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/ed/0fa67476182ac6d097abff85a5e965/germline_control_1.dv_only_sites.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/a4f4fab6897c3bfc78449702b1c3c5/.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/a7/3c4be24150a8745172b27c7cc104ed/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/3c4be24150a8745172b27c7cc104ed/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/f6/a4f4fab6897c3bfc78449702b1c3c5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/0fa67476182ac6d097abff85a5e965/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% @chr2:29694850, elapsed 0.0s, est remaining 0.2s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 3
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 133
progress 15% @chr3:142533832, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 354
progress 20% @chr5:112818952, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 536
progress 25% @chr7:5999106, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 668
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 714
progress 35% @chr9:21973481, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 847
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 995
progress 45% @chr11:61444108, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1111
progress 50% @chr12:11776559, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1293
progress 55% @chr12:11792759, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1305
progress 60% @chr12:11831519, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1322
progress 65% @chr12:132660824, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1382
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1560
progress 75% @chr15:89306007, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1715
progress 80% @chr17:7678839, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1950
progress 85% @chr17:39530604, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 131
progress 90% @chr17:61679140, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 232
progress 95% @chr19:52170836, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 416
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 82MB, user 0.1s, sys 0.2s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71637313
output file size: 22311
reads: 1001089
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.002 real
advance: 3049 calls 0.052 user 0.040 sys 0.101 real
calc: 5761 calls 0.002 user 0.000 sys 0.018 real
clip_region: 7 calls 0.000 user 0.000 sys 0.002 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.002 sys 0.097 real
fetch: 5761 calls 0.005 user 0.007 sys 0.009 real
fetch_ref: 5768 calls 0.001 user 0.000 sys 0.025 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 24 calls 0.003 user 0.004 sys 12.428 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.000 user 0.000 sys 0.004 real
tracker: 5761 calls 0.000 user 0.000 sys 0.007 real
overall: 86732800 mem 0.182 user 0.466 sys 1.147 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory