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/c2/370f49ab9e003226ef97140c52a35b/.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/53/ceed4bf612d62859d876f95d1d2d6f/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/ceed4bf612d62859d876f95d1d2d6f/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/370f49ab9e003226ef97140c52a35b/.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% @chr8:144250212, elapsed 0.0s, est remaining 0.9s, peak mem 72MB, user 0.0s, sys 0.2s, output queue size 2281
progress 10% @chr9:36833270, elapsed 0.1s, est remaining 0.9s, peak mem 78MB, user 0.0s, sys 0.4s, output queue size 355
progress 15% @chr9:96763118, elapsed 0.1s, est remaining 0.7s, peak mem 84MB, user 0.0s, sys 0.5s, output queue size 2138
progress 20% @chr9:128916096, elapsed 0.2s, est remaining 0.8s, peak mem 87MB, user 0.1s, sys 0.7s, output queue size 4755
progress 25% @chr10:14932854, elapsed 0.4s, est remaining 1.2s, peak mem 90MB, user 0.1s, sys 1.0s, output queue size 7514
progress 30% @chr10:69200280, elapsed 0.5s, est remaining 1.1s, peak mem 90MB, user 0.1s, sys 1.2s, output queue size 9898
progress 35% @chr10:100509007, elapsed 0.6s, est remaining 1.0s, peak mem 96MB, user 0.2s, sys 1.4s, output queue size 12555
progress 40% @chr11:294556, elapsed 0.6s, est remaining 1.0s, peak mem 99MB, user 0.2s, sys 1.6s, output queue size 15137
progress 45% @chr11:17959470, elapsed 0.7s, est remaining 0.9s, peak mem 99MB, user 0.2s, sys 1.9s, output queue size 17291
progress 50% @chr11:61397774, elapsed 0.8s, est remaining 0.8s, peak mem 105MB, user 0.3s, sys 2.2s, output queue size 19657
progress 55% @chr11:72988964, elapsed 0.9s, est remaining 0.7s, peak mem 111MB, user 0.3s, sys 2.6s, output queue size 22328
progress 60% @chr11:114407445, elapsed 0.9s, est remaining 0.6s, peak mem 129MB, user 0.3s, sys 2.9s, output queue size 24617
progress 65% @chr12:6457406, elapsed 1.0s, est remaining 0.6s, peak mem 132MB, user 0.4s, sys 3.3s, output queue size 26980
progress 70% @chr12:31672304, elapsed 1.1s, est remaining 0.5s, peak mem 144MB, user 0.4s, sys 3.5s, output queue size 29067
progress 75% @chr12:55986961, elapsed 1.2s, est remaining 0.4s, peak mem 147MB, user 0.4s, sys 3.8s, output queue size 31548
progress 80% @chr12:100051079, elapsed 1.3s, est remaining 0.3s, peak mem 150MB, user 0.5s, sys 4.1s, output queue size 34277
progress 85% @chr12:123796656, elapsed 1.4s, est remaining 0.2s, peak mem 156MB, user 0.5s, sys 4.4s, output queue size 37135
progress 90% @chr13:48464982, elapsed 1.5s, est remaining 0.2s, peak mem 174MB, user 0.5s, sys 4.6s, output queue size 39497
progress 95% @chr14:22633768, elapsed 1.6s, est remaining 0.1s, peak mem 174MB, user 0.6s, sys 4.8s, output queue size 41753
progress 100% @chr14:59331813, elapsed 1.7s, est remaining 0.0s, peak mem 174MB, user 0.6s, sys 5.0s, output queue size 44307
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: 71692764
output file size: 22308
reads: 1001089
contig: 48642 intervals 9000010 bases
active: 98785 calls 0.001 user 0.002 sys 0.017 real
advance: 50143 calls 0.004 user 0.002 sys 0.023 real
calc: 98785 calls 0.000 user 0.009 sys 0.017 real
done: 1 calls 0.002 user 0.000 sys 0.002 real
execute: 1 calls 0.009 user 0.000 sys 3.210 real
fetch: 98785 calls 0.007 user 0.000 sys 0.018 real
fetch_ref: 98785 calls 0.079 user 0.067 sys 0.418 real
idle: 51 calls 0.004 user 0.006 sys 31.208 real
init: 1 calls 0.049 user 0.000 sys 0.044 real
region: 98785 calls 0.002 user 0.006 sys 0.019 real
tracker: 98785 calls 0.010 user 0.002 sys 0.098 real
overall: 182571008 mem 1.398 user 8.629 sys 4.340 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory