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/fe/91f754e863bf68cf22f64454ef6bcb/.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/a7/3c4be24150a8745172b27c7cc104ed/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/3c4be24150a8745172b27c7cc104ed/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/fe/91f754e863bf68cf22f64454ef6bcb/.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 82MB, user 0.1s, sys 0.1s, output queue size 1800
progress 10% @chr4:152352429, elapsed 0.1s, est remaining 0.9s, peak mem 91MB, user 0.1s, sys 0.3s, output queue size 4198
progress 15% @chr5:36166519, elapsed 0.1s, est remaining 0.8s, peak mem 99MB, user 0.1s, sys 0.4s, output queue size 6665
progress 20% @chr5:91374114, elapsed 0.2s, est remaining 0.8s, peak mem 109MB, user 0.2s, sys 0.6s, output queue size 9245
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.7s, peak mem 117MB, user 0.2s, sys 0.7s, output queue size 1101
progress 30% @chr5:177293824, elapsed 0.3s, est remaining 0.7s, peak mem 124MB, user 0.2s, sys 0.8s, output queue size 3218
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.6s, peak mem 138MB, user 0.2s, sys 0.9s, output queue size 5409
progress 40% @chr6:43645099, elapsed 0.4s, est remaining 0.6s, peak mem 145MB, user 0.3s, sys 1.1s, output queue size 7958
progress 45% @chr6:106527305, elapsed 0.4s, est remaining 0.5s, peak mem 153MB, user 0.3s, sys 1.2s, output queue size 10421
progress 50% @chr6:149450683, elapsed 0.5s, est remaining 0.5s, peak mem 162MB, user 0.3s, sys 1.3s, output queue size 12516
progress 55% @chr7:13911239, elapsed 0.5s, est remaining 0.4s, peak mem 169MB, user 0.3s, sys 1.5s, output queue size 14777
progress 60% @chr7:64219314, elapsed 0.6s, est remaining 0.4s, peak mem 177MB, user 0.4s, sys 1.6s, output queue size 16846
progress 65% @chr7:100951841, elapsed 0.6s, est remaining 0.3s, peak mem 187MB, user 0.4s, sys 1.8s, output queue size 19359
progress 70% @chr7:139341385, elapsed 0.7s, est remaining 0.3s, peak mem 193MB, user 0.4s, sys 1.9s, output queue size 21728
progress 75% @chr8:13110742, elapsed 0.7s, est remaining 0.2s, peak mem 204MB, user 0.5s, sys 2.0s, output queue size 23788
progress 80% @chr8:38977953, elapsed 0.8s, est remaining 0.2s, peak mem 213MB, user 0.5s, sys 2.2s, output queue size 25435
progress 85% @chrX:15566253, elapsed 0.8s, est remaining 0.1s, peak mem 216MB, user 0.5s, sys 2.3s, output queue size 27928
progress 90% @chrX:55001546, elapsed 0.9s, est remaining 0.1s, peak mem 226MB, user 0.6s, sys 2.4s, output queue size 30287
progress 95% @chrX:111736714, elapsed 1.0s, est remaining 0.1s, peak mem 231MB, user 0.6s, sys 2.5s, output queue size 32230
progress 100% @chrX:154984687, elapsed 1.0s, est remaining 0.0s, peak mem 240MB, user 0.6s, sys 2.7s, output queue size 34438
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: 71637313
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 0.000 sys 0.018 real
advance: 47638 calls 0.004 user 0.001 sys 0.028 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.000 user 0.002 sys 0.018 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 0.008 user 0.002 sys 1.970 real
fetch: 93348 calls 0.000 user 0.000 sys 0.019 real
fetch_ref: 93349 calls 0.020 user 0.030 sys 0.374 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.003 user 0.007 sys 24.081 real
init: 1 calls 0.040 user 0.000 sys 0.044 real
region: 93348 calls 0.000 user 0.001 sys 0.021 real
tracker: 93348 calls 0.004 user 0.000 sys 0.094 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 253464576 mem 1.270 user 4.407 sys 3.104 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory