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/a6/fbb2bcc6f6046cd5ab60ab096900c9/germline_control_1.dv_only_sites.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/690dbae98fb373cfe512e4a077a6c1/.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/e8/c0a67c1d98a52e016e1ee4b829f9ba/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/c0a67c1d98a52e016e1ee4b829f9ba/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/44/690dbae98fb373cfe512e4a077a6c1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/fbb2bcc6f6046cd5ab60ab096900c9/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 50MB, user 0.0s, sys 0.0s, output queue size 48
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 50MB, user 0.0s, sys 0.0s, output queue size 176
progress 15% @chr3:142540904, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 221
progress 20% @chr5:112821885, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 402
progress 25% @chr7:6002447, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 536
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 575
progress 35% @chr9:21974436, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 712
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 859
progress 45% @chr11:61437994, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 976
progress 50% @chr12:11699469, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 1158
progress 55% @chr12:11809199, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 1172
progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.1s, output queue size 1189
progress 65% @chr12:132657862, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.1s, output queue size 1248
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 1427
progress 75% @chr15:90720120, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 1587
progress 80% @chr17:7683999, elapsed 0.0s, est remaining 0.0s, peak mem 58MB, user 0.0s, sys 0.1s, output queue size 1818
progress 85% @chr17:39532155, elapsed 0.1s, est remaining 0.0s, peak mem 58MB, user 0.0s, sys 0.1s, output queue size 1995
progress 90% @chr17:61681285, elapsed 0.1s, est remaining 0.0s, peak mem 59MB, user 0.0s, sys 0.1s, output queue size 2098
progress 95% @chr19:50416610, elapsed 0.1s, est remaining 0.0s, peak mem 60MB, user 0.0s, sys 0.1s, output queue size 2281
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 90MB, user 0.2s, sys 0.2s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef 40417f5e
  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: 71692772
output file size: 22311
reads: 1001089
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.003 real
advance: 3049 calls 0.099 user 0.022 sys 0.122 real
calc: 5761 calls 0.022 user 0.000 sys 0.030 real
clip_region: 7 calls 0.001 user 0.000 sys 0.002 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.003 sys 0.130 real
fetch: 5761 calls 0.000 user 0.000 sys 0.007 real
fetch_ref: 5768 calls 0.004 user 0.002 sys 0.025 real
fetch_region: 7 calls 0.012 user 0.000 sys 0.001 real
idle: 25 calls 0.009 user 0.016 sys 12.672 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.013 user 0.000 sys 0.005 real
tracker: 5761 calls 0.000 user 0.000 sys 0.009 real
overall: 94744576 mem 0.253 user 0.535 sys 1.198 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory