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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/fb83e4a098b9ce74fe79a269bc29c0/.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/96/fb83e4a098b9ce74fe79a269bc29c0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/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% @chr19:49138205, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 427
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1024
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 1390
progress 20% @chr19:54803652, elapsed 0.0s, est remaining 0.1s, peak mem 79MB, user 0.0s, sys 0.1s, output queue size 1777
progress 25% @chr19:56221575, elapsed 0.0s, est remaining 0.1s, peak mem 79MB, user 0.0s, sys 0.1s, output queue size 2213
progress 30% @chr19:58243965, elapsed 0.0s, est remaining 0.1s, peak mem 79MB, user 0.0s, sys 0.1s, output queue size 2456
progress 35% @chr21:30425394, elapsed 0.1s, est remaining 0.2s, peak mem 118MB, user 0.7s, sys 0.2s, output queue size 118
progress 40% @chr21:35048842, elapsed 0.3s, est remaining 0.4s, peak mem 166MB, user 1.7s, sys 0.2s, output queue size 107
progress 45% @chr21:42543436, elapsed 1.1s, est remaining 1.4s, peak mem 300MB, user 9.3s, sys 0.3s, output queue size 148
progress 50% @chr21:45514976, elapsed 1.4s, est remaining 1.4s, peak mem 310MB, user 12.4s, sys 0.4s, output queue size 7
progress 55% @chr22:19455680, elapsed 1.5s, est remaining 1.2s, peak mem 310MB, user 12.9s, sys 0.4s, output queue size 88
progress 60% @chr22:22244946, elapsed 1.5s, est remaining 1.0s, peak mem 310MB, user 12.9s, sys 0.4s, output queue size 559
progress 65% @chr22:23957723, elapsed 1.5s, est remaining 0.8s, peak mem 310MB, user 12.9s, sys 0.4s, output queue size 782
progress 70% @chr22:29288004, elapsed 1.5s, est remaining 0.6s, peak mem 310MB, user 12.9s, sys 0.5s, output queue size 1287
progress 75% @chr22:31814992, elapsed 1.5s, est remaining 0.5s, peak mem 310MB, user 12.9s, sys 0.5s, output queue size 1825
progress 80% @chr22:37959346, elapsed 1.5s, est remaining 0.4s, peak mem 310MB, user 12.9s, sys 0.5s, output queue size 2392
progress 85% @chr22:37074610, elapsed 1.5s, est remaining 0.3s, peak mem 310MB, user 12.9s, sys 0.6s, output queue size 2911
progress 90% @chr22:46256561, elapsed 1.5s, est remaining 0.2s, peak mem 310MB, user 13.0s, sys 0.6s, output queue size 3521
progress 95% @chr22:50739271, elapsed 1.5s, est remaining 0.1s, peak mem 310MB, user 13.0s, sys 0.6s, output queue size 4095
progress 100% @chrY:21903896, elapsed 1.5s, est remaining 0.0s, peak mem 310MB, user 13.0s, sys 0.6s, output queue size 4671
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: 74586807
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.497 user 0.049 sys 0.811 real
"assemble_addRead": 324 calls 0.016 user 0.000 sys 0.039 real
"assemble_buildGraph": 688 calls 0.230 user 0.018 sys 0.409 real
"assemble_computecigar": 523 calls 0.279 user 0.008 sys 0.378 real
"assemble_kg_build_calcsize": 688 calls 0.119 user 0.000 sys 0.229 real
"assemble_kg_build_clear": 826 calls 0.002 user 0.000 sys 0.019 real
"assemble_kg_build_prepare": 1376 calls 0.082 user 0.030 sys 0.189 real
"assemble_kg_build_threading": 550 calls 0.111 user 0.018 sys 0.175 real
"assemble_kg_op1": 550 calls 0.021 user 0.000 sys 0.035 real
"assemble_kg_op2": 550 calls 0.000 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.006 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.052 user 0.000 sys 0.042 real
"assemble_sg_create": 523 calls 0.056 user 0.001 sys 0.054 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.297 user 0.008 sys 0.397 real
active: 19646 calls 0.012 user 0.004 sys 0.015 real
advance: 10022 calls 2.388 user 0.075 sys 2.994 real
annotate: 394 calls 0.031 user 0.000 sys 0.032 real
assemble_region: 324 calls 0.811 user 0.057 sys 1.251 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.267 user 0.000 sys 0.307 real
calc_region: 322 calls 6.146 user 0.062 sys 6.513 real
call_region: 322 calls 0.033 user 0.000 sys 0.061 real
clip_region: 646 calls 0.047 user 0.000 sys 0.078 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.002 sys 1.594 real
fetch: 19646 calls 0.182 user 0.018 sys 0.145 real
fetch_db: 322 calls 0.046 user 0.000 sys 0.083 real
fetch_ref: 19970 calls 0.015 user 0.000 sys 0.072 real
fetch_region: 324 calls 0.010 user 0.000 sys 0.021 real
idle: 39 calls 0.003 user 0.001 sys 13.117 real
init: 1 calls 0.029 user 0.011 sys 0.041 real
pairhmm: 2270 calls 9.992 user 0.027 sys 10.670 real
realign: 697 calls 0.605 user 0.001 sys 0.714 real
region: 19646 calls 9.765 user 0.103 sys 9.795 real
tracker: 19646 calls 0.010 user 0.000 sys 0.024 real
trim_region: 324 calls 0.000 user 0.000 sys 0.005 real
overall: 325722112 mem 16.628 user 1.021 sys 2.705 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory