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/7b/ebcb01a9484eefe78a6d4926fe14b5/.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-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/7b/ebcb01a9484eefe78a6d4926fe14b5/.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% @chr1:18376310, elapsed 0.1s, est remaining 1.1s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 2235
progress 10% @chr1:37799567, elapsed 0.1s, est remaining 1.1s, peak mem 75MB, user 0.1s, sys 0.4s, output queue size 4890
progress 15% @chr1:65401761, elapsed 0.2s, est remaining 1.1s, peak mem 78MB, user 0.1s, sys 0.7s, output queue size 1893
progress 20% @chr1:113848540, elapsed 0.3s, est remaining 1.0s, peak mem 93MB, user 0.1s, sys 0.9s, output queue size 4656
progress 25% @chr1:155247782, elapsed 0.3s, est remaining 1.0s, peak mem 93MB, user 0.2s, sys 1.1s, output queue size 6997
progress 30% @chr1:179102287, elapsed 0.4s, est remaining 0.9s, peak mem 105MB, user 0.2s, sys 1.4s, output queue size 9472
progress 35% @chr1:209789667, elapsed 0.4s, est remaining 0.8s, peak mem 111MB, user 0.3s, sys 1.6s, output queue size 11903
progress 40% @chr1:246916142, elapsed 0.5s, est remaining 0.8s, peak mem 126MB, user 0.3s, sys 1.9s, output queue size 14306
progress 45% @chr2:32547850, elapsed 0.6s, est remaining 0.7s, peak mem 132MB, user 0.3s, sys 2.0s, output queue size 16593
progress 50% @chr2:74461275, elapsed 0.6s, est remaining 0.6s, peak mem 138MB, user 0.4s, sys 2.2s, output queue size 19081
progress 55% @chr2:113499257, elapsed 0.9s, est remaining 0.7s, peak mem 141MB, user 0.4s, sys 2.5s, output queue size 21612
progress 60% @chr2:170993780, elapsed 1.0s, est remaining 0.7s, peak mem 150MB, user 0.4s, sys 2.7s, output queue size 24308
progress 65% @chr2:202765446, elapsed 1.1s, est remaining 0.6s, peak mem 156MB, user 0.5s, sys 2.9s, output queue size 26581
progress 70% @chr2:233779359, elapsed 1.2s, est remaining 0.5s, peak mem 159MB, user 0.5s, sys 3.0s, output queue size 29061
progress 75% @chr3:25624297, elapsed 1.3s, est remaining 0.4s, peak mem 162MB, user 0.6s, sys 3.2s, output queue size 31284
progress 80% @chr3:49804181, elapsed 1.4s, est remaining 0.3s, peak mem 168MB, user 0.6s, sys 3.3s, output queue size 33758
progress 85% @chr3:102468964, elapsed 1.4s, est remaining 0.2s, peak mem 180MB, user 0.6s, sys 3.5s, output queue size 36403
progress 90% @chr3:139573598, elapsed 1.5s, est remaining 0.2s, peak mem 180MB, user 0.7s, sys 3.7s, output queue size 38989
progress 95% @chr3:187942990, elapsed 1.6s, est remaining 0.1s, peak mem 183MB, user 0.7s, sys 3.9s, output queue size 41400
progress 100% @chr4:25757534, elapsed 1.6s, est remaining 0.0s, peak mem 186MB, user 0.7s, sys 4.1s, output queue size 43634
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: 71692764
output file size: 22304
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.007 user 0.000 sys 0.019 real
advance: 51084 calls 0.003 user 0.007 sys 0.027 real
calc: 100735 calls 0.000 user 0.000 sys 0.019 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.004 sys 3.088 real
fetch: 100735 calls 0.001 user 0.000 sys 0.020 real
fetch_ref: 100735 calls 0.069 user 0.054 sys 0.417 real
idle: 51 calls 0.003 user 0.006 sys 30.156 real
init: 1 calls 0.029 user 0.011 sys 0.042 real
region: 100735 calls 0.001 user 0.001 sys 0.023 real
tracker: 100735 calls 0.025 user 0.004 sys 0.096 real
overall: 198316032 mem 1.405 user 7.300 sys 4.216 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory