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/3f/01e1a1debe9d7c068e082a00e45f42/.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/d5/f0f78c58c00045bc57d71e33fbf1a9/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/f0f78c58c00045bc57d71e33fbf1a9/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/01e1a1debe9d7c068e082a00e45f42/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr8_93795409-93795507.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 chr8_93795409-93795507.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr8:144255509, elapsed 0.0s, est remaining 0.8s, peak mem 84MB, user 0.0s, sys 0.1s, output queue size 809
progress 10% @chr9:36833270, elapsed 0.1s, est remaining 0.7s, peak mem 90MB, user 0.0s, sys 0.2s, output queue size 3023
progress 15% @chr9:96651659, elapsed 0.1s, est remaining 0.6s, peak mem 99MB, user 0.1s, sys 0.3s, output queue size 4804
progress 20% @chr9:128945687, elapsed 0.1s, est remaining 0.6s, peak mem 109MB, user 0.1s, sys 0.5s, output queue size 7428
progress 25% @chr10:14908408, elapsed 0.2s, est remaining 0.5s, peak mem 121MB, user 0.1s, sys 0.7s, output queue size 10177
progress 30% @chr10:69208600, elapsed 0.2s, est remaining 0.5s, peak mem 132MB, user 0.2s, sys 0.8s, output queue size 12571
progress 35% @chr10:100498029, elapsed 0.3s, est remaining 0.5s, peak mem 145MB, user 0.2s, sys 1.0s, output queue size 15221
progress 40% @chr11:319838, elapsed 0.3s, est remaining 0.5s, peak mem 151MB, user 0.3s, sys 1.1s, output queue size 17803
progress 45% @chr11:17771665, elapsed 0.3s, est remaining 0.4s, peak mem 163MB, user 0.3s, sys 1.3s, output queue size 19961
progress 50% @chr11:61416105, elapsed 0.4s, est remaining 0.4s, peak mem 174MB, user 0.4s, sys 1.5s, output queue size 22325
progress 55% @chr11:72902543, elapsed 0.4s, est remaining 0.3s, peak mem 177MB, user 0.4s, sys 1.6s, output queue size 24994
progress 60% @chr11:114444541, elapsed 0.5s, est remaining 0.3s, peak mem 187MB, user 0.5s, sys 1.7s, output queue size 27283
progress 65% @chr12:6458645, elapsed 0.5s, est remaining 0.3s, peak mem 195MB, user 0.5s, sys 1.8s, output queue size 29643
progress 70% @chr12:31667647, elapsed 0.5s, est remaining 0.2s, peak mem 204MB, user 0.5s, sys 2.0s, output queue size 31734
progress 75% @chr12:55967857, elapsed 0.6s, est remaining 0.2s, peak mem 213MB, user 0.6s, sys 2.1s, output queue size 34210
progress 80% @chr12:99984104, elapsed 0.6s, est remaining 0.2s, peak mem 220MB, user 0.6s, sys 2.4s, output queue size 36944
progress 85% @chr12:123756815, elapsed 0.7s, est remaining 0.1s, peak mem 232MB, user 0.7s, sys 2.6s, output queue size 39798
progress 90% @chr13:48479980, elapsed 0.7s, est remaining 0.1s, peak mem 240MB, user 0.7s, sys 2.7s, output queue size 42178
progress 95% @chr14:22769791, elapsed 0.8s, est remaining 0.0s, peak mem 255MB, user 0.7s, sys 2.9s, output queue size 225
progress 100% @chr14:64001934, elapsed 0.8s, est remaining 0.0s, peak mem 261MB, user 0.8s, sys 3.1s, output queue size 2776
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692769
output file size: 22308
reads: 1001089
contig: 48642 intervals 9000010 bases
active: 98785 calls 0.000 user 0.000 sys 0.018 real
advance: 50143 calls 0.002 user 0.005 sys 0.019 real
calc: 98785 calls 0.008 user 0.003 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.002 sys 2.509 real
fetch: 98785 calls 0.000 user 0.001 sys 0.019 real
fetch_ref: 98785 calls 0.128 user 0.087 sys 0.368 real
idle: 51 calls 0.002 user 0.007 sys 32.589 real
init: 1 calls 0.041 user 0.000 sys 0.041 real
region: 98785 calls 0.007 user 0.007 sys 0.022 real
tracker: 98785 calls 0.012 user 0.001 sys 0.088 real
overall: 273944576 mem 1.397 user 5.013 sys 3.640 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory