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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/b940e1f67f5c630b9fb2b630dddb12/.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/d1/7fb75bb19bef014eecf269a038384b/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/7fb75bb19bef014eecf269a038384b/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/b940e1f67f5c630b9fb2b630dddb12/.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 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 467
progress 10% @chr19:50632286, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 1064
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 75MB, user 0.0s, sys 0.0s, output queue size 74
progress 20% @chr19:54813842, elapsed 0.0s, est remaining 0.1s, peak mem 76MB, user 0.0s, sys 0.1s, output queue size 463
progress 25% @chr19:56207059, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.0s, sys 0.1s, output queue size 904
progress 30% @chr19:58212161, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.0s, sys 0.1s, output queue size 1146
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 103MB, user 0.5s, sys 0.2s, output queue size 83
progress 40% @chr21:35048842, elapsed 0.3s, est remaining 0.4s, peak mem 157MB, user 1.5s, sys 0.2s, output queue size 113
progress 45% @chr21:42395324, elapsed 0.8s, est remaining 1.0s, peak mem 261MB, user 6.8s, sys 0.3s, output queue size 113
progress 50% @chr21:45510064, elapsed 1.0s, est remaining 1.0s, peak mem 265MB, user 8.4s, sys 0.3s, output queue size 116
progress 55% @chr22:19434736, elapsed 1.1s, est remaining 0.9s, peak mem 265MB, user 9.1s, sys 0.3s, output queue size 173
progress 60% @chr22:22214908, elapsed 1.1s, est remaining 0.8s, peak mem 265MB, user 9.1s, sys 0.3s, output queue size 653
progress 65% @chr22:23884623, elapsed 1.1s, est remaining 0.6s, peak mem 265MB, user 9.1s, sys 0.3s, output queue size 871
progress 70% @chr22:29288004, elapsed 1.1s, est remaining 0.5s, peak mem 265MB, user 9.1s, sys 0.3s, output queue size 1379
progress 75% @chr22:31873255, elapsed 1.1s, est remaining 0.4s, peak mem 265MB, user 9.1s, sys 0.4s, output queue size 1926
progress 80% @chr22:37959346, elapsed 1.2s, est remaining 0.3s, peak mem 265MB, user 9.1s, sys 0.4s, output queue size 2485
progress 85% @chr22:41237176, elapsed 1.2s, est remaining 0.2s, peak mem 265MB, user 9.1s, sys 0.4s, output queue size 3000
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 265MB, user 9.2s, sys 0.4s, output queue size 3613
progress 95% @chr22:50730721, elapsed 1.2s, est remaining 0.1s, peak mem 265MB, user 9.2s, sys 0.5s, output queue size 4182
progress 100% @chrY:2425197, elapsed 1.2s, est remaining 0.0s, peak mem 265MB, user 9.2s, sys 0.5s, output queue size 4763
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: 71692770
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.462 user 0.021 sys 0.679 real
"assemble_addRead": 315 calls 0.032 user 0.000 sys 0.031 real
"assemble_buildGraph": 650 calls 0.208 user 0.009 sys 0.335 real
"assemble_computecigar": 513 calls 0.300 user 0.013 sys 0.368 real
"assemble_kg_build_calcsize": 650 calls 0.126 user 0.000 sys 0.183 real
"assemble_kg_build_clear": 775 calls 0.000 user 0.000 sys 0.014 real
"assemble_kg_build_prepare": 1300 calls 0.128 user 0.009 sys 0.152 real
"assemble_kg_build_threading": 525 calls 0.083 user 0.005 sys 0.148 real
"assemble_kg_op1": 525 calls 0.027 user 0.006 sys 0.032 real
"assemble_kg_op2": 525 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.009 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.022 user 0.000 sys 0.040 real
"assemble_sg_create": 513 calls 0.038 user 0.001 sys 0.052 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.321 user 0.013 sys 0.386 real
active: 19646 calls 0.000 user 0.000 sys 0.013 real
advance: 10022 calls 2.185 user 0.066 sys 3.051 real
annotate: 358 calls 0.022 user 0.000 sys 0.025 real
assemble_region: 315 calls 0.819 user 0.035 sys 1.100 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.177 user 0.000 sys 0.296 real
calc_region: 312 calls 3.848 user 0.011 sys 4.237 real
call_region: 312 calls 0.042 user 0.000 sys 0.049 real
clip_region: 627 calls 0.079 user 0.015 sys 0.062 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.000 sys 1.263 real
fetch: 19646 calls 0.176 user 0.017 sys 0.131 real
fetch_db: 312 calls 0.011 user 0.000 sys 0.081 real
fetch_ref: 19961 calls 0.007 user 0.021 sys 0.075 real
fetch_region: 315 calls 0.010 user 0.000 sys 0.014 real
idle: 43 calls 0.005 user 0.000 sys 13.176 real
init: 1 calls 0.039 user 0.010 sys 0.041 real
pairhmm: 1803 calls 6.545 user 0.003 sys 6.944 real
realign: 598 calls 0.467 user 0.000 sys 0.518 real
region: 19646 calls 6.230 user 0.079 sys 6.196 real
tracker: 19646 calls 0.011 user 0.001 sys 0.024 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 278630400 mem 12.691 user 0.910 sys 2.375 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory