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/80/df9cd0f8f285b6ab0b55d677146c3f/.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/80/df9cd0f8f285b6ab0b55d677146c3f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/afbce3389bf5bcfac4e357eeed7653/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/afbce3389bf5bcfac4e357eeed7653/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% @chr19:49148993, elapsed 0.0s, est remaining 0.3s, peak mem 66MB, user 0.0s, sys 0.0s, output queue size 283
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.3s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 869
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 1237
progress 20% @chr19:54819713, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.2s, output queue size 1623
progress 25% @chr19:56223631, elapsed 0.1s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.2s, output queue size 2060
progress 30% @chr19:58212161, elapsed 0.1s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.2s, output queue size 2305
progress 35% @chr21:26844225, elapsed 0.2s, est remaining 0.3s, peak mem 102MB, user 0.7s, sys 0.3s, output queue size 118
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.5s, peak mem 153MB, user 1.6s, sys 0.4s, output queue size 106
progress 45% @chr21:42426697, elapsed 1.2s, est remaining 1.5s, peak mem 267MB, user 9.2s, sys 0.5s, output queue size 121
progress 50% @chr21:45497599, elapsed 1.5s, est remaining 1.5s, peak mem 267MB, user 12.7s, sys 0.6s, output queue size 66
progress 55% @chr22:19447378, elapsed 1.5s, est remaining 1.3s, peak mem 270MB, user 13.2s, sys 0.6s, output queue size 219
progress 60% @chr22:22201834, elapsed 1.6s, est remaining 1.0s, peak mem 270MB, user 13.2s, sys 0.7s, output queue size 694
progress 65% @chr22:23882759, elapsed 1.6s, est remaining 0.8s, peak mem 270MB, user 13.2s, sys 0.7s, output queue size 911
progress 70% @chr22:29288004, elapsed 1.6s, est remaining 0.7s, peak mem 270MB, user 13.2s, sys 0.7s, output queue size 1421
progress 75% @chr22:31821502, elapsed 1.6s, est remaining 0.5s, peak mem 270MB, user 13.2s, sys 0.8s, output queue size 1960
progress 80% @chr22:37951460, elapsed 1.6s, est remaining 0.4s, peak mem 270MB, user 13.3s, sys 0.9s, output queue size 2524
progress 85% @chr22:41280933, elapsed 1.6s, est remaining 0.3s, peak mem 270MB, user 13.3s, sys 0.9s, output queue size 3052
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 270MB, user 13.3s, sys 1.0s, output queue size 3656
progress 95% @chr22:50720184, elapsed 1.7s, est remaining 0.1s, peak mem 270MB, user 13.3s, sys 1.0s, output queue size 72
progress 100% @chrY:57196336, elapsed 1.7s, est remaining 0.0s, peak mem 270MB, user 13.3s, sys 1.2s, output queue size 643
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586803
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.742 user 0.035 sys 0.847 real
"assemble_addRead": 324 calls 0.052 user 0.000 sys 0.051 real
"assemble_buildGraph": 688 calls 0.312 user 0.012 sys 0.422 real
"assemble_computecigar": 523 calls 0.336 user 0.018 sys 0.402 real
"assemble_kg_build_calcsize": 688 calls 0.180 user 0.000 sys 0.237 real
"assemble_kg_build_clear": 826 calls 0.021 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 1376 calls 0.268 user 0.021 sys 0.205 real
"assemble_kg_build_threading": 550 calls 0.123 user 0.012 sys 0.179 real
"assemble_kg_op1": 550 calls 0.018 user 0.000 sys 0.036 real
"assemble_kg_op2": 550 calls 0.010 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.008 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.014 user 0.000 sys 0.042 real
"assemble_sg_create": 523 calls 0.072 user 0.002 sys 0.056 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.364 user 0.018 sys 0.422 real
active: 19646 calls 0.004 user 0.000 sys 0.015 real
advance: 10022 calls 2.554 user 0.162 sys 3.145 real
annotate: 394 calls 0.022 user 0.000 sys 0.036 real
assemble_region: 324 calls 1.177 user 0.053 sys 1.323 real
build_variants: 322 calls 0.010 user 0.000 sys 0.002 real
calc: 19646 calls 0.174 user 0.006 sys 0.318 real
calc_region: 322 calls 6.477 user 0.086 sys 6.852 real
call_region: 322 calls 0.035 user 0.000 sys 0.069 real
clip_region: 646 calls 0.064 user 0.000 sys 0.087 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.009 sys 1.786 real
fetch: 19646 calls 0.104 user 0.003 sys 0.173 real
fetch_db: 322 calls 0.036 user 0.000 sys 0.086 real
fetch_ref: 19970 calls 0.006 user 0.043 sys 0.090 real
fetch_region: 324 calls 0.021 user 0.000 sys 0.018 real
idle: 39 calls 0.003 user 0.002 sys 13.766 real
init: 1 calls 0.026 user 0.011 sys 0.042 real
pairhmm: 2270 calls 10.264 user 0.081 sys 10.947 real
realign: 697 calls 0.514 user 0.002 sys 0.737 real
region: 19646 calls 10.045 user 0.178 sys 10.201 real
tracker: 19646 calls 0.015 user 0.000 sys 0.026 real
trim_region: 324 calls 0.000 user 0.000 sys 0.005 real
overall: 283234304 mem 17.140 user 1.804 sys 2.896 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory