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/8a/ea1df65ed7e4716300b5b31ad8c794/.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/f0/61734391e4f47c8b44be28e79e0683/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/61734391e4f47c8b44be28e79e0683/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/8a/ea1df65ed7e4716300b5b31ad8c794/.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% @chr4:86799101, elapsed 0.1s, est remaining 1.2s, peak mem 72MB, user 0.0s, sys 0.3s, output queue size 2297
progress 10% @chr4:152888133, elapsed 0.1s, est remaining 1.1s, peak mem 72MB, user 0.0s, sys 0.5s, output queue size 2473
progress 15% @chr5:36181818, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.1s, sys 0.7s, output queue size 4912
progress 20% @chr5:91374114, elapsed 0.3s, est remaining 1.0s, peak mem 93MB, user 0.1s, sys 0.9s, output queue size 7488
progress 25% @chr5:141192553, elapsed 0.3s, est remaining 1.0s, peak mem 96MB, user 0.1s, sys 1.0s, output queue size 9889
progress 30% @chr5:177302752, elapsed 0.4s, est remaining 0.9s, peak mem 105MB, user 0.2s, sys 1.1s, output queue size 12009
progress 35% @chr6:30948547, elapsed 0.5s, est remaining 0.8s, peak mem 117MB, user 0.2s, sys 1.3s, output queue size 14199
progress 40% @chr6:43640021, elapsed 0.5s, est remaining 0.8s, peak mem 123MB, user 0.2s, sys 1.5s, output queue size 16745
progress 45% @chr6:106519131, elapsed 0.6s, est remaining 0.7s, peak mem 135MB, user 0.3s, sys 1.6s, output queue size 19208
progress 50% @chr6:149450683, elapsed 0.6s, est remaining 0.6s, peak mem 141MB, user 0.3s, sys 1.8s, output queue size 21307
progress 55% @chr7:13911239, elapsed 0.7s, est remaining 0.6s, peak mem 153MB, user 0.3s, sys 1.9s, output queue size 23564
progress 60% @chr7:64219314, elapsed 0.8s, est remaining 0.5s, peak mem 159MB, user 0.4s, sys 2.0s, output queue size 25635
progress 65% @chr7:100951841, elapsed 0.8s, est remaining 0.4s, peak mem 162MB, user 0.4s, sys 2.3s, output queue size 1616
progress 70% @chr7:139293232, elapsed 0.9s, est remaining 0.4s, peak mem 171MB, user 0.4s, sys 2.6s, output queue size 3982
progress 75% @chr8:13099347, elapsed 0.9s, est remaining 0.3s, peak mem 180MB, user 0.5s, sys 2.8s, output queue size 6040
progress 80% @chr8:41609655, elapsed 1.0s, est remaining 0.2s, peak mem 183MB, user 0.5s, sys 3.0s, output queue size 7829
progress 85% @chrX:15534212, elapsed 1.0s, est remaining 0.2s, peak mem 195MB, user 0.5s, sys 3.3s, output queue size 10179
progress 90% @chrX:54951905, elapsed 1.1s, est remaining 0.1s, peak mem 204MB, user 0.6s, sys 3.5s, output queue size 12536
progress 95% @chrX:111728185, elapsed 1.1s, est remaining 0.1s, peak mem 207MB, user 0.6s, sys 3.8s, output queue size 14478
progress 100% @chrX:156009816, elapsed 1.2s, est remaining 0.0s, peak mem 219MB, user 0.6s, sys 4.0s, output queue size 16691
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: 71692764
output file size: 22308
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 0.010 sys 0.014 real
advance: 47638 calls 0.002 user 0.016 sys 0.021 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.008 user 0.000 sys 0.015 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 0.003 sys 2.287 real
fetch: 93348 calls 0.000 user 0.008 sys 0.015 real
fetch_ref: 93349 calls 0.153 user 0.121 sys 0.367 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 51 calls 0.007 user 0.022 sys 25.604 real
init: 1 calls 0.038 user 0.002 sys 0.042 real
region: 93348 calls 0.001 user 0.010 sys 0.017 real
tracker: 93348 calls 0.033 user 0.010 sys 0.082 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 229818368 mem 1.066 user 5.718 sys 3.407 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory