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/eb/c22ace01d2c582d39f4f1535772d60/.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/45/2c338fb82705e4e0b4e7a512d35d58/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/2c338fb82705e4e0b4e7a512d35d58/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/eb/c22ace01d2c582d39f4f1535772d60/.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% @chr1:18630847, elapsed 0.0s, est remaining 0.8s, peak mem 78MB, user 0.0s, sys 0.1s, output queue size 2453
progress 10% @chr1:37761367, elapsed 0.1s, est remaining 0.7s, peak mem 84MB, user 0.1s, sys 0.2s, output queue size 2319
progress 15% @chr1:65405870, elapsed 0.1s, est remaining 0.7s, peak mem 102MB, user 0.1s, sys 0.4s, output queue size 5046
progress 20% @chr1:113814905, elapsed 0.2s, est remaining 0.7s, peak mem 105MB, user 0.1s, sys 0.5s, output queue size 7806
progress 25% @chr1:155250276, elapsed 0.2s, est remaining 0.6s, peak mem 114MB, user 0.2s, sys 0.6s, output queue size 10151
progress 30% @chr1:179102287, elapsed 0.2s, est remaining 0.6s, peak mem 132MB, user 0.2s, sys 0.7s, output queue size 12628
progress 35% @chr1:209796348, elapsed 0.3s, est remaining 0.5s, peak mem 141MB, user 0.2s, sys 0.8s, output queue size 15054
progress 40% @chr1:246986967, elapsed 0.3s, est remaining 0.5s, peak mem 147MB, user 0.3s, sys 1.0s, output queue size 17461
progress 45% @chr2:32543241, elapsed 0.4s, est remaining 0.4s, peak mem 153MB, user 0.3s, sys 1.1s, output queue size 19750
progress 50% @chr2:74460221, elapsed 0.4s, est remaining 0.4s, peak mem 168MB, user 0.3s, sys 1.2s, output queue size 22234
progress 55% @chr2:113499257, elapsed 0.4s, est remaining 0.4s, peak mem 174MB, user 0.3s, sys 1.3s, output queue size 24769
progress 60% @chr2:170965790, elapsed 0.5s, est remaining 0.3s, peak mem 186MB, user 0.4s, sys 1.5s, output queue size 27462
progress 65% @chr2:202765446, elapsed 0.5s, est remaining 0.3s, peak mem 195MB, user 0.4s, sys 1.6s, output queue size 29734
progress 70% @chr2:233772261, elapsed 0.6s, est remaining 0.2s, peak mem 201MB, user 0.4s, sys 1.8s, output queue size 32212
progress 75% @chr3:25618654, elapsed 0.6s, est remaining 0.2s, peak mem 210MB, user 0.4s, sys 1.9s, output queue size 34435
progress 80% @chr3:49805308, elapsed 0.6s, est remaining 0.2s, peak mem 225MB, user 0.5s, sys 2.0s, output queue size 36914
progress 85% @chr3:101859272, elapsed 0.7s, est remaining 0.1s, peak mem 231MB, user 0.5s, sys 2.1s, output queue size 39547
progress 90% @chr3:139578872, elapsed 0.7s, est remaining 0.1s, peak mem 243MB, user 0.5s, sys 2.3s, output queue size 42143
progress 95% @chr3:188760113, elapsed 0.8s, est remaining 0.0s, peak mem 252MB, user 0.6s, sys 2.4s, output queue size 44562
progress 100% @chr4:23813690, elapsed 0.8s, est remaining 0.0s, peak mem 258MB, user 0.6s, sys 2.5s, output queue size 46787
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: 71692773
output file size: 22305
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.000 sys 0.020 real
advance: 51084 calls 0.004 user 0.018 sys 0.025 real
calc: 100735 calls 0.000 user 0.000 sys 0.020 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.001 sys 1.665 real
fetch: 100735 calls 0.006 user 0.000 sys 0.021 real
fetch_ref: 100735 calls 0.087 user 0.059 sys 0.377 real
idle: 39 calls 0.002 user 0.010 sys 22.581 real
init: 1 calls 0.040 user 0.000 sys 0.042 real
region: 100735 calls 0.000 user 0.004 sys 0.024 real
tracker: 100735 calls 0.036 user 0.006 sys 0.095 real
overall: 273813504 mem 1.338 user 5.141 sys 2.779 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory