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/bb/be0070733c332481adf0f5a51026b1/.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/bb/be0070733c332481adf0f5a51026b1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8eee459d74eba64dfe5bc8368d5cb4/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8eee459d74eba64dfe5bc8368d5cb4/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% @chr19:49136724, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 426
progress 10% @chr19:50625393, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1023
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1392
progress 20% @chr19:54818315, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1778
progress 25% @chr19:56224663, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 2215
progress 30% @chr19:58260851, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 910
progress 35% @chr21:30425394, elapsed 0.1s, est remaining 0.2s, peak mem 102MB, user 0.6s, sys 0.3s, output queue size 118
progress 40% @chr21:36723045, elapsed 0.3s, est remaining 0.5s, peak mem 141MB, user 1.6s, sys 0.3s, output queue size 107
progress 45% @chr21:41492213, elapsed 1.2s, est remaining 1.5s, peak mem 276MB, user 10.0s, sys 0.4s, output queue size 106
progress 50% @chr21:45505838, elapsed 1.5s, est remaining 1.5s, peak mem 282MB, user 12.8s, sys 0.5s, output queue size 8
progress 55% @chr22:19405786, elapsed 1.5s, est remaining 1.3s, peak mem 282MB, user 13.3s, sys 0.5s, output queue size 41
progress 60% @chr22:22195903, elapsed 1.5s, est remaining 1.0s, peak mem 282MB, user 13.3s, sys 0.6s, output queue size 521
progress 65% @chr22:23877721, elapsed 1.5s, est remaining 0.8s, peak mem 282MB, user 13.3s, sys 0.6s, output queue size 738
progress 70% @chr22:29286684, elapsed 1.6s, est remaining 0.7s, peak mem 282MB, user 13.3s, sys 0.6s, output queue size 1251
progress 75% @chr22:31836972, elapsed 1.6s, est remaining 0.5s, peak mem 282MB, user 13.3s, sys 0.7s, output queue size 1788
progress 80% @chr22:37947281, elapsed 1.6s, est remaining 0.4s, peak mem 282MB, user 13.3s, sys 0.8s, output queue size 2352
progress 85% @chr22:41256191, elapsed 1.6s, est remaining 0.3s, peak mem 282MB, user 13.3s, sys 0.8s, output queue size 2872
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 282MB, user 13.3s, sys 0.9s, output queue size 3482
progress 95% @chr22:50730721, elapsed 1.6s, est remaining 0.1s, peak mem 282MB, user 13.3s, sys 0.9s, output queue size 4056
progress 100% @chr6_GL000254v2_alt:3891538, elapsed 1.6s, est remaining 0.0s, peak mem 282MB, user 13.3s, sys 1.0s, output queue size 4634
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: 74586809
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.671 user 0.045 sys 0.836 real
"assemble_addRead": 324 calls 0.034 user 0.000 sys 0.052 real
"assemble_buildGraph": 688 calls 0.328 user 0.009 sys 0.416 real
"assemble_computecigar": 523 calls 0.312 user 0.040 sys 0.390 real
"assemble_kg_build_calcsize": 688 calls 0.195 user 0.000 sys 0.233 real
"assemble_kg_build_clear": 826 calls 0.028 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 1376 calls 0.174 user 0.041 sys 0.203 real
"assemble_kg_build_threading": 550 calls 0.131 user 0.001 sys 0.177 real
"assemble_kg_op1": 550 calls 0.034 user 0.001 sys 0.036 real
"assemble_kg_op2": 550 calls 0.010 user 0.000 sys 0.009 real
"assemble_kg_op3": 550 calls 0.000 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.025 user 0.001 sys 0.041 real
"assemble_sg_create": 523 calls 0.051 user 0.001 sys 0.055 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.334 user 0.042 sys 0.411 real
active: 19646 calls 0.000 user 0.001 sys 0.015 real
advance: 10022 calls 2.345 user 0.126 sys 3.112 real
annotate: 394 calls 0.034 user 0.000 sys 0.034 real
assemble_region: 324 calls 1.039 user 0.087 sys 1.302 real
build_variants: 322 calls 0.010 user 0.000 sys 0.003 real
calc: 19646 calls 0.233 user 0.000 sys 0.315 real
calc_region: 322 calls 6.215 user 0.080 sys 6.679 real
call_region: 322 calls 0.075 user 0.000 sys 0.065 real
clip_region: 646 calls 0.071 user 0.013 sys 0.088 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.002 sys 1.725 real
fetch: 19646 calls 0.243 user 0.026 sys 0.173 real
fetch_db: 322 calls 0.005 user 0.000 sys 0.085 real
fetch_ref: 19970 calls 0.022 user 0.022 sys 0.086 real
fetch_region: 324 calls 0.000 user 0.000 sys 0.017 real
idle: 39 calls 0.008 user 0.001 sys 13.452 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
pairhmm: 2270 calls 9.969 user 0.036 sys 10.929 real
realign: 697 calls 0.661 user 0.000 sys 0.724 real
region: 19646 calls 9.951 user 0.158 sys 10.263 real
tracker: 19646 calls 0.025 user 0.000 sys 0.026 real
trim_region: 324 calls 0.001 user 0.001 sys 0.005 real
overall: 295833600 mem 17.019 user 1.556 sys 2.839 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory