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/e6/ca40473d501cf2a62b43d0bc6a0283/.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/39/26289db7549e63f8f8b4e32bd08c0f/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-rnd-pltf-dev-nextflow-scratch-01/work/e6/ca40473d501cf2a62b43d0bc6a0283/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/26289db7549e63f8f8b4e32bd08c0f/Sig_18_Blood.dv_only_sites.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
==> 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.recalibrated.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% @chr2:29531915, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 48
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 35
progress 15% @chr3:142536108, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 254
progress 20% @chr5:112827091, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 435
progress 25% @chr7:6000358, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 569
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 608
progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 747
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 893
progress 45% @chr11:61437994, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1009
progress 50% @chr12:11776559, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1192
progress 55% @chr12:11792759, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1205
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progress 65% @chr12:132667502, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1282
progress 70% @chr14:67819780, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1463
progress 75% @chr15:90743438, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1627
progress 80% @chr17:7685679, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1854
progress 85% @chr17:39525864, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 2023
progress 90% @chr17:61679140, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 2135
progress 95% @chr19:50416391, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 2316
progress 100% @chr21:34787802, elapsed 0.2s, est remaining 0.0s, peak mem 123MB, user 0.2s, sys 0.1s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 208827488
output file size: 22302
reads: 2481283
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.002 real
advance: 3049 calls 0.150 user 0.048 sys 0.231 real
calc: 5761 calls 0.009 user 0.001 sys 0.044 real
clip_region: 7 calls 0.005 user 0.000 sys 0.004 real
done: 1 calls 0.001 user 0.001 sys 0.002 real
execute: 1 calls 0.004 user 0.004 sys 0.159 real
fetch: 5761 calls 0.027 user 0.017 sys 0.020 real
fetch_ref: 5768 calls 0.005 user 0.002 sys 0.024 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.003 real
idle: 25 calls 0.022 user 0.011 sys 13.083 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.005 user 0.000 sys 0.008 real
tracker: 5761 calls 0.000 user 0.000 sys 0.006 real
overall: 129110016 mem 0.389 user 0.322 sys 1.210 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory