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/fb/7a62d020ae46f064d420fcc722bc77/.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/ad/ded0dc28f0bedef0afd0b3c848896c/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/ded0dc28f0bedef0afd0b3c848896c/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/7a62d020ae46f064d420fcc722bc77/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr19_47340800-47341813.bed.gz
  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 chr19_47340800-47341813.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49139668, elapsed 0.0s, est remaining 0.3s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 426
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.3s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 1024
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 1389
progress 20% @chr19:54803891, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.1s, sys 0.1s, output queue size 1776
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 69MB, user 0.1s, sys 0.1s, output queue size 416
progress 30% @chr19:58212161, elapsed 0.1s, est remaining 0.2s, peak mem 69MB, user 0.1s, sys 0.2s, output queue size 662
progress 35% @chr21:28966370, elapsed 0.1s, est remaining 0.2s, peak mem 84MB, user 0.7s, sys 0.2s, output queue size 180
progress 40% @chr21:36245048, elapsed 0.3s, est remaining 0.4s, peak mem 138MB, user 1.6s, sys 0.2s, output queue size 111
progress 45% @chr21:42383033, elapsed 0.9s, est remaining 1.1s, peak mem 252MB, user 7.1s, sys 0.3s, output queue size 112
progress 50% @chr21:44573759, elapsed 1.1s, est remaining 1.1s, peak mem 255MB, user 9.0s, sys 0.3s, output queue size 120
progress 55% @chr22:19408483, elapsed 1.1s, est remaining 0.9s, peak mem 255MB, user 9.7s, sys 0.4s, output queue size 317
progress 60% @chr22:22162280, elapsed 1.1s, est remaining 0.8s, peak mem 255MB, user 9.7s, sys 0.4s, output queue size 801
progress 65% @chr22:23308561, elapsed 1.1s, est remaining 0.6s, peak mem 255MB, user 9.7s, sys 0.4s, output queue size 1016
progress 70% @chr22:29294124, elapsed 1.2s, est remaining 0.5s, peak mem 255MB, user 9.8s, sys 0.5s, output queue size 586
progress 75% @chr22:31833915, elapsed 1.2s, est remaining 0.4s, peak mem 255MB, user 9.8s, sys 0.5s, output queue size 1127
progress 80% @chr22:37970687, elapsed 1.2s, est remaining 0.3s, peak mem 255MB, user 9.8s, sys 0.5s, output queue size 1698
progress 85% @chr22:41257948, elapsed 1.2s, est remaining 0.2s, peak mem 255MB, user 9.8s, sys 0.6s, output queue size 2215
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 255MB, user 9.8s, sys 0.6s, output queue size 2825
progress 95% @chr22:50720184, elapsed 1.2s, est remaining 0.1s, peak mem 255MB, user 9.8s, sys 0.6s, output queue size 3402
progress 100% @chrY:7087267, elapsed 1.2s, est remaining 0.0s, peak mem 255MB, user 9.8s, sys 0.7s, output queue size 3974
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: 71692760
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.505 user 0.008 sys 0.686 real
"assemble_addRead": 315 calls 0.000 user 0.000 sys 0.037 real
"assemble_buildGraph": 650 calls 0.270 user 0.003 sys 0.333 real
"assemble_computecigar": 513 calls 0.325 user 0.015 sys 0.370 real
"assemble_kg_build_calcsize": 650 calls 0.162 user 0.000 sys 0.181 real
"assemble_kg_build_clear": 775 calls 0.010 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 1300 calls 0.142 user 0.005 sys 0.159 real
"assemble_kg_build_threading": 525 calls 0.108 user 0.003 sys 0.148 real
"assemble_kg_op1": 525 calls 0.009 user 0.000 sys 0.032 real
"assemble_kg_op2": 525 calls 0.002 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.007 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.004 user 0.000 sys 0.040 real
"assemble_sg_create": 513 calls 0.041 user 0.000 sys 0.052 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.351 user 0.015 sys 0.388 real
active: 19646 calls 0.017 user 0.000 sys 0.013 real
advance: 10022 calls 2.353 user 0.074 sys 2.980 real
annotate: 358 calls 0.020 user 0.000 sys 0.027 real
assemble_region: 315 calls 0.865 user 0.023 sys 1.114 real
build_variants: 312 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.188 user 0.000 sys 0.295 real
calc_region: 312 calls 3.842 user 0.023 sys 4.180 real
call_region: 312 calls 0.041 user 0.000 sys 0.052 real
clip_region: 627 calls 0.040 user 0.000 sys 0.063 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.003 sys 1.327 real
fetch: 19646 calls 0.195 user 0.013 sys 0.132 real
fetch_db: 312 calls 0.012 user 0.000 sys 0.081 real
fetch_ref: 19961 calls 0.022 user 0.026 sys 0.086 real
fetch_region: 315 calls 0.023 user 0.000 sys 0.013 real
idle: 39 calls 0.002 user 0.012 sys 13.537 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
pairhmm: 1803 calls 6.282 user 0.021 sys 6.878 real
realign: 598 calls 0.317 user 0.011 sys 0.517 real
region: 19646 calls 6.458 user 0.064 sys 6.501 real
tracker: 19646 calls 0.003 user 0.001 sys 0.023 real
trim_region: 315 calls 0.005 user 0.000 sys 0.004 real
overall: 267522048 mem 12.513 user 1.366 sys 2.446 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory