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/d7/77e00cf04b13fa0bc978658b325b48/germline_control_1.dv_only_sites.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/dfbbfbd15ca0d68430c68d16ade401/.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/25/42f5334e31345bae82309fbb4f085c/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/42f5334e31345bae82309fbb4f085c/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/47/dfbbfbd15ca0d68430c68d16ade401/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/77e00cf04b13fa0bc978658b325b48/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% @chr2:29451636, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 10
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 141
progress 15% @chr3:142522728, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 177
progress 20% @chr5:112827910, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 358
progress 25% @chr7:6002447, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 491
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 532
progress 35% @chr9:21974436, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 669
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 814
progress 45% @chr11:61445932, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 931
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1113
progress 55% @chr12:11792759, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1126
progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1143
progress 65% @chr12:132663994, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1205
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1386
progress 75% @chr15:89305605, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1537
progress 80% @chr17:7682559, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1770
progress 85% @chr17:39532155, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1951
progress 90% @chr17:61679140, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 2052
progress 95% @chr19:52170836, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 2238
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 85MB, 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: 71343278
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 0.039 user 0.022 sys 0.094 real
calc: 5761 calls 0.000 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 0.001 user 0.000 sys 0.096 real
fetch: 5761 calls 0.011 user 0.003 sys 0.008 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: 25 calls 0.009 user 0.026 sys 12.424 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 0.001 user 0.002 sys 0.007 real
overall: 89931776 mem 0.161 user 0.443 sys 1.145 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory