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/e5/1525dda5badbdff12a80cb04c26268/.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/e6/1c36638b2f3ef9e6b9417b252dfc07/germline_control_2.dv_only_sites.vcf.gz
  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/e6/1c36638b2f3ef9e6b9417b252dfc07/germline_control_2.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/1525dda5badbdff12a80cb04c26268/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/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 germline_control_2.dv_only_sites.vcf.gz --emit_mode variant germline_control_2.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 45MB, user 0.0s, sys 0.0s, output queue size 18
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 147
progress 15% @chr4:54229921, elapsed 0.0s, est remaining 0.1s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 390
progress 20% @chr5:112821885, elapsed 0.0s, est remaining 0.1s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 549
progress 25% @chr7:6002447, elapsed 0.0s, est remaining 0.1s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 684
progress 30% @chr7:55204953, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 723
progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 860
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 1007
progress 45% @chr11:64804862, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 1125
progress 51% @chr12:11760959, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 1308
progress 55% @chr12:11799959, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 1320
progress 60% @chr12:11860606, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 1339
progress 65% @chr12:132660824, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.0s, output queue size 1399
progress 70% @chr14:65084870, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.1s, output queue size 40
progress 75% @chr15:90803508, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.1s, output queue size 227
progress 80% @chr17:17212802, elapsed 0.0s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.1s, output queue size 437
progress 85% @chr17:43049007, elapsed 0.1s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.1s, output queue size 617
progress 90% @chr17:61785237, elapsed 0.1s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.1s, output queue size 729
progress 95% @chr19:52170836, elapsed 0.1s, est remaining 0.0s, peak mem 45MB, user 0.0s, sys 0.1s, output queue size 891
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 69MB, 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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586807
output file size: 22314
reads: 1001133
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.003 real
advance: 3049 calls 0.061 user 0.031 sys 0.115 real
calc: 5761 calls 0.009 user 0.000 sys 0.020 real
clip_region: 7 calls 0.000 user 0.002 sys 0.002 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.001 sys 0.114 real
fetch: 5761 calls 0.008 user 0.002 sys 0.010 real
fetch_ref: 5768 calls 0.001 user 0.001 sys 0.027 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 25 calls 0.007 user 0.008 sys 12.503 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.000 user 0.002 sys 0.005 real
tracker: 5761 calls 0.000 user 0.001 sys 0.008 real
overall: 72486912 mem 0.254 user 0.487 sys 1.174 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory