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/d2/16c7c7024d9eabcb3c292d9c034c36/.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/chr4_30730753-30730788.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/16c7c7024d9eabcb3c292d9c034c36/.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 chr4_30730753-30730788.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86814456, elapsed 0.1s, est remaining 1.0s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 1690
progress 10% @chr4:152332564, elapsed 0.1s, est remaining 0.9s, peak mem 81MB, user 0.1s, sys 0.2s, output queue size 4079
progress 15% @chr5:36181818, elapsed 0.2s, est remaining 0.9s, peak mem 93MB, user 0.1s, sys 0.4s, output queue size 6554
progress 20% @chr5:91374114, elapsed 0.2s, est remaining 0.8s, peak mem 99MB, user 0.1s, sys 0.6s, output queue size 9132
progress 25% @chr5:141192553, elapsed 0.3s, est remaining 0.8s, peak mem 105MB, user 0.1s, sys 0.7s, output queue size 11532
progress 30% @chr5:177293824, elapsed 0.3s, est remaining 0.7s, peak mem 114MB, user 0.1s, sys 0.9s, output queue size 13657
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.6s, peak mem 126MB, user 0.2s, sys 1.0s, output queue size 15849
progress 40% @chr6:43640021, elapsed 0.4s, est remaining 0.6s, peak mem 135MB, user 0.2s, sys 1.2s, output queue size 18389
progress 45% @chr6:106527305, elapsed 0.4s, est remaining 0.5s, peak mem 138MB, user 0.2s, sys 1.4s, output queue size 1163
progress 50% @chr6:149450683, elapsed 0.5s, est remaining 0.5s, peak mem 138MB, user 0.2s, sys 1.6s, output queue size 3260
progress 55% @chr7:13911239, elapsed 0.6s, est remaining 0.5s, peak mem 144MB, user 0.3s, sys 1.8s, output queue size 5528
progress 60% @chr7:64219314, elapsed 0.6s, est remaining 0.4s, peak mem 150MB, user 0.3s, sys 1.9s, output queue size 7591
progress 65% @chr7:100951841, elapsed 0.7s, est remaining 0.4s, peak mem 153MB, user 0.3s, sys 2.1s, output queue size 10110
progress 70% @chr7:139345501, elapsed 0.7s, est remaining 0.3s, peak mem 165MB, user 0.4s, sys 2.4s, output queue size 12474
progress 75% @chr8:13110742, elapsed 0.8s, est remaining 0.3s, peak mem 171MB, user 0.4s, sys 2.6s, output queue size 14534
progress 80% @chr8:38975031, elapsed 0.8s, est remaining 0.2s, peak mem 174MB, user 0.4s, sys 2.8s, output queue size 16178
progress 85% @chrX:15511437, elapsed 0.9s, est remaining 0.2s, peak mem 177MB, user 0.4s, sys 3.0s, output queue size 18664
progress 90% @chrX:54993911, elapsed 1.0s, est remaining 0.1s, peak mem 186MB, user 0.5s, sys 3.3s, output queue size 21029
progress 95% @chrX:111721603, elapsed 1.0s, est remaining 0.1s, peak mem 195MB, user 0.5s, sys 3.6s, output queue size 22966
progress 100% @chrX:153786355, elapsed 1.1s, est remaining 0.0s, peak mem 210MB, user 0.5s, sys 3.8s, output queue size 25182
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: 71692764
output file size: 22307
reads: 1001089
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_addRead": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_buildGraph": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_computecigar": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_calcsize": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_clear": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_prepare": 4 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_threading": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op1": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op2": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op3": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_clean": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_create": 2 calls 0.000 user 0.000 sys 0.000 real
"checkGraph": 1 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 1 calls 0.000 user 0.000 sys 0.000 real
active: 93348 calls 0.000 user 0.003 sys 0.016 real
advance: 47638 calls 0.005 user 0.007 sys 0.025 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.000 user 0.014 sys 0.016 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.002 sys 2.969 real
fetch: 93348 calls 0.000 user 0.010 sys 0.017 real
fetch_ref: 93349 calls 0.070 user 0.082 sys 0.403 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 51 calls 0.003 user 0.024 sys 35.129 real
init: 1 calls 0.024 user 0.026 sys 0.042 real
region: 93348 calls 0.000 user 0.015 sys 0.020 real
tracker: 93348 calls 0.021 user 0.004 sys 0.088 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 220336128 mem 1.241 user 6.388 sys 4.087 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory