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/78/26d0b09982f58438f78936207e1443/germline_control_1.dv_only_sites.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/e049c5b9376bc5fe2f899a85cd4521/.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/e7/493cf948b1d450f8051fba2ea0097a/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/493cf948b1d450f8051fba2ea0097a/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/3c/e049c5b9376bc5fe2f899a85cd4521/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/26d0b09982f58438f78936207e1443/germline_control_1.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 germline_control_1.dv_only_sites.vcf.gz --emit_mode variant germline_control_1.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 0
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 101
progress 15% @chr3:142522728, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 219
progress 20% @chr5:112837544, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 407
progress 25% @chr7:6002447, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 532
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 572
progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 709
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 856
progress 45% @chr11:64803513, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 971
progress 50% @chr12:11752419, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1151
progress 55% @chr12:11809199, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1165
progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1180
progress 65% @chr12:132659281, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1245
progress 70% @chr14:67946271, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 288
progress 75% @chr15:89312894, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 439
progress 80% @chr17:7679679, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 669
progress 85% @chr17:39532155, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 851
progress 90% @chr17:61685832, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 953
progress 95% @chr19:52201094, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 1136
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 87MB, user 0.1s, 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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692765
output file size: 22309
reads: 1001089
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.002 real
advance: 3049 calls 0.031 user 0.045 sys 0.093 real
calc: 5761 calls 0.002 user 0.002 sys 0.017 real
clip_region: 7 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 0.005 user 0.002 sys 0.093 real
fetch: 5761 calls 0.010 user 0.001 sys 0.007 real
fetch_ref: 5768 calls 0.000 user 0.001 sys 0.023 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 24 calls 0.006 user 0.010 sys 12.398 real
init: 1 calls 0.000 user 0.000 sys 0.001 real
region: 5761 calls 0.000 user 0.000 sys 0.004 real
tracker: 5761 calls 0.000 user 0.000 sys 0.006 real
overall: 91504640 mem 0.184 user 0.335 sys 1.146 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory