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/ba/0f360c861c92fa64e23bfacecaabd8/.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/5d/3cfabeb790a6f016a7b8ea9337df7f/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/3cfabeb790a6f016a7b8ea9337df7f/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/ba/0f360c861c92fa64e23bfacecaabd8/.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% @chr1:18365223, elapsed 0.0s, est remaining 0.8s, peak mem 85MB, user 0.0s, sys 0.2s, output queue size 2177
progress 10% @chr1:37752876, elapsed 0.1s, est remaining 0.7s, peak mem 96MB, user 0.1s, sys 0.3s, output queue size 4831
progress 15% @chr1:65405870, elapsed 0.1s, est remaining 0.7s, peak mem 111MB, user 0.1s, sys 0.6s, output queue size 7554
progress 20% @chr1:113837590, elapsed 0.2s, est remaining 0.7s, peak mem 120MB, user 0.1s, sys 0.7s, output queue size 2124
progress 25% @chr1:155250276, elapsed 0.2s, est remaining 0.6s, peak mem 129MB, user 0.1s, sys 1.0s, output queue size 4469
progress 30% @chr1:179102287, elapsed 0.3s, est remaining 0.6s, peak mem 144MB, user 0.1s, sys 1.2s, output queue size 6942
progress 35% @chr1:209828064, elapsed 0.3s, est remaining 0.5s, peak mem 151MB, user 0.2s, sys 1.3s, output queue size 9373
progress 40% @chr1:246986967, elapsed 0.3s, est remaining 0.5s, peak mem 163MB, user 0.2s, sys 1.5s, output queue size 11777
progress 45% @chr2:32811024, elapsed 0.4s, est remaining 0.5s, peak mem 169MB, user 0.2s, sys 1.7s, output queue size 14091
progress 50% @chr2:74461275, elapsed 0.4s, est remaining 0.4s, peak mem 183MB, user 0.2s, sys 1.8s, output queue size 16553
progress 55% @chr2:113499257, elapsed 0.5s, est remaining 0.4s, peak mem 193MB, user 0.3s, sys 2.0s, output queue size 19083
progress 60% @chr2:171053761, elapsed 0.5s, est remaining 0.3s, peak mem 207MB, user 0.3s, sys 2.3s, output queue size 21792
progress 65% @chr2:202779533, elapsed 0.5s, est remaining 0.3s, peak mem 214MB, user 0.3s, sys 2.4s, output queue size 24052
progress 70% @chr2:233772261, elapsed 0.6s, est remaining 0.3s, peak mem 222MB, user 0.4s, sys 2.6s, output queue size 26529
progress 75% @chr3:25612515, elapsed 0.6s, est remaining 0.2s, peak mem 232MB, user 0.4s, sys 2.7s, output queue size 28753
progress 80% @chr3:49805308, elapsed 0.7s, est remaining 0.2s, peak mem 244MB, user 0.4s, sys 2.9s, output queue size 31226
progress 85% @chr3:101857073, elapsed 0.7s, est remaining 0.1s, peak mem 252MB, user 0.4s, sys 3.0s, output queue size 33868
progress 90% @chr3:139582927, elapsed 0.8s, est remaining 0.1s, peak mem 265MB, user 0.5s, sys 3.1s, output queue size 36463
progress 95% @chr3:188239635, elapsed 0.8s, est remaining 0.0s, peak mem 274MB, user 0.5s, sys 3.3s, output queue size 38868
progress 100% @chr4:25396664, elapsed 0.8s, est remaining 0.0s, peak mem 285MB, user 0.5s, sys 3.5s, output queue size 41104
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71699821
output file size: 22306
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.023 sys 0.018 real
advance: 51084 calls 0.002 user 0.020 sys 0.023 real
calc: 100735 calls 0.008 user 0.013 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.001 sys 1.469 real
fetch: 100735 calls 0.000 user 0.012 sys 0.019 real
fetch_ref: 100735 calls 0.131 user 0.099 sys 0.411 real
idle: 39 calls 0.003 user 0.007 sys 19.995 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
region: 100735 calls 0.000 user 0.010 sys 0.021 real
tracker: 100735 calls 0.045 user 0.008 sys 0.090 real
overall: 300675072 mem 1.064 user 5.311 sys 2.588 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory