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/63/dd8e25047a90dfffbce806f52a64db/.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/63/dd8e25047a90dfffbce806f52a64db/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/55e68b26048fb02e6d377a2b8f5bd1/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr8_93795409-93795507.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/55e68b26048fb02e6d377a2b8f5bd1/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 chr8_93795409-93795507.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr8:144254813, elapsed 0.0s, est remaining 0.8s, peak mem 82MB, user 0.0s, sys 0.2s, output queue size 1806
progress 10% @chr9:36833270, elapsed 0.1s, est remaining 0.7s, peak mem 93MB, user 0.0s, sys 0.2s, output queue size 4022
progress 15% @chr9:96645893, elapsed 0.1s, est remaining 0.6s, peak mem 102MB, user 0.0s, sys 0.3s, output queue size 5805
progress 20% @chr9:128940369, elapsed 0.1s, est remaining 0.6s, peak mem 111MB, user 0.1s, sys 0.5s, output queue size 8423
progress 25% @chr10:14908408, elapsed 0.2s, est remaining 0.6s, peak mem 121MB, user 0.1s, sys 0.7s, output queue size 11175
progress 30% @chr10:69186443, elapsed 0.2s, est remaining 0.5s, peak mem 135MB, user 0.1s, sys 0.8s, output queue size 1086
progress 35% @chr10:100502254, elapsed 0.3s, est remaining 0.5s, peak mem 141MB, user 0.2s, sys 1.0s, output queue size 3743
progress 40% @chr11:298501, elapsed 0.3s, est remaining 0.5s, peak mem 156MB, user 0.2s, sys 1.2s, output queue size 6325
progress 45% @chr11:17788085, elapsed 0.3s, est remaining 0.4s, peak mem 165MB, user 0.2s, sys 1.3s, output queue size 8479
progress 50% @chr11:61416105, elapsed 0.4s, est remaining 0.4s, peak mem 174MB, user 0.3s, sys 1.5s, output queue size 10844
progress 55% @chr11:73234160, elapsed 0.4s, est remaining 0.3s, peak mem 187MB, user 0.3s, sys 1.6s, output queue size 13520
progress 60% @chr11:114440656, elapsed 0.5s, est remaining 0.3s, peak mem 195MB, user 0.3s, sys 1.8s, output queue size 15804
progress 65% @chr12:6495099, elapsed 0.5s, est remaining 0.3s, peak mem 204MB, user 0.4s, sys 2.0s, output queue size 18176
progress 70% @chr12:31590706, elapsed 0.5s, est remaining 0.2s, peak mem 214MB, user 0.4s, sys 2.2s, output queue size 20260
progress 75% @chr12:55966831, elapsed 0.6s, est remaining 0.2s, peak mem 226MB, user 0.4s, sys 2.4s, output queue size 22732
progress 80% @chr12:100047943, elapsed 0.6s, est remaining 0.2s, peak mem 238MB, user 0.5s, sys 2.5s, output queue size 25464
progress 85% @chr12:123781080, elapsed 0.7s, est remaining 0.1s, peak mem 249MB, user 0.5s, sys 2.8s, output queue size 28320
progress 90% @chr13:48456200, elapsed 0.7s, est remaining 0.1s, peak mem 259MB, user 0.5s, sys 3.0s, output queue size 30686
progress 95% @chr14:22610859, elapsed 0.7s, est remaining 0.0s, peak mem 268MB, user 0.6s, sys 3.1s, output queue size 32948
progress 100% @chr14:64089574, elapsed 0.8s, est remaining 0.0s, peak mem 280MB, user 0.6s, sys 3.3s, output queue size 35496
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 22310
reads: 1001133
contig: 48642 intervals 9000010 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": 1 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": 3 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": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op1": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op2": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op3": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_clean": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_create": 1 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: 98785 calls 0.000 user 0.012 sys 0.018 real
advance: 50143 calls 0.014 user 0.005 sys 0.021 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 98785 calls 0.000 user 0.025 sys 0.018 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 0.006 user 0.001 sys 1.380 real
fetch: 98785 calls 0.000 user 0.000 sys 0.019 real
fetch_ref: 98786 calls 0.101 user 0.031 sys 0.352 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.003 user 0.001 sys 19.780 real
init: 1 calls 0.049 user 0.001 sys 0.042 real
region: 98785 calls 0.000 user 0.012 sys 0.022 real
tracker: 98785 calls 0.024 user 0.003 sys 0.087 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 295956480 mem 1.211 user 4.920 sys 2.499 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory