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/fe/98dadf328c468d44aa74a7c1a666b8/.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/f0/61734391e4f47c8b44be28e79e0683/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/61734391e4f47c8b44be28e79e0683/HCC1395_BL.recalibrated.bam.bai
  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/fe/98dadf328c468d44aa74a7c1a666b8/.command.run
  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 HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:18480982, elapsed 0.1s, est remaining 1.2s, peak mem 75MB, user 0.1s, sys 0.2s, output queue size 2146
progress 10% @chr1:37794183, elapsed 0.1s, est remaining 1.1s, peak mem 84MB, user 0.1s, sys 0.4s, output queue size 4797
progress 15% @chr1:65619928, elapsed 0.2s, est remaining 1.1s, peak mem 93MB, user 0.1s, sys 0.7s, output queue size 7544
progress 20% @chr1:113859352, elapsed 0.3s, est remaining 1.1s, peak mem 108MB, user 0.2s, sys 0.9s, output queue size 2395
progress 25% @chr1:155253625, elapsed 0.3s, est remaining 1.0s, peak mem 111MB, user 0.2s, sys 1.0s, output queue size 4735
progress 30% @chr1:179102287, elapsed 0.4s, est remaining 0.9s, peak mem 120MB, user 0.2s, sys 1.3s, output queue size 7201
progress 35% @chr1:209830803, elapsed 0.4s, est remaining 0.8s, peak mem 129MB, user 0.2s, sys 1.6s, output queue size 9635
progress 40% @chr1:246986967, elapsed 0.5s, est remaining 0.8s, peak mem 141MB, user 0.3s, sys 1.8s, output queue size 12038
progress 45% @chr2:32547850, elapsed 0.6s, est remaining 0.7s, peak mem 150MB, user 0.3s, sys 2.1s, output queue size 14327
progress 50% @chr2:74459873, elapsed 0.6s, est remaining 0.6s, peak mem 159MB, user 0.3s, sys 2.3s, output queue size 16816
progress 55% @chr2:113499257, elapsed 0.7s, est remaining 0.6s, peak mem 168MB, user 0.3s, sys 2.7s, output queue size 19348
progress 60% @chr2:170956436, elapsed 0.7s, est remaining 0.5s, peak mem 177MB, user 0.4s, sys 3.0s, output queue size 22042
progress 65% @chr2:202815911, elapsed 0.8s, est remaining 0.4s, peak mem 186MB, user 0.4s, sys 3.2s, output queue size 24320
progress 70% @chr2:233770694, elapsed 0.9s, est remaining 0.4s, peak mem 192MB, user 0.4s, sys 3.5s, output queue size 26798
progress 75% @chr3:25635936, elapsed 0.9s, est remaining 0.3s, peak mem 201MB, user 0.5s, sys 3.8s, output queue size 29028
progress 80% @chr3:49804181, elapsed 1.0s, est remaining 0.2s, peak mem 210MB, user 0.5s, sys 4.0s, output queue size 31489
progress 85% @chr3:101857073, elapsed 1.0s, est remaining 0.2s, peak mem 216MB, user 0.5s, sys 4.3s, output queue size 34131
progress 90% @chr3:139582927, elapsed 1.1s, est remaining 0.1s, peak mem 219MB, user 0.6s, sys 4.7s, output queue size 36723
progress 95% @chr3:187741772, elapsed 1.2s, est remaining 0.1s, peak mem 234MB, user 0.6s, sys 5.0s, output queue size 39130
progress 100% @chr4:26489233, elapsed 1.2s, est remaining 0.0s, peak mem 237MB, user 0.6s, sys 5.2s, output queue size 41367
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: 22305
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.008 user 0.011 sys 0.015 real
advance: 51084 calls 0.004 user 0.011 sys 0.023 real
calc: 100735 calls 0.000 user 0.000 sys 0.016 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.010 sys 2.218 real
fetch: 100735 calls 0.000 user 0.010 sys 0.016 real
fetch_ref: 100735 calls 0.082 user 0.120 sys 0.392 real
idle: 39 calls 0.003 user 0.004 sys 24.335 real
init: 1 calls 0.028 user 0.011 sys 0.044 real
region: 100735 calls 0.004 user 0.000 sys 0.017 real
tracker: 100735 calls 0.058 user 0.006 sys 0.087 real
overall: 251793408 mem 0.984 user 7.121 sys 3.347 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory