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/93/6e4307e8b010b247f428b3887dc49a/.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/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam
  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/93/6e4307e8b010b247f428b3887dc49a/.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% @chr4:86775442, elapsed 0.0s, est remaining 0.7s, peak mem 82MB, user 0.0s, sys 0.0s, output queue size 706
progress 10% @chr4:152329639, elapsed 0.1s, est remaining 0.7s, peak mem 91MB, user 0.1s, sys 0.2s, output queue size 3098
progress 15% @chr5:36176965, elapsed 0.1s, est remaining 0.6s, peak mem 100MB, user 0.1s, sys 0.4s, output queue size 5574
progress 20% @chr5:91373684, elapsed 0.2s, est remaining 0.6s, peak mem 117MB, user 0.1s, sys 0.6s, output queue size 8152
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.6s, peak mem 127MB, user 0.1s, sys 0.7s, output queue size 10560
progress 30% @chr5:177304625, elapsed 0.2s, est remaining 0.5s, peak mem 135MB, user 0.2s, sys 0.8s, output queue size 12678
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.5s, peak mem 142MB, user 0.2s, sys 1.0s, output queue size 14865
progress 40% @chr6:43636381, elapsed 0.3s, est remaining 0.4s, peak mem 154MB, user 0.2s, sys 1.1s, output queue size 17410
progress 45% @chr6:106519131, elapsed 0.3s, est remaining 0.4s, peak mem 166MB, user 0.2s, sys 1.3s, output queue size 19873
progress 50% @chr6:149400392, elapsed 0.4s, est remaining 0.4s, peak mem 175MB, user 0.2s, sys 1.4s, output queue size 21975
progress 55% @chr7:13911239, elapsed 0.4s, est remaining 0.3s, peak mem 181MB, user 0.3s, sys 1.5s, output queue size 24230
progress 60% @chr7:64219314, elapsed 0.4s, est remaining 0.3s, peak mem 187MB, user 0.3s, sys 1.7s, output queue size 26300
progress 65% @chr7:100951841, elapsed 0.5s, est remaining 0.3s, peak mem 204MB, user 0.4s, sys 1.9s, output queue size 28818
progress 70% @chr7:139376062, elapsed 0.5s, est remaining 0.2s, peak mem 213MB, user 0.4s, sys 2.0s, output queue size 31185
progress 75% @chr8:13099347, elapsed 0.5s, est remaining 0.2s, peak mem 223MB, user 0.4s, sys 2.1s, output queue size 33246
progress 80% @chr8:38827168, elapsed 0.6s, est remaining 0.1s, peak mem 229MB, user 0.5s, sys 2.2s, output queue size 34865
progress 85% @chrX:15537134, elapsed 0.6s, est remaining 0.1s, peak mem 238MB, user 0.5s, sys 2.4s, output queue size 37376
progress 90% @chrX:54951905, elapsed 0.6s, est remaining 0.1s, peak mem 253MB, user 0.6s, sys 2.5s, output queue size 39737
progress 95% @chrX:111720095, elapsed 0.7s, est remaining 0.0s, peak mem 258MB, user 0.6s, sys 2.6s, output queue size 41672
progress 100% @chrX:154478283, elapsed 0.7s, est remaining 0.0s, peak mem 268MB, user 0.6s, sys 2.7s, output queue size 43891
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692767
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 0.014 sys 0.015 real
advance: 47638 calls 0.012 user 0.003 sys 0.030 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.002 user 0.000 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 0.006 user 0.004 sys 1.311 real
fetch: 93348 calls 0.000 user 0.000 sys 0.016 real
fetch_ref: 93349 calls 0.064 user 0.076 sys 0.355 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.002 user 0.002 sys 19.643 real
init: 1 calls 0.020 user 0.020 sys 0.041 real
region: 93348 calls 0.000 user 0.001 sys 0.018 real
tracker: 93348 calls 0.026 user 0.005 sys 0.082 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 284954624 mem 1.243 user 4.607 sys 2.425 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory