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/d7/a0c7d9d74940c4ed0a1cd45408ba3d/.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/d7/a0c7d9d74940c4ed0a1cd45408ba3d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/Sig_18_Blood.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr19_47340800-47341813.bed.gz
  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 chr19_47340800-47341813.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49142804, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 464
progress 10% @chr19:50632286, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 795
progress 15% @chr19:51645477, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 1166
progress 20% @chr19:54192116, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 1551
progress 25% @chr19:55762598, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 1998
progress 30% @chr19:58294098, elapsed 0.1s, est remaining 0.1s, peak mem 73MB, user 0.1s, sys 0.0s, output queue size 2236
progress 35% @chr21:30425394, elapsed 0.1s, est remaining 0.3s, peak mem 112MB, user 0.8s, sys 0.1s, output queue size 118
progress 40% @chr21:36719821, elapsed 0.3s, est remaining 0.5s, peak mem 162MB, user 1.8s, sys 0.2s, output queue size 107
progress 45% @chr21:41492213, elapsed 1.2s, est remaining 1.4s, peak mem 283MB, user 8.8s, sys 0.3s, output queue size 130
progress 50% @chr21:45505838, elapsed 1.4s, est remaining 1.4s, peak mem 293MB, user 11.9s, sys 0.4s, output queue size 34
progress 55% @chr22:19405786, elapsed 1.5s, est remaining 1.2s, peak mem 296MB, user 12.4s, sys 0.4s, output queue size 109
progress 60% @chr22:22201834, elapsed 1.5s, est remaining 1.0s, peak mem 296MB, user 12.5s, sys 0.4s, output queue size 594
progress 65% @chr22:23877042, elapsed 1.5s, est remaining 0.8s, peak mem 296MB, user 12.5s, sys 0.4s, output queue size 808
progress 70% @chr22:29286684, elapsed 1.5s, est remaining 0.6s, peak mem 296MB, user 12.5s, sys 0.4s, output queue size 1319
progress 75% @chr22:31874273, elapsed 1.5s, est remaining 0.5s, peak mem 296MB, user 12.5s, sys 0.5s, output queue size 1867
progress 80% @chr22:37972301, elapsed 1.5s, est remaining 0.4s, peak mem 296MB, user 12.5s, sys 0.5s, output queue size 2432
progress 85% @chr22:41252872, elapsed 1.5s, est remaining 0.3s, peak mem 296MB, user 12.5s, sys 0.5s, output queue size 2941
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 296MB, user 12.5s, sys 0.6s, output queue size 3554
progress 95% @chr22:50627556, elapsed 1.6s, est remaining 0.1s, peak mem 296MB, user 12.5s, sys 0.6s, output queue size 4127
progress 100% @chrY:57194043, elapsed 1.6s, est remaining 0.0s, peak mem 296MB, user 12.6s, sys 0.6s, output queue size 4702
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74381931
output file size: 79910
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.679 user 0.018 sys 0.837 real
"assemble_addRead": 324 calls 0.007 user 0.000 sys 0.039 real
"assemble_buildGraph": 688 calls 0.292 user 0.010 sys 0.429 real
"assemble_computecigar": 523 calls 0.264 user 0.019 sys 0.383 real
"assemble_kg_build_calcsize": 688 calls 0.210 user 0.000 sys 0.235 real
"assemble_kg_build_clear": 826 calls 0.025 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 1376 calls 0.175 user 0.001 sys 0.192 real
"assemble_kg_build_threading": 550 calls 0.077 user 0.010 sys 0.188 real
"assemble_kg_op1": 550 calls 0.015 user 0.006 sys 0.035 real
"assemble_kg_op2": 550 calls 0.010 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.002 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.041 user 0.000 sys 0.042 real
"assemble_sg_create": 523 calls 0.062 user 0.000 sys 0.055 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.273 user 0.019 sys 0.403 real
active: 19646 calls 0.012 user 0.008 sys 0.015 real
advance: 10022 calls 2.212 user 0.102 sys 3.030 real
annotate: 394 calls 0.053 user 0.000 sys 0.034 real
assemble_region: 324 calls 0.963 user 0.037 sys 1.282 real
build_variants: 322 calls 0.020 user 0.000 sys 0.002 real
calc: 19646 calls 0.205 user 0.006 sys 0.310 real
calc_region: 322 calls 5.883 user 0.098 sys 6.323 real
call_region: 322 calls 0.063 user 0.000 sys 0.063 real
clip_region: 646 calls 0.055 user 0.002 sys 0.079 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.000 user 0.002 sys 1.635 real
fetch: 19646 calls 0.162 user 0.019 sys 0.151 real
fetch_db: 322 calls 0.028 user 0.000 sys 0.086 real
fetch_ref: 19970 calls 0.015 user 0.006 sys 0.075 real
fetch_region: 324 calls 0.010 user 0.000 sys 0.017 real
idle: 39 calls 0.003 user 0.001 sys 13.175 real
init: 1 calls 0.046 user 0.003 sys 0.042 real
pairhmm: 2270 calls 10.272 user 0.067 sys 10.783 real
realign: 697 calls 0.339 user 0.000 sys 0.713 real
region: 19646 calls 9.247 user 0.135 sys 9.352 real
tracker: 19646 calls 0.000 user 0.003 sys 0.024 real
trim_region: 324 calls 0.008 user 0.000 sys 0.005 real
overall: 310849536 mem 16.864 user 1.007 sys 2.750 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory