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/1a/b2c3eba1c3188a0c09a69058be60cc/.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/1a/b2c3eba1c3188a0c09a69058be60cc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b8328367b22c15bd3300ec483b8d21/Sig_18_Blood.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b8328367b22c15bd3300ec483b8d21/Sig_18_Blood.recalibrated.bam.bai
  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 81MB, user 0.0s, sys 0.1s, output queue size 1923
progress 10% @chr1:37752876, elapsed 0.1s, est remaining 0.8s, peak mem 91MB, user 0.1s, sys 0.2s, output queue size 4579
progress 15% @chr1:65408641, elapsed 0.1s, est remaining 0.7s, peak mem 105MB, user 0.1s, sys 0.4s, output queue size 7303
progress 20% @chr1:113834309, elapsed 0.2s, est remaining 0.7s, peak mem 118MB, user 0.2s, sys 0.5s, output queue size 10063
progress 25% @chr1:155248405, elapsed 0.2s, est remaining 0.7s, peak mem 129MB, user 0.2s, sys 0.6s, output queue size 12405
progress 30% @chr1:179102287, elapsed 0.3s, est remaining 0.6s, peak mem 138MB, user 0.2s, sys 0.8s, output queue size 14885
progress 35% @chr1:209835075, elapsed 0.3s, est remaining 0.6s, peak mem 148MB, user 0.3s, sys 0.9s, output queue size 3537
progress 40% @chr1:246986967, elapsed 0.3s, est remaining 0.5s, peak mem 159MB, user 0.3s, sys 1.0s, output queue size 5937
progress 45% @chr2:32547850, elapsed 0.4s, est remaining 0.5s, peak mem 169MB, user 0.3s, sys 1.2s, output queue size 8223
progress 50% @chr2:74463190, elapsed 0.4s, est remaining 0.4s, peak mem 175MB, user 0.3s, sys 1.3s, output queue size 10712
progress 55% @chr2:113499257, elapsed 0.5s, est remaining 0.4s, peak mem 184MB, user 0.3s, sys 1.5s, output queue size 13249
progress 60% @chr2:170993780, elapsed 0.5s, est remaining 0.3s, peak mem 196MB, user 0.4s, sys 1.6s, output queue size 15940
progress 65% @chr2:202759233, elapsed 0.5s, est remaining 0.3s, peak mem 205MB, user 0.4s, sys 1.8s, output queue size 18211
progress 70% @chr2:233771174, elapsed 0.6s, est remaining 0.3s, peak mem 219MB, user 0.5s, sys 1.9s, output queue size 20691
progress 75% @chr3:25615431, elapsed 0.6s, est remaining 0.2s, peak mem 223MB, user 0.5s, sys 2.0s, output queue size 22913
progress 80% @chr3:49810984, elapsed 0.7s, est remaining 0.2s, peak mem 237MB, user 0.5s, sys 2.2s, output queue size 25399
progress 85% @chr3:101859272, elapsed 0.7s, est remaining 0.1s, peak mem 246MB, user 0.6s, sys 2.3s, output queue size 28024
progress 90% @chr3:140682462, elapsed 0.8s, est remaining 0.1s, peak mem 256MB, user 0.6s, sys 2.5s, output queue size 30638
progress 95% @chr3:188239635, elapsed 0.8s, est remaining 0.0s, peak mem 264MB, user 0.6s, sys 2.6s, output queue size 33027
progress 100% @chr4:7984839, elapsed 0.9s, est remaining 0.0s, peak mem 276MB, user 0.6s, sys 2.7s, output queue size 35264
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: 74732894
output file size: 22307
reads: 1001133
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.000 sys 0.018 real
advance: 51084 calls 0.002 user 0.013 sys 0.022 real
calc: 100735 calls 0.006 user 0.002 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.001 sys 1.541 real
fetch: 100735 calls 0.000 user 0.005 sys 0.019 real
fetch_ref: 100735 calls 0.065 user 0.074 sys 0.391 real
idle: 39 calls 0.009 user 0.023 sys 20.624 real
init: 1 calls 0.042 user 0.000 sys 0.042 real
region: 100735 calls 0.011 user 0.013 sys 0.022 real
tracker: 100735 calls 0.026 user 0.006 sys 0.092 real
overall: 291237888 mem 1.327 user 4.990 sys 2.668 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory