Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/5df8f52d305ac0a41ae26d1a51ef52/.command.sh
  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-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/d5/f0f78c58c00045bc57d71e33fbf1a9/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/f0f78c58c00045bc57d71e33fbf1a9/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/e9/5df8f52d305ac0a41ae26d1a51ef52/.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 0.0s, est remaining 0.8s, peak mem 85MB, user 0.0s, sys 0.1s, output queue size 755
progress 10% @chr1:37799567, elapsed 0.1s, est remaining 0.8s, peak mem 96MB, user 0.1s, sys 0.3s, output queue size 3409
progress 15% @chr1:65405870, elapsed 0.1s, est remaining 0.7s, peak mem 109MB, user 0.1s, sys 0.5s, output queue size 6131
progress 20% @chr1:113837590, elapsed 0.2s, est remaining 0.7s, peak mem 118MB, user 0.1s, sys 0.7s, output queue size 8894
progress 25% @chr1:155239886, elapsed 0.2s, est remaining 0.6s, peak mem 124MB, user 0.2s, sys 0.9s, output queue size 11232
progress 30% @chr1:179102287, elapsed 0.3s, est remaining 0.6s, peak mem 136MB, user 0.2s, sys 1.1s, output queue size 13714
progress 35% @chr1:209789667, elapsed 0.3s, est remaining 0.6s, peak mem 144MB, user 0.2s, sys 1.3s, output queue size 16139
progress 40% @chr1:246918250, elapsed 0.3s, est remaining 0.5s, peak mem 154MB, user 0.2s, sys 1.5s, output queue size 18542
progress 45% @chr2:32543241, elapsed 0.4s, est remaining 0.5s, peak mem 166MB, user 0.3s, sys 1.7s, output queue size 20833
progress 50% @chr2:74460221, elapsed 0.4s, est remaining 0.4s, peak mem 172MB, user 0.3s, sys 1.8s, output queue size 23319
progress 55% @chr2:113499257, elapsed 0.5s, est remaining 0.4s, peak mem 183MB, user 0.4s, sys 2.0s, output queue size 25856
progress 60% @chr2:170993780, elapsed 0.5s, est remaining 0.3s, peak mem 193MB, user 0.4s, sys 2.2s, output queue size 28546
progress 65% @chr2:202828848, elapsed 0.6s, est remaining 0.3s, peak mem 207MB, user 0.4s, sys 2.3s, output queue size 30829
progress 70% @chr2:233771174, elapsed 0.6s, est remaining 0.3s, peak mem 216MB, user 0.4s, sys 2.5s, output queue size 33299
progress 75% @chr3:25620682, elapsed 0.6s, est remaining 0.2s, peak mem 226MB, user 0.4s, sys 2.7s, output queue size 35518
progress 80% @chr3:49807736, elapsed 0.7s, est remaining 0.2s, peak mem 234MB, user 0.5s, sys 2.8s, output queue size 37993
progress 85% @chr3:101860457, elapsed 0.7s, est remaining 0.1s, peak mem 249MB, user 0.5s, sys 3.0s, output queue size 40630
progress 90% @chr3:139539460, elapsed 0.8s, est remaining 0.1s, peak mem 258MB, user 0.6s, sys 3.2s, output queue size 43228
progress 95% @chr3:188609161, elapsed 0.8s, est remaining 0.0s, peak mem 267MB, user 0.6s, sys 3.4s, output queue size 45640
progress 100% @chr4:5708286, elapsed 0.9s, est remaining 0.0s, peak mem 282MB, user 0.6s, sys 3.5s, output queue size 1216
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692769
output file size: 22305
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.004 user 0.008 sys 0.019 real
advance: 51084 calls 0.010 user 0.008 sys 0.024 real
calc: 100735 calls 0.007 user 0.001 sys 0.019 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.000 sys 1.544 real
fetch: 100735 calls 0.011 user 0.007 sys 0.020 real
fetch_ref: 100735 calls 0.121 user 0.058 sys 0.388 real
idle: 39 calls 0.006 user 0.019 sys 20.515 real
init: 1 calls 0.040 user 0.000 sys 0.041 real
region: 100735 calls 0.007 user 0.011 sys 0.023 real
tracker: 100735 calls 0.035 user 0.013 sys 0.094 real
overall: 295964672 mem 1.266 user 5.761 sys 2.660 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory