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/e9/a65d2327a9fc390e546bf1814f6759/.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-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr1_69091-70008.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/a65d2327a9fc390e546bf1814f6759/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8eee459d74eba64dfe5bc8368d5cb4/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8eee459d74eba64dfe5bc8368d5cb4/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 chr1_69091-70008.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:18376800, elapsed 0.0s, est remaining 0.8s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 2301
progress 10% @chr1:37761367, elapsed 0.1s, est remaining 0.8s, peak mem 81MB, user 0.1s, sys 0.3s, output queue size 4952
progress 15% @chr1:65392431, elapsed 0.1s, est remaining 0.8s, peak mem 96MB, user 0.1s, sys 0.4s, output queue size 2157
progress 20% @chr1:113837590, elapsed 0.2s, est remaining 0.7s, peak mem 105MB, user 0.1s, sys 0.6s, output queue size 4916
progress 25% @chr1:155247782, elapsed 0.2s, est remaining 0.7s, peak mem 123MB, user 0.1s, sys 0.7s, output queue size 7259
progress 30% @chr1:179102287, elapsed 0.3s, est remaining 0.6s, peak mem 123MB, user 0.2s, sys 0.9s, output queue size 9738
progress 35% @chr1:209801240, elapsed 0.3s, est remaining 0.6s, peak mem 129MB, user 0.2s, sys 1.0s, output queue size 12164
progress 40% @chr1:246999348, elapsed 0.4s, est remaining 0.5s, peak mem 144MB, user 0.2s, sys 1.2s, output queue size 14567
progress 45% @chr2:32597751, elapsed 0.4s, est remaining 0.5s, peak mem 156MB, user 0.3s, sys 1.3s, output queue size 16860
progress 50% @chr2:74461275, elapsed 0.4s, est remaining 0.4s, peak mem 162MB, user 0.3s, sys 1.5s, output queue size 19345
progress 55% @chr2:113499257, elapsed 0.5s, est remaining 0.4s, peak mem 171MB, user 0.4s, sys 1.6s, output queue size 21878
progress 60% @chr2:170993780, elapsed 0.5s, est remaining 0.4s, peak mem 183MB, user 0.4s, sys 1.8s, output queue size 24572
progress 65% @chr2:202759233, elapsed 0.6s, est remaining 0.3s, peak mem 198MB, user 0.4s, sys 1.9s, output queue size 26842
progress 70% @chr2:233772261, elapsed 0.6s, est remaining 0.3s, peak mem 210MB, user 0.5s, sys 2.1s, output queue size 29326
progress 75% @chr3:25619862, elapsed 0.7s, est remaining 0.2s, peak mem 213MB, user 0.5s, sys 2.2s, output queue size 31544
progress 80% @chr3:49804181, elapsed 0.7s, est remaining 0.2s, peak mem 222MB, user 0.5s, sys 2.4s, output queue size 34020
progress 85% @chr3:101857073, elapsed 0.8s, est remaining 0.1s, peak mem 234MB, user 0.6s, sys 2.5s, output queue size 36660
progress 90% @chr3:139538781, elapsed 0.8s, est remaining 0.1s, peak mem 243MB, user 0.6s, sys 2.7s, output queue size 39254
progress 95% @chr3:188239635, elapsed 0.8s, est remaining 0.0s, peak mem 249MB, user 0.6s, sys 2.8s, output queue size 41661
progress 100% @chr4:30721423, elapsed 0.9s, est remaining 0.0s, peak mem 258MB, user 0.6s, sys 2.9s, output queue size 43896
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: 74586809
output file size: 22307
reads: 1001133
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.007 sys 0.017 real
advance: 51084 calls 0.001 user 0.002 sys 0.024 real
calc: 100735 calls 0.001 user 0.007 sys 0.016 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.004 sys 1.616 real
fetch: 100735 calls 0.002 user 0.003 sys 0.017 real
fetch_ref: 100735 calls 0.092 user 0.040 sys 0.384 real
idle: 39 calls 0.015 user 0.034 sys 21.216 real
init: 1 calls 0.036 user 0.004 sys 0.042 real
region: 100735 calls 0.002 user 0.000 sys 0.021 real
tracker: 100735 calls 0.027 user 0.002 sys 0.089 real
overall: 273825792 mem 1.318 user 5.297 sys 2.738 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory