real
pairhmm: 815 calls 5.206 user 0.030 sys 5.462 real
realign: 246 calls 0.230 user 0.000 sys 0.301 real
region: 1044 calls 5.076 user 0.078 sys 5.210 real
tracker: 1044 calls 0.000 user 0.000 sys 0.003 real
trim_region: 89 calls 0.000 user 0.000 sys 0.002 real
overall: 245518336 mem 8.385 user 0.237 sys 1.845 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory