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/f1/9491b9ffa18dafa64e3511829f95e1/.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/f1/9491b9ffa18dafa64e3511829f95e1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr14_64122012-64122133.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 chr14_64122012-64122133.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr14:100880712, elapsed 0.0s, est remaining 0.8s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 2028
progress 10% @chr15:40929847, elapsed 0.1s, est remaining 0.7s, peak mem 81MB, user 0.0s, sys 0.3s, output queue size 4271
progress 15% @chr15:63908520, elapsed 0.1s, est remaining 0.7s, peak mem 87MB, user 0.1s, sys 0.4s, output queue size 6891
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 0.6s, peak mem 102MB, user 0.1s, sys 0.5s, output queue size 9177
progress 25% @chr16:1941257, elapsed 0.2s, est remaining 0.5s, peak mem 108MB, user 0.1s, sys 0.5s, output queue size 10863
progress 30% @chr16:23582284, elapsed 0.2s, est remaining 0.5s, peak mem 114MB, user 0.2s, sys 0.7s, output queue size 13359
progress 35% @chr16:66566514, elapsed 0.3s, est remaining 0.5s, peak mem 123MB, user 0.2s, sys 0.8s, output queue size 2919
progress 40% @chr16:89279067, elapsed 0.3s, est remaining 0.5s, peak mem 132MB, user 0.3s, sys 1.0s, output queue size 5390
progress 45% @chr17:10309234, elapsed 0.4s, est remaining 0.5s, peak mem 135MB, user 0.3s, sys 1.3s, output queue size 8005
progress 50% @chr17:36330448, elapsed 0.7s, est remaining 0.7s, peak mem 135MB, user 0.3s, sys 1.5s, output queue size 10605
progress 55% @chr17:45114250, elapsed 0.8s, est remaining 0.7s, peak mem 138MB, user 0.4s, sys 1.6s, output queue size 12845
progress 60% @chr17:68370444, elapsed 0.9s, est remaining 0.6s, peak mem 141MB, user 0.4s, sys 1.9s, output queue size 15378
progress 65% @chr18:5890198, elapsed 1.0s, est remaining 0.5s, peak mem 147MB, user 0.5s, sys 2.2s, output queue size 18098
progress 70% @chr18:62895781, elapsed 1.1s, est remaining 0.5s, peak mem 159MB, user 0.5s, sys 2.4s, output queue size 20482
progress 75% @chr19:6903810, elapsed 1.1s, est remaining 0.4s, peak mem 165MB, user 0.5s, sys 2.8s, output queue size 22864
progress 80% @chr19:15263420, elapsed 1.2s, est remaining 0.3s, peak mem 171MB, user 0.5s, sys 3.0s, output queue size 25119
progress 85% @chr19:36891492, elapsed 1.3s, est remaining 0.2s, peak mem 180MB, user 0.6s, sys 3.2s, output queue size 27435
progress 90% @chr19:46525663, elapsed 1.3s, est remaining 0.1s, peak mem 183MB, user 0.6s, sys 3.3s, output queue size 29608
progress 95% @chr20:36905333, elapsed 1.4s, est remaining 0.1s, peak mem 183MB, user 0.6s, sys 3.5s, output queue size 32246
progress 100% @chr20:63889850, elapsed 1.4s, est remaining 0.0s, peak mem 192MB, user 0.7s, sys 3.6s, output queue size 34683
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: 22306
reads: 1001089
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.000 user 0.000 sys 0.016 real
advance: 49760 calls 0.000 user 0.010 sys 0.023 real
calc: 97912 calls 0.000 user 0.003 sys 0.016 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.004 sys 2.433 real
fetch: 97912 calls 0.000 user 0.009 sys 0.017 real
fetch_ref: 97912 calls 0.095 user 0.039 sys 0.381 real
idle: 51 calls 0.005 user 0.003 sys 25.039 real
init: 1 calls 0.063 user 0.000 sys 0.064 real
region: 97912 calls 0.002 user 0.006 sys 0.020 real
tracker: 97912 calls 0.026 user 0.004 sys 0.092 real
overall: 201490432 mem 1.520 user 6.416 sys 3.598 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory