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/0f/69eb37538244495d555e0c13edf846/.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-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/0f/69eb37538244495d555e0c13edf846/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b9327ccd07f95c93afdb2eed727086/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b9327ccd07f95c93afdb2eed727086/Sig_18_Blood.recalibrated.bam
  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 Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:18634302, elapsed 0.0s, est remaining 0.9s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 2300
progress 10% @chr1:37761367, elapsed 0.1s, est remaining 0.9s, peak mem 75MB, user 0.0s, sys 0.3s, output queue size 592
progress 15% @chr1:65401761, elapsed 0.2s, est remaining 0.9s, peak mem 78MB, user 0.0s, sys 0.4s, output queue size 3320
progress 20% @chr1:113814905, elapsed 0.2s, est remaining 0.9s, peak mem 84MB, user 0.1s, sys 0.7s, output queue size 6080
progress 25% @chr1:155240630, elapsed 0.3s, est remaining 0.8s, peak mem 90MB, user 0.1s, sys 0.9s, output queue size 8422
progress 30% @chr1:179102287, elapsed 0.3s, est remaining 0.8s, peak mem 93MB, user 0.1s, sys 1.0s, output queue size 10896
progress 35% @chr1:209833185, elapsed 0.4s, est remaining 0.7s, peak mem 96MB, user 0.2s, sys 1.2s, output queue size 13331
progress 40% @chr1:246986967, elapsed 0.4s, est remaining 0.6s, peak mem 102MB, user 0.2s, sys 1.4s, output queue size 15733
progress 45% @chr2:32545643, elapsed 0.5s, est remaining 0.6s, peak mem 111MB, user 0.3s, sys 1.6s, output queue size 18019
progress 50% @chr2:74464496, elapsed 0.6s, est remaining 0.6s, peak mem 117MB, user 0.3s, sys 1.9s, output queue size 20509
progress 55% @chr2:113499257, elapsed 0.6s, est remaining 0.5s, peak mem 126MB, user 0.4s, sys 2.2s, output queue size 23039
progress 60% @chr2:170996653, elapsed 0.7s, est remaining 0.5s, peak mem 135MB, user 0.4s, sys 2.6s, output queue size 25737
progress 65% @chr2:202695881, elapsed 0.8s, est remaining 0.4s, peak mem 150MB, user 0.4s, sys 2.7s, output queue size 28009
progress 70% @chr2:233772261, elapsed 0.9s, est remaining 0.4s, peak mem 159MB, user 0.5s, sys 3.0s, output queue size 30487
progress 75% @chr3:25626560, elapsed 0.9s, est remaining 0.3s, peak mem 168MB, user 0.5s, sys 3.1s, output queue size 32712
progress 80% @chr3:49807736, elapsed 1.0s, est remaining 0.2s, peak mem 174MB, user 0.6s, sys 3.5s, output queue size 35184
progress 85% @chr3:101859272, elapsed 1.2s, est remaining 0.2s, peak mem 174MB, user 0.6s, sys 3.7s, output queue size 37819
progress 90% @chr3:139582927, elapsed 1.4s, est remaining 0.2s, peak mem 174MB, user 0.7s, sys 3.9s, output queue size 40417
progress 95% @chr3:188241640, elapsed 1.6s, est remaining 0.1s, peak mem 177MB, user 0.7s, sys 4.2s, output queue size 42825
progress 100% @chr4:26614408, elapsed 1.9s, est remaining 0.0s, peak mem 177MB, user 0.8s, sys 4.5s, output queue size 45061
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: 74586810
output file size: 22307
reads: 1001133
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.001 sys 0.017 real
advance: 51084 calls 0.018 user 0.003 sys 0.024 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 0.004 user 0.000 sys 3.791 real
fetch: 100735 calls 0.000 user 0.003 sys 0.018 real
fetch_ref: 100735 calls 0.078 user 0.054 sys 0.431 real
idle: 51 calls 0.002 user 0.007 sys 35.404 real
init: 1 calls 0.035 user 0.000 sys 0.043 real
region: 100735 calls 0.000 user 0.000 sys 0.020 real
tracker: 100735 calls 0.024 user 0.005 sys 0.095 real
overall: 188870656 mem 1.434 user 7.664 sys 4.921 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory