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/2c/9d3e8fae49aab0eb93b6eaa11c4189/.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-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/2c/9d3e8fae49aab0eb93b6eaa11c4189/.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% @chr4:86785231, elapsed 0.1s, est remaining 1.0s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 1192
progress 10% @chr4:152337759, elapsed 0.1s, est remaining 0.9s, peak mem 87MB, user 0.1s, sys 0.4s, output queue size 3584
progress 15% @chr5:36168313, elapsed 0.2s, est remaining 0.9s, peak mem 93MB, user 0.1s, sys 0.6s, output queue size 6057
progress 20% @chr5:94520243, elapsed 0.2s, est remaining 0.8s, peak mem 96MB, user 0.1s, sys 0.8s, output queue size 8674
progress 25% @chr5:141192553, elapsed 0.3s, est remaining 0.8s, peak mem 105MB, user 0.1s, sys 1.1s, output queue size 11039
progress 30% @chr5:177303986, elapsed 0.3s, est remaining 0.7s, peak mem 111MB, user 0.2s, sys 1.3s, output queue size 13164
progress 35% @chr6:31025502, elapsed 0.4s, est remaining 0.7s, peak mem 114MB, user 0.2s, sys 1.5s, output queue size 15357
progress 40% @chr6:43629750, elapsed 0.4s, est remaining 0.6s, peak mem 132MB, user 0.2s, sys 1.8s, output queue size 17895
progress 45% @chr6:106665782, elapsed 0.5s, est remaining 0.6s, peak mem 138MB, user 0.2s, sys 2.0s, output queue size 20394
progress 50% @chr6:149461831, elapsed 0.5s, est remaining 0.5s, peak mem 147MB, user 0.3s, sys 2.2s, output queue size 22457
progress 55% @chr7:13911239, elapsed 0.6s, est remaining 0.5s, peak mem 159MB, user 0.3s, sys 2.5s, output queue size 24714
progress 60% @chr7:64077276, elapsed 0.6s, est remaining 0.4s, peak mem 162MB, user 0.4s, sys 2.7s, output queue size 26788
progress 65% @chr7:100951841, elapsed 0.7s, est remaining 0.4s, peak mem 171MB, user 0.4s, sys 3.0s, output queue size 555
progress 70% @chr7:139374414, elapsed 0.7s, est remaining 0.3s, peak mem 177MB, user 0.4s, sys 3.2s, output queue size 2921
progress 75% @chr8:13099347, elapsed 0.8s, est remaining 0.3s, peak mem 195MB, user 0.5s, sys 3.4s, output queue size 4976
progress 80% @chr8:38819522, elapsed 0.8s, est remaining 0.2s, peak mem 201MB, user 0.5s, sys 3.6s, output queue size 6602
progress 85% @chrX:15522346, elapsed 0.9s, est remaining 0.2s, peak mem 210MB, user 0.5s, sys 4.0s, output queue size 9107
progress 90% @chrX:55000423, elapsed 1.0s, est remaining 0.1s, peak mem 213MB, user 0.5s, sys 4.2s, output queue size 11477
progress 95% @chrX:111722793, elapsed 1.0s, est remaining 0.1s, peak mem 213MB, user 0.5s, sys 4.4s, output queue size 13409
progress 100% @chrX:154466150, elapsed 1.1s, est remaining 0.0s, peak mem 213MB, user 0.6s, sys 4.7s, output queue size 15628
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692770
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 0.005 user 0.000 sys 0.017 real
advance: 47638 calls 0.018 user 0.002 sys 0.023 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.012 user 0.003 sys 0.016 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 0.003 user 0.002 sys 3.048 real
fetch: 93348 calls 0.000 user 0.000 sys 0.017 real
fetch_ref: 93349 calls 0.087 user 0.137 sys 0.411 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 51 calls 0.009 user 0.006 sys 36.236 real
init: 1 calls 0.030 user 0.020 sys 0.042 real
region: 93348 calls 0.001 user 0.004 sys 0.019 real
tracker: 93348 calls 0.015 user 0.022 sys 0.083 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 223502336 mem 1.015 user 7.375 sys 4.178 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory