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/93/0b348a0fb015ab558f21b7cba196ff/.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/d1/b4859e2819e5c08f9ce4cd4fa95b10/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/b4859e2819e5c08f9ce4cd4fa95b10/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/0b348a0fb015ab558f21b7cba196ff/.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 1.4s, est remaining 26.0s, peak mem 72MB, user 0.1s, sys 0.1s, output queue size 715
progress 10% @chr15:40899144, elapsed 1.4s, est remaining 12.7s, peak mem 72MB, user 0.2s, sys 0.3s, output queue size 2959
progress 15% @chr15:63774694, elapsed 1.5s, est remaining 8.3s, peak mem 84MB, user 0.2s, sys 0.5s, output queue size 5583
progress 20% @chr15:87989891, elapsed 1.5s, est remaining 6.0s, peak mem 93MB, user 0.2s, sys 0.7s, output queue size 7871
progress 25% @chr16:1961497, elapsed 1.5s, est remaining 4.6s, peak mem 102MB, user 0.3s, sys 0.9s, output queue size 9564
progress 30% @chr16:23529502, elapsed 1.6s, est remaining 3.7s, peak mem 111MB, user 0.3s, sys 1.0s, output queue size 12034
progress 35% @chr16:66566514, elapsed 1.6s, est remaining 3.1s, peak mem 120MB, user 0.3s, sys 1.3s, output queue size 14639
progress 40% @chr16:89286670, elapsed 1.7s, est remaining 2.5s, peak mem 129MB, user 0.4s, sys 1.5s, output queue size 17113
progress 45% @chr17:10312574, elapsed 1.7s, est remaining 2.1s, peak mem 147MB, user 0.4s, sys 1.7s, output queue size 19727
progress 50% @chr17:36260780, elapsed 1.8s, est remaining 1.8s, peak mem 159MB, user 0.4s, sys 1.8s, output queue size 22321
progress 55% @chr17:45099405, elapsed 1.8s, est remaining 1.5s, peak mem 165MB, user 0.5s, sys 2.0s, output queue size 24564
progress 60% @chr17:68420189, elapsed 1.9s, est remaining 1.2s, peak mem 174MB, user 0.5s, sys 2.2s, output queue size 27097
progress 65% @chr18:5433903, elapsed 1.9s, est remaining 1.0s, peak mem 186MB, user 0.6s, sys 2.4s, output queue size 29816
progress 70% @chr18:62574057, elapsed 2.0s, est remaining 0.8s, peak mem 198MB, user 0.6s, sys 2.7s, output queue size 2280
progress 75% @chr19:6921713, elapsed 2.0s, est remaining 0.7s, peak mem 207MB, user 0.7s, sys 2.8s, output queue size 4670
progress 80% @chr19:15371952, elapsed 2.1s, est remaining 0.5s, peak mem 213MB, user 0.7s, sys 3.0s, output queue size 6941
progress 85% @chr19:36949512, elapsed 2.1s, est remaining 0.4s, peak mem 219MB, user 0.7s, sys 3.2s, output queue size 9245
progress 90% @chr19:46493558, elapsed 2.2s, est remaining 0.2s, peak mem 234MB, user 0.8s, sys 3.5s, output queue size 11414
progress 95% @chr20:36916678, elapsed 2.3s, est remaining 0.1s, peak mem 240MB, user 0.8s, sys 3.8s, output queue size 14050
progress 100% @chr20:63741370, elapsed 2.3s, est remaining 0.0s, peak mem 252MB, user 0.8s, sys 4.1s, output queue size 16490
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692759
output file size: 22307
reads: 1001089
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.003 user 0.003 sys 0.018 real
advance: 49760 calls 0.001 user 0.014 sys 0.023 real
calc: 97912 calls 0.012 user 0.006 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.001 sys 3.168 real
fetch: 97912 calls 0.000 user 0.000 sys 0.018 real
fetch_ref: 97912 calls 0.138 user 0.063 sys 0.364 real
idle: 39 calls 0.003 user 0.002 sys 22.565 real
init: 1 calls 0.049 user 0.001 sys 0.042 real
region: 97912 calls 0.001 user 0.005 sys 0.023 real
tracker: 97912 calls 0.012 user 0.004 sys 0.088 real
overall: 264376320 mem 1.591 user 6.192 sys 4.288 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory