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/15/7a5d00c319358fb4829cb35c8177cb/.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/25/42f5334e31345bae82309fbb4f085c/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/42f5334e31345bae82309fbb4f085c/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/15/7a5d00c319358fb4829cb35c8177cb/.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% @chr4:86784465, elapsed 0.1s, est remaining 1.0s, peak mem 78MB, user 0.1s, sys 0.1s, output queue size 1444
progress 10% @chr4:152337759, elapsed 0.1s, est remaining 0.9s, peak mem 85MB, user 0.1s, sys 0.3s, output queue size 3840
progress 15% @chr5:36168313, elapsed 0.2s, est remaining 0.9s, peak mem 93MB, user 0.1s, sys 0.4s, output queue size 6311
progress 20% @chr5:91373684, elapsed 0.2s, est remaining 0.8s, peak mem 106MB, user 0.1s, sys 0.6s, output queue size 8891
progress 25% @chr5:141192553, elapsed 0.3s, est remaining 0.8s, peak mem 117MB, user 0.1s, sys 0.7s, output queue size 11295
progress 30% @chr5:177306422, elapsed 0.3s, est remaining 0.7s, peak mem 126MB, user 0.2s, sys 0.8s, output queue size 13416
progress 35% @chr6:30986237, elapsed 0.4s, est remaining 0.7s, peak mem 136MB, user 0.2s, sys 1.0s, output queue size 15607
progress 40% @chr6:43636381, elapsed 0.4s, est remaining 0.6s, peak mem 145MB, user 0.2s, sys 1.1s, output queue size 18149
progress 45% @chr6:106519131, elapsed 0.5s, est remaining 0.6s, peak mem 154MB, user 0.3s, sys 1.3s, output queue size 1414
progress 50% @chr6:149572507, elapsed 0.5s, est remaining 0.5s, peak mem 166MB, user 0.3s, sys 1.4s, output queue size 3530
progress 55% @chr7:13903840, elapsed 0.6s, est remaining 0.5s, peak mem 174MB, user 0.3s, sys 1.5s, output queue size 5770
progress 60% @chr7:64265896, elapsed 0.6s, est remaining 0.4s, peak mem 181MB, user 0.3s, sys 1.7s, output queue size 7842
progress 65% @chr7:100951841, elapsed 0.6s, est remaining 0.3s, peak mem 193MB, user 0.4s, sys 1.8s, output queue size 10362
progress 70% @chr7:139376062, elapsed 0.7s, est remaining 0.3s, peak mem 202MB, user 0.4s, sys 2.0s, output queue size 12728
progress 75% @chr8:13099347, elapsed 0.7s, est remaining 0.2s, peak mem 213MB, user 0.4s, sys 2.1s, output queue size 14784
progress 80% @chr8:38819522, elapsed 0.8s, est remaining 0.2s, peak mem 216MB, user 0.5s, sys 2.2s, output queue size 16405
progress 85% @chrX:15815677, elapsed 0.8s, est remaining 0.1s, peak mem 228MB, user 0.5s, sys 2.4s, output queue size 18963
progress 90% @chrX:54959827, elapsed 0.9s, est remaining 0.1s, peak mem 237MB, user 0.5s, sys 2.5s, output queue size 21277
progress 95% @chrX:111713225, elapsed 0.9s, est remaining 0.0s, peak mem 246MB, user 0.5s, sys 2.6s, output queue size 23211
progress 100% @chrX:156007523, elapsed 0.9s, est remaining 0.0s, peak mem 255MB, user 0.5s, sys 2.8s, output queue size 25433
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 71343278
output file size: 22309
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 0.002 sys 0.020 real
advance: 47638 calls 0.021 user 0.000 sys 0.028 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.006 user 0.003 sys 0.019 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.000 sys 1.915 real
fetch: 93348 calls 0.000 user 0.002 sys 0.020 real
fetch_ref: 93349 calls 0.082 user 0.056 sys 0.380 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.002 user 0.002 sys 24.097 real
init: 1 calls 0.037 user 0.012 sys 0.043 real
region: 93348 calls 0.002 user 0.001 sys 0.022 real
tracker: 93348 calls 0.013 user 0.013 sys 0.096 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 267616256 mem 1.228 user 5.188 sys 3.046 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory