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/1b/aec1df52b4d83222278dce4ca20d05/.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/1b/aec1df52b4d83222278dce4ca20d05/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/9b9bdd2e3a62b63766fd1bff60945d/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/9b9bdd2e3a62b63766fd1bff60945d/Sig_18_Blood.recalibrated.bam
  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 Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49139961, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 159
progress 10% @chr19:50632286, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 755
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 1122
progress 20% @chr19:54803891, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 1508
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 1945
progress 30% @chr19:58243965, elapsed 0.1s, est remaining 0.1s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 2187
progress 35% @chr21:30425394, elapsed 0.2s, est remaining 0.3s, peak mem 102MB, user 0.7s, sys 0.2s, output queue size 118
progress 40% @chr21:36412884, elapsed 0.4s, est remaining 0.5s, peak mem 159MB, user 1.6s, sys 0.2s, output queue size 107
progress 45% @chr21:42381982, elapsed 1.2s, est remaining 1.5s, peak mem 270MB, user 9.2s, sys 0.4s, output queue size 113
progress 50% @chr21:45497599, elapsed 1.5s, est remaining 1.5s, peak mem 282MB, user 11.9s, sys 0.4s, output queue size 34
progress 55% @chr22:19444265, elapsed 1.5s, est remaining 1.3s, peak mem 285MB, user 12.5s, sys 0.5s, output queue size 315
progress 60% @chr22:22195903, elapsed 1.6s, est remaining 1.0s, peak mem 285MB, user 12.5s, sys 0.6s, output queue size 795
progress 65% @chr22:23882459, elapsed 1.6s, est remaining 0.8s, peak mem 285MB, user 12.5s, sys 0.6s, output queue size 1011
progress 70% @chr22:29293284, elapsed 1.6s, est remaining 0.7s, peak mem 285MB, user 12.5s, sys 0.6s, output queue size 260
progress 75% @chr22:31836972, elapsed 1.6s, est remaining 0.5s, peak mem 285MB, user 12.5s, sys 0.6s, output queue size 800
progress 80% @chr22:37959346, elapsed 1.6s, est remaining 0.4s, peak mem 285MB, user 12.5s, sys 0.7s, output queue size 1367
progress 85% @chr22:41274600, elapsed 1.6s, est remaining 0.3s, peak mem 285MB, user 12.5s, sys 0.7s, output queue size 1887
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 285MB, user 12.5s, sys 0.7s, output queue size 2500
progress 95% @chr22:50744061, elapsed 1.7s, est remaining 0.1s, peak mem 285MB, user 12.6s, sys 0.9s, output queue size 3072
progress 100% @chrY:24834127, elapsed 1.7s, est remaining 0.0s, peak mem 285MB, user 12.6s, sys 0.9s, output queue size 3646
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: 74586803
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.615 user 0.025 sys 0.828 real
"assemble_addRead": 324 calls 0.022 user 0.000 sys 0.049 real
"assemble_buildGraph": 688 calls 0.300 user 0.011 sys 0.413 real
"assemble_computecigar": 523 calls 0.339 user 0.023 sys 0.392 real
"assemble_kg_build_calcsize": 688 calls 0.164 user 0.000 sys 0.231 real
"assemble_kg_build_clear": 826 calls 0.024 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 1376 calls 0.194 user 0.012 sys 0.198 real
"assemble_kg_build_threading": 550 calls 0.125 user 0.011 sys 0.176 real
"assemble_kg_op1": 550 calls 0.032 user 0.000 sys 0.036 real
"assemble_kg_op2": 550 calls 0.015 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.013 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.000 user 0.000 sys 0.042 real
"assemble_sg_create": 523 calls 0.044 user 0.002 sys 0.055 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.346 user 0.025 sys 0.411 real
active: 19646 calls 0.000 user 0.000 sys 0.015 real
advance: 10022 calls 2.723 user 0.117 sys 3.115 real
annotate: 394 calls 0.012 user 0.000 sys 0.036 real
assemble_region: 324 calls 0.983 user 0.050 sys 1.292 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.231 user 0.011 sys 0.311 real
calc_region: 322 calls 5.797 user 0.050 sys 6.157 real
call_region: 322 calls 0.043 user 0.000 sys 0.067 real
clip_region: 646 calls 0.081 user 0.004 sys 0.083 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.000 sys 1.787 real
fetch: 19646 calls 0.142 user 0.012 sys 0.164 real
fetch_db: 322 calls 0.030 user 0.007 sys 0.086 real
fetch_ref: 19970 calls 0.025 user 0.034 sys 0.086 real
fetch_region: 324 calls 0.007 user 0.000 sys 0.019 real
idle: 39 calls 0.004 user 0.003 sys 13.788 real
init: 1 calls 0.041 user 0.009 sys 0.042 real
pairhmm: 2270 calls 9.633 user 0.055 sys 10.716 real
realign: 697 calls 0.602 user 0.004 sys 0.715 real
region: 19646 calls 9.060 user 0.142 sys 9.262 real
tracker: 19646 calls 0.015 user 0.000 sys 0.025 real
trim_region: 324 calls 0.000 user 0.000 sys 0.005 real
overall: 298979328 mem 16.744 user 1.548 sys 2.906 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory