Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/592944dcc0335bee194e890ffe5cb9/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_Blood/Sig_18_Blood.recal.bam
  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/e1/86847d6e48ff7034f8a5ce42eb2400/Sig_18_Blood.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/germline_rescue_targets.bed
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_Blood/Sig_18_Blood.recal.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/592944dcc0335bee194e890ffe5cb9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/86847d6e48ff7034f8a5ce42eb2400/Sig_18_Blood.dv_only_sites.vcf.gz
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval germline_rescue_targets.bed -i Sig_18_Blood.recal.bam --algo Haplotyper --given Sig_18_Blood.dv_only_sites.vcf.gz --emit_mode variant Sig_18_Blood.forcecall.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:29451636, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 19
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 150
progress 15% @chr3:142535080, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 368
progress 20% @chr5:112821885, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 549
progress 25% @chr7:6000358, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 684
progress 30% @chr7:55204953, elapsed 0.0s, est remaining 0.0s, peak mem 53MB, user 0.0s, sys 0.0s, output queue size 725
progress 35% @chr9:21969676, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.0s, output queue size 859
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.0s, output queue size 1007
progress 45% @chr11:61445932, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.0s, output queue size 1124
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.0s, output queue size 1305
progress 55% @chr12:11796959, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.0s, output queue size 1317
progress 60% @chr12:11831519, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.0s, output queue size 1335
progress 65% @chr12:132660824, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.0s, output queue size 1396
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.0s, output queue size 718
progress 75% @chr15:89314597, elapsed 0.0s, est remaining 0.0s, peak mem 58MB, user 0.0s, sys 0.1s, output queue size 878
progress 80% @chr17:7679679, elapsed 0.0s, est remaining 0.0s, peak mem 58MB, user 0.0s, sys 0.1s, output queue size 1108
progress 85% @chr17:39532155, elapsed 0.0s, est remaining 0.0s, peak mem 60MB, user 0.0s, sys 0.1s, output queue size 1289
progress 90% @chr17:61681285, elapsed 0.0s, est remaining 0.0s, peak mem 60MB, user 0.0s, sys 0.1s, output queue size 1391
progress 95% @chr19:52185532, elapsed 0.0s, est remaining 0.0s, peak mem 62MB, user 0.0s, sys 0.1s, output queue size 1576
progress 100% @chr21:34787802, elapsed 0.2s, est remaining 0.0s, peak mem 138MB, user 0.3s, sys 0.2s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 138653580
output file size: 22295
reads: 1685487
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.004 real
advance: 3049 calls 0.173 user 0.080 sys 0.251 real
calc: 5761 calls 0.032 user 0.000 sys 0.059 real
clip_region: 7 calls 0.005 user 0.000 sys 0.004 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.010 user 0.000 sys 0.191 real
fetch: 5761 calls 0.032 user 0.006 sys 0.022 real
fetch_ref: 5768 calls 0.001 user 0.010 sys 0.022 real
fetch_region: 7 calls 0.010 user 0.000 sys 0.004 real
idle: 25 calls 0.017 user 0.016 sys 13.354 real
init: 1 calls 0.000 user 0.000 sys 0.003 real
region: 5761 calls 0.015 user 0.000 sys 0.010 real
tracker: 5761 calls 0.000 user 0.000 sys 0.008 real
overall: 145166336 mem 0.445 user 0.324 sys 1.258 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory