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/86/23a0262544e25fed6078fcc5c051c1/.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/ad/ded0dc28f0bedef0afd0b3c848896c/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/ded0dc28f0bedef0afd0b3c848896c/HCC1395_BL.recalibrated.bam.bai
  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/86/23a0262544e25fed6078fcc5c051c1/.command.run
  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 HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:18365223, elapsed 0.1s, est remaining 1.0s, peak mem 78MB, user 0.0s, sys 0.2s, output queue size 1112
progress 10% @chr1:37764961, elapsed 0.1s, est remaining 1.0s, peak mem 84MB, user 0.1s, sys 0.5s, output queue size 3765
progress 15% @chr1:65405870, elapsed 0.2s, est remaining 0.9s, peak mem 90MB, user 0.1s, sys 0.8s, output queue size 6491
progress 20% @chr1:113837590, elapsed 0.2s, est remaining 0.9s, peak mem 108MB, user 0.1s, sys 1.1s, output queue size 9251
progress 25% @chr1:155238517, elapsed 0.3s, est remaining 0.8s, peak mem 120MB, user 0.2s, sys 1.3s, output queue size 11594
progress 30% @chr1:179099331, elapsed 0.3s, est remaining 0.8s, peak mem 129MB, user 0.2s, sys 1.5s, output queue size 14078
progress 35% @chr1:209801240, elapsed 0.4s, est remaining 0.7s, peak mem 138MB, user 0.2s, sys 1.7s, output queue size 16497
progress 40% @chr1:246918250, elapsed 0.4s, est remaining 0.6s, peak mem 150MB, user 0.3s, sys 1.9s, output queue size 18900
progress 45% @chr2:32575156, elapsed 0.5s, est remaining 0.6s, peak mem 156MB, user 0.3s, sys 2.2s, output queue size 21191
progress 50% @chr2:74460221, elapsed 0.5s, est remaining 0.5s, peak mem 162MB, user 0.3s, sys 2.4s, output queue size 23682
progress 55% @chr2:113499257, elapsed 0.6s, est remaining 0.5s, peak mem 180MB, user 0.4s, sys 2.7s, output queue size 26209
progress 60% @chr2:171855834, elapsed 0.7s, est remaining 0.4s, peak mem 189MB, user 0.4s, sys 2.8s, output queue size 471
progress 65% @chr2:202765446, elapsed 0.7s, est remaining 0.4s, peak mem 198MB, user 0.5s, sys 3.0s, output queue size 2663
progress 70% @chr2:233772261, elapsed 0.7s, est remaining 0.3s, peak mem 213MB, user 0.5s, sys 3.2s, output queue size 5142
progress 75% @chr3:25618654, elapsed 0.8s, est remaining 0.3s, peak mem 216MB, user 0.6s, sys 3.4s, output queue size 7361
progress 80% @chr3:49809978, elapsed 0.8s, est remaining 0.2s, peak mem 228MB, user 0.6s, sys 3.6s, output queue size 9847
progress 85% @chr3:101859272, elapsed 0.9s, est remaining 0.2s, peak mem 243MB, user 0.6s, sys 3.8s, output queue size 12474
progress 90% @chr3:139578872, elapsed 0.9s, est remaining 0.1s, peak mem 249MB, user 0.7s, sys 4.0s, output queue size 15072
progress 95% @chr3:187741772, elapsed 1.0s, est remaining 0.1s, peak mem 258MB, user 0.7s, sys 4.2s, output queue size 17480
progress 100% @chr4:8235433, elapsed 1.0s, est remaining 0.0s, peak mem 264MB, user 0.8s, sys 4.3s, output queue size 19716
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: 71692760
output file size: 22305
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.006 user 0.034 sys 0.016 real
advance: 51084 calls 0.002 user 0.015 sys 0.020 real
calc: 100735 calls 0.000 user 0.018 sys 0.016 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.001 sys 1.680 real
fetch: 100735 calls 0.000 user 0.004 sys 0.016 real
fetch_ref: 100735 calls 0.165 user 0.073 sys 0.410 real
idle: 39 calls 0.007 user 0.024 sys 20.514 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
region: 100735 calls 0.002 user 0.000 sys 0.018 real
tracker: 100735 calls 0.026 user 0.000 sys 0.085 real
overall: 276942848 mem 1.231 user 6.143 sys 2.797 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory