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/cb/2155027aabf5864eebafdd6870c779/.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/cb/2155027aabf5864eebafdd6870c779/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/381faa0df790cd8579fab559ff3f2b/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/381faa0df790cd8579fab559ff3f2b/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% @chr1:18630847, elapsed 0.1s, est remaining 1.0s, peak mem 78MB, user 0.1s, sys 0.1s, output queue size 992
progress 10% @chr1:37761367, elapsed 0.1s, est remaining 0.9s, peak mem 78MB, user 0.1s, sys 0.3s, output queue size 3645
progress 15% @chr1:65405870, elapsed 0.2s, est remaining 0.9s, peak mem 87MB, user 0.1s, sys 0.6s, output queue size 6370
progress 20% @chr1:113829592, elapsed 0.2s, est remaining 0.8s, peak mem 93MB, user 0.1s, sys 0.7s, output queue size 9131
progress 25% @chr1:155250276, elapsed 0.3s, est remaining 0.8s, peak mem 108MB, user 0.1s, sys 0.9s, output queue size 11477
progress 30% @chr1:179102287, elapsed 0.3s, est remaining 0.7s, peak mem 111MB, user 0.1s, sys 1.1s, output queue size 13954
progress 35% @chr1:209795290, elapsed 0.4s, est remaining 0.7s, peak mem 123MB, user 0.1s, sys 1.2s, output queue size 16377
progress 40% @chr1:247037449, elapsed 0.4s, est remaining 0.7s, peak mem 123MB, user 0.1s, sys 1.4s, output queue size 18784
progress 45% @chr2:32595034, elapsed 0.5s, est remaining 0.6s, peak mem 123MB, user 0.2s, sys 1.6s, output queue size 21071
progress 50% @chr2:74460221, elapsed 0.9s, est remaining 0.9s, peak mem 129MB, user 0.3s, sys 1.8s, output queue size 2132
progress 55% @chr2:115689840, elapsed 1.0s, est remaining 0.8s, peak mem 135MB, user 0.3s, sys 2.0s, output queue size 4718
progress 60% @chr2:170954650, elapsed 1.0s, est remaining 0.7s, peak mem 144MB, user 0.3s, sys 2.2s, output queue size 7363
progress 65% @chr2:202817418, elapsed 1.1s, est remaining 0.6s, peak mem 162MB, user 0.3s, sys 2.4s, output queue size 9641
progress 70% @chr2:233772261, elapsed 1.2s, est remaining 0.5s, peak mem 165MB, user 0.4s, sys 2.6s, output queue size 12111
progress 75% @chr3:25624297, elapsed 1.2s, est remaining 0.4s, peak mem 165MB, user 0.5s, sys 2.7s, output queue size 14335
progress 80% @chr3:49805308, elapsed 1.4s, est remaining 0.3s, peak mem 171MB, user 0.5s, sys 2.9s, output queue size 16807
progress 85% @chr3:101361715, elapsed 1.5s, est remaining 0.3s, peak mem 174MB, user 0.6s, sys 3.1s, output queue size 19451
progress 90% @chr3:140562811, elapsed 1.6s, est remaining 0.2s, peak mem 183MB, user 0.6s, sys 3.2s, output queue size 22057
progress 95% @chr3:188240450, elapsed 1.7s, est remaining 0.1s, peak mem 189MB, user 0.7s, sys 3.4s, output queue size 24450
progress 100% @chr4:25667880, elapsed 1.8s, est remaining 0.0s, peak mem 198MB, user 0.7s, sys 3.5s, output queue size 26686
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: 74586800
output file size: 22307
reads: 1001133
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.003 sys 0.019 real
advance: 51084 calls 0.003 user 0.006 sys 0.027 real
calc: 100735 calls 0.000 user 0.000 sys 0.019 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.000 user 0.003 sys 3.789 real
fetch: 100735 calls 0.001 user 0.000 sys 0.020 real
fetch_ref: 100735 calls 0.045 user 0.022 sys 0.400 real
idle: 51 calls 0.003 user 0.008 sys 36.052 real
init: 1 calls 0.031 user 0.009 sys 0.043 real
region: 100735 calls 0.000 user 0.000 sys 0.022 real
tracker: 100735 calls 0.018 user 0.010 sys 0.101 real
overall: 207749120 mem 1.275 user 6.642 sys 4.948 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory