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/df/330191d67418925f91587a105d913c/.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/53/ceed4bf612d62859d876f95d1d2d6f/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/ceed4bf612d62859d876f95d1d2d6f/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/330191d67418925f91587a105d913c/.command.run
  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 HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49138205, elapsed 0.0s, est remaining 0.3s, peak mem 66MB, user 0.0s, sys 0.0s, output queue size 521
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.0s, output queue size 381
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.0s, output queue size 747
progress 20% @chr19:54805951, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.0s, output queue size 1130
progress 25% @chr19:56221575, elapsed 0.0s, est remaining 0.1s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 1570
progress 30% @chr19:58212161, elapsed 0.1s, est remaining 0.1s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 1809
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 84MB, user 0.6s, sys 0.1s, output queue size 83
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 135MB, user 1.5s, sys 0.2s, output queue size 105
progress 45% @chr21:42383033, elapsed 0.9s, est remaining 1.1s, peak mem 243MB, user 7.2s, sys 0.3s, output queue size 113
progress 50% @chr21:45511111, elapsed 1.1s, est remaining 1.1s, peak mem 243MB, user 9.0s, sys 0.3s, output queue size 115
progress 55% @chr22:19407184, elapsed 1.2s, est remaining 1.0s, peak mem 246MB, user 9.8s, sys 0.4s, output queue size 345
progress 60% @chr22:22380959, elapsed 1.2s, est remaining 0.8s, peak mem 246MB, user 9.8s, sys 0.4s, output queue size 845
progress 65% @chr22:24042904, elapsed 1.2s, est remaining 0.6s, peak mem 246MB, user 9.8s, sys 0.4s, output queue size 433
progress 70% @chr22:29288004, elapsed 1.2s, est remaining 0.5s, peak mem 246MB, user 9.8s, sys 0.4s, output queue size 909
progress 75% @chr22:31838685, elapsed 1.2s, est remaining 0.4s, peak mem 246MB, user 9.8s, sys 0.5s, output queue size 1450
progress 80% @chr22:37956773, elapsed 1.2s, est remaining 0.3s, peak mem 246MB, user 9.8s, sys 0.5s, output queue size 2016
progress 85% @chr22:41257948, elapsed 1.2s, est remaining 0.2s, peak mem 246MB, user 9.8s, sys 0.5s, output queue size 2535
progress 90% @chr22:46256561, elapsed 1.3s, est remaining 0.1s, peak mem 246MB, user 9.8s, sys 0.6s, output queue size 3143
progress 95% @chr22:50720184, elapsed 1.3s, est remaining 0.1s, peak mem 246MB, user 9.9s, sys 0.6s, output queue size 3721
progress 100% @chrY:1190897, elapsed 1.3s, est remaining 0.0s, peak mem 246MB, user 9.9s, sys 0.6s, output queue size 4295
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: 71692764
output file size: 77723
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.521 user 0.016 sys 0.719 real
"assemble_addRead": 315 calls 0.025 user 0.000 sys 0.036 real
"assemble_buildGraph": 650 calls 0.190 user 0.004 sys 0.351 real
"assemble_computecigar": 513 calls 0.322 user 0.025 sys 0.390 real
"assemble_kg_build_calcsize": 650 calls 0.104 user 0.000 sys 0.190 real
"assemble_kg_build_clear": 775 calls 0.011 user 0.000 sys 0.016 real
"assemble_kg_build_prepare": 1300 calls 0.115 user 0.011 sys 0.162 real
"assemble_kg_build_threading": 525 calls 0.083 user 0.004 sys 0.157 real
"assemble_kg_op1": 525 calls 0.013 user 0.000 sys 0.034 real
"assemble_kg_op2": 525 calls 0.009 user 0.000 sys 0.009 real
"assemble_kg_op3": 525 calls 0.012 user 0.000 sys 0.012 real
"assemble_sg_clean": 513 calls 0.073 user 0.000 sys 0.043 real
"assemble_sg_create": 513 calls 0.059 user 0.001 sys 0.055 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.334 user 0.025 sys 0.410 real
active: 19646 calls 0.010 user 0.000 sys 0.015 real
advance: 10022 calls 2.396 user 0.093 sys 3.121 real
annotate: 358 calls 0.022 user 0.000 sys 0.029 real
assemble_region: 315 calls 0.879 user 0.041 sys 1.169 real
build_variants: 312 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.225 user 0.006 sys 0.307 real
calc_region: 312 calls 3.875 user 0.027 sys 4.290 real
call_region: 312 calls 0.033 user 0.000 sys 0.055 real
clip_region: 627 calls 0.042 user 0.000 sys 0.069 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.001 sys 1.410 real
fetch: 19646 calls 0.157 user 0.017 sys 0.164 real
fetch_db: 312 calls 0.011 user 0.002 sys 0.084 real
fetch_ref: 19961 calls 0.015 user 0.016 sys 0.082 real
fetch_region: 315 calls 0.004 user 0.000 sys 0.015 real
idle: 39 calls 0.004 user 0.016 sys 14.000 real
init: 1 calls 0.048 user 0.002 sys 0.044 real
pairhmm: 1803 calls 6.444 user 0.027 sys 7.095 real
realign: 598 calls 0.491 user 0.004 sys 0.533 real
region: 19646 calls 6.506 user 0.080 sys 6.637 real
tracker: 19646 calls 0.006 user 0.011 sys 0.025 real
trim_region: 315 calls 0.003 user 0.000 sys 0.004 real
overall: 258084864 mem 12.925 user 1.232 sys 2.523 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory