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/fe/835c05f39fc51aee60985d2b091ac9/.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-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/df31cbdca311f9a894932ecec74001/HCC1395_BL.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/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  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/fe/835c05f39fc51aee60985d2b091ac9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/df31cbdca311f9a894932ecec74001/HCC1395_BL.dv_only_sites.vcf.gz.tbi
==> 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 HCC1395_BL.recalibrated.bam --algo Haplotyper --given HCC1395_BL.dv_only_sites.vcf.gz --emit_mode variant HCC1395_BL.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 48MB, user 0.0s, sys 0.0s, output queue size 29
progress 10% @chr2:214807967, elapsed 0.0s, est remaining 0.1s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 170
progress 15% @chr3:142533832, elapsed 0.0s, est remaining 0.1s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 380
progress 20% @chr5:132556020, elapsed 0.0s, est remaining 0.1s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 266
progress 25% @chr7:6006303, elapsed 0.0s, est remaining 0.1s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 398
progress 30% @chr7:55204953, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 430
progress 35% @chr9:21973481, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 573
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 717
progress 45% @chr11:64803513, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 836
progress 50% @chr12:11776559, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 1018
progress 55% @chr12:11796959, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 1030
progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 1048
progress 65% @chr12:132668356, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 1117
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 1287
progress 75% @chr15:89316396, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.0s, output queue size 1454
progress 80% @chr17:7682559, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.1s, output queue size 1682
progress 85% @chr17:39532155, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.1s, output queue size 1856
progress 90% @chr17:61685832, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.1s, output queue size 1958
progress 95% @chr19:52170836, elapsed 0.0s, est remaining 0.0s, peak mem 48MB, user 0.0s, sys 0.1s, output queue size 2143
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 99MB, 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: 163002590
output file size: 22292
reads: 1955548
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.002 real
advance: 3049 calls 0.110 user 0.041 sys 0.197 real
calc: 5761 calls 0.043 user 0.003 sys 0.030 real
clip_region: 8 calls 0.000 user 0.000 sys 0.002 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.001 sys 0.135 real
fetch: 5761 calls 0.003 user 0.010 sys 0.014 real
fetch_ref: 5769 calls 0.005 user 0.001 sys 0.023 real
fetch_region: 8 calls 0.006 user 0.004 sys 0.002 real
idle: 25 calls 0.016 user 0.009 sys 12.780 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.007 user 0.004 sys 0.006 real
tracker: 5761 calls 0.000 user 0.000 sys 0.007 real
overall: 103944192 mem 0.314 user 0.342 sys 1.187 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory