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/cf/baf084e91054735d91fcbdb1dbb35f/.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-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/cf/baf084e91054735d91fcbdb1dbb35f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/Sig_18_Blood.recalibrated.bam
  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 Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86807560, elapsed 0.1s, est remaining 1.0s, peak mem 76MB, user 0.0s, sys 0.1s, output queue size 225
progress 10% @chr4:152330694, elapsed 0.1s, est remaining 1.1s, peak mem 91MB, user 0.0s, sys 0.3s, output queue size 2614
progress 15% @chr5:36171603, elapsed 0.2s, est remaining 1.0s, peak mem 99MB, user 0.1s, sys 0.4s, output queue size 5086
progress 20% @chr5:91376621, elapsed 0.2s, est remaining 0.9s, peak mem 111MB, user 0.1s, sys 0.5s, output queue size 7670
progress 25% @chr5:141192553, elapsed 0.3s, est remaining 0.9s, peak mem 120MB, user 0.1s, sys 0.7s, output queue size 10069
progress 30% @chr5:177304625, elapsed 0.3s, est remaining 0.8s, peak mem 129MB, user 0.1s, sys 0.8s, output queue size 12193
progress 35% @chr6:30948547, elapsed 0.4s, est remaining 0.7s, peak mem 138MB, user 0.2s, sys 0.9s, output queue size 14376
progress 40% @chr6:43640021, elapsed 0.4s, est remaining 0.7s, peak mem 145MB, user 0.2s, sys 1.0s, output queue size 16923
progress 45% @chr6:106640349, elapsed 0.5s, est remaining 0.6s, peak mem 159MB, user 0.3s, sys 1.1s, output queue size 19415
progress 50% @chr6:149450683, elapsed 0.6s, est remaining 0.6s, peak mem 166MB, user 0.3s, sys 1.2s, output queue size 1956
progress 55% @chr7:13903840, elapsed 0.6s, est remaining 0.5s, peak mem 175MB, user 0.3s, sys 1.3s, output queue size 4215
progress 60% @chr7:64348090, elapsed 0.7s, est remaining 0.4s, peak mem 181MB, user 0.4s, sys 1.4s, output queue size 6287
progress 65% @chr7:100951841, elapsed 0.7s, est remaining 0.4s, peak mem 192MB, user 0.4s, sys 1.6s, output queue size 8797
progress 70% @chr7:139345501, elapsed 0.8s, est remaining 0.3s, peak mem 201MB, user 0.5s, sys 1.7s, output queue size 11167
progress 75% @chr8:13115586, elapsed 0.8s, est remaining 0.3s, peak mem 211MB, user 0.5s, sys 1.8s, output queue size 13229
progress 80% @chr8:38831125, elapsed 0.8s, est remaining 0.2s, peak mem 214MB, user 0.6s, sys 1.9s, output queue size 14852
progress 85% @chrX:15531328, elapsed 0.9s, est remaining 0.2s, peak mem 226MB, user 0.6s, sys 2.0s, output queue size 17361
progress 90% @chrX:55000423, elapsed 0.9s, est remaining 0.1s, peak mem 238MB, user 0.6s, sys 2.1s, output queue size 19725
progress 95% @chrX:111718112, elapsed 0.9s, est remaining 0.0s, peak mem 247MB, user 0.7s, sys 2.2s, output queue size 21658
progress 100% @chrX:153872152, elapsed 1.0s, est remaining 0.0s, peak mem 256MB, user 0.7s, sys 2.4s, output queue size 23877
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: 74586807
output file size: 22311
reads: 1001133
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.001 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 0.002 user 0.000 sys 0.017 real
advance: 47638 calls 0.017 user 0.008 sys 0.025 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.003 user 0.000 sys 0.017 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 0.005 user 0.004 sys 1.710 real
fetch: 93348 calls 0.000 user 0.000 sys 0.017 real
fetch_ref: 93349 calls 0.047 user 0.010 sys 0.365 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.002 user 0.014 sys 21.155 real
init: 1 calls 0.034 user 0.005 sys 0.042 real
region: 93348 calls 0.007 user 0.005 sys 0.021 real
tracker: 93348 calls 0.014 user 0.000 sys 0.086 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 269209600 mem 1.074 user 3.494 sys 2.829 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory