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/e0/c6e286c0c08dac984a859e37efe139/.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/e7/493cf948b1d450f8051fba2ea0097a/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/493cf948b1d450f8051fba2ea0097a/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/e0/c6e286c0c08dac984a859e37efe139/.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% @chr4:86775171, elapsed 0.0s, est remaining 0.9s, peak mem 79MB, user 0.1s, sys 0.1s, output queue size 1971
progress 10% @chr4:152330694, elapsed 0.1s, est remaining 0.8s, peak mem 91MB, user 0.1s, sys 0.3s, output queue size 4365
progress 15% @chr5:36171603, elapsed 0.2s, est remaining 0.9s, peak mem 102MB, user 0.1s, sys 0.5s, output queue size 6839
progress 20% @chr5:93587917, elapsed 0.2s, est remaining 0.9s, peak mem 109MB, user 0.1s, sys 0.6s, output queue size 1063
progress 25% @chr5:141192553, elapsed 0.3s, est remaining 0.8s, peak mem 120MB, user 0.1s, sys 0.8s, output queue size 3458
progress 30% @chr5:177306098, elapsed 0.3s, est remaining 0.7s, peak mem 130MB, user 0.2s, sys 1.0s, output queue size 5579
progress 35% @chr6:30986237, elapsed 0.3s, est remaining 0.6s, peak mem 139MB, user 0.2s, sys 1.1s, output queue size 7769
progress 40% @chr6:43636381, elapsed 0.4s, est remaining 0.6s, peak mem 148MB, user 0.2s, sys 1.2s, output queue size 10312
progress 45% @chr6:106541586, elapsed 0.5s, est remaining 0.6s, peak mem 159MB, user 0.3s, sys 1.4s, output queue size 12779
progress 50% @chr6:149450683, elapsed 0.6s, est remaining 0.6s, peak mem 165MB, user 0.3s, sys 1.5s, output queue size 14872
progress 55% @chr7:13903840, elapsed 0.7s, est remaining 0.5s, peak mem 169MB, user 0.4s, sys 1.6s, output queue size 17130
progress 60% @chr7:64219314, elapsed 0.7s, est remaining 0.5s, peak mem 180MB, user 0.4s, sys 1.7s, output queue size 19202
progress 65% @chr7:100951841, elapsed 0.8s, est remaining 0.4s, peak mem 189MB, user 0.4s, sys 1.9s, output queue size 21714
progress 70% @chr7:139345501, elapsed 0.8s, est remaining 0.3s, peak mem 198MB, user 0.5s, sys 2.0s, output queue size 24084
progress 75% @chr8:13499049, elapsed 0.8s, est remaining 0.3s, peak mem 207MB, user 0.5s, sys 2.1s, output queue size 26152
progress 80% @chr8:38827168, elapsed 0.9s, est remaining 0.2s, peak mem 213MB, user 0.5s, sys 2.3s, output queue size 27769
progress 85% @chrX:15549840, elapsed 0.9s, est remaining 0.2s, peak mem 222MB, user 0.5s, sys 2.5s, output queue size 30282
progress 90% @chrX:55006518, elapsed 1.0s, est remaining 0.1s, peak mem 232MB, user 0.6s, sys 2.6s, output queue size 32647
progress 95% @chrX:111721603, elapsed 1.0s, est remaining 0.1s, peak mem 241MB, user 0.6s, sys 2.8s, output queue size 34576
progress 100% @chrX:156009816, elapsed 1.0s, est remaining 0.0s, peak mem 250MB, user 0.7s, sys 2.9s, output queue size 36794
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692765
output file size: 22308
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 0.000 sys 0.015 real
advance: 47638 calls 0.012 user 0.009 sys 0.023 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.000 user 0.004 sys 0.015 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 0.000 user 0.007 sys 1.883 real
fetch: 93348 calls 0.002 user 0.010 sys 0.015 real
fetch_ref: 93349 calls 0.064 user 0.038 sys 0.341 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.020 user 0.083 sys 22.900 real
init: 1 calls 0.049 user 0.011 sys 0.057 real
region: 93348 calls 0.003 user 0.004 sys 0.017 real
tracker: 93348 calls 0.055 user 0.010 sys 0.084 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 264556544 mem 1.193 user 4.410 sys 3.036 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory