Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/3f4672bf93af7c1ba3868e23cf5bd7/.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/0e/1efc95d887ebdaf1c9892b5421119a/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/1efc95d887ebdaf1c9892b5421119a/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/3f4672bf93af7c1ba3868e23cf5bd7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr8_93795409-93795507.bed.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr8_93795409-93795507.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr8:144260677, elapsed 0.0s, est remaining 0.9s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 772
progress 10% @chr9:36888555, elapsed 0.1s, est remaining 0.8s, peak mem 78MB, user 0.1s, sys 0.3s, output queue size 2979
progress 15% @chr9:96758778, elapsed 0.1s, est remaining 0.7s, peak mem 90MB, user 0.1s, sys 0.5s, output queue size 4761
progress 20% @chr9:128907165, elapsed 0.2s, est remaining 0.7s, peak mem 105MB, user 0.2s, sys 0.8s, output queue size 7379
progress 25% @chr10:14908408, elapsed 0.2s, est remaining 0.7s, peak mem 114MB, user 0.2s, sys 1.0s, output queue size 10133
progress 30% @chr10:69196992, elapsed 0.3s, est remaining 0.6s, peak mem 126MB, user 0.2s, sys 1.3s, output queue size 12519
progress 35% @chr10:100506040, elapsed 0.3s, est remaining 0.6s, peak mem 138MB, user 0.3s, sys 1.5s, output queue size 15175
progress 40% @chr11:309013, elapsed 0.4s, est remaining 0.6s, peak mem 141MB, user 0.3s, sys 1.8s, output queue size 17757
progress 45% @chr11:17788085, elapsed 0.4s, est remaining 0.5s, peak mem 165MB, user 0.3s, sys 2.0s, output queue size 19913
progress 50% @chr11:56417258, elapsed 0.5s, est remaining 0.5s, peak mem 165MB, user 0.4s, sys 2.2s, output queue size 22285
progress 55% @chr11:73000990, elapsed 0.5s, est remaining 0.4s, peak mem 174MB, user 0.5s, sys 2.4s, output queue size 24952
progress 60% @chr11:114521968, elapsed 0.6s, est remaining 0.4s, peak mem 186MB, user 0.5s, sys 2.7s, output queue size 27242
progress 65% @chr12:6457406, elapsed 0.6s, est remaining 0.3s, peak mem 195MB, user 0.5s, sys 3.0s, output queue size 29604
progress 70% @chr12:31590706, elapsed 0.7s, est remaining 0.3s, peak mem 204MB, user 0.5s, sys 3.1s, output queue size 31695
progress 75% @chr12:55968778, elapsed 0.7s, est remaining 0.2s, peak mem 216MB, user 0.6s, sys 3.3s, output queue size 34169
progress 80% @chr12:100057571, elapsed 0.8s, est remaining 0.2s, peak mem 228MB, user 0.6s, sys 3.6s, output queue size 36900
progress 85% @chr12:123757927, elapsed 0.8s, est remaining 0.1s, peak mem 243MB, user 0.6s, sys 3.8s, output queue size 2123
progress 90% @chr13:48495261, elapsed 0.9s, est remaining 0.1s, peak mem 252MB, user 0.7s, sys 4.0s, output queue size 4499
progress 95% @chr14:22770193, elapsed 0.9s, est remaining 0.0s, peak mem 258MB, user 0.7s, sys 4.3s, output queue size 6749
progress 100% @chr14:52864747, elapsed 1.0s, est remaining 0.0s, peak mem 273MB, user 0.8s, sys 4.6s, output queue size 9299
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692776
output file size: 22309
reads: 1001089
contig: 48642 intervals 9000010 bases
active: 98785 calls 0.017 user 0.010 sys 0.015 real
advance: 50143 calls 0.005 user 0.003 sys 0.017 real
calc: 98785 calls 0.002 user 0.001 sys 0.015 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.001 sys 1.870 real
fetch: 98785 calls 0.000 user 0.011 sys 0.015 real
fetch_ref: 98785 calls 0.160 user 0.092 sys 0.385 real
idle: 39 calls 0.002 user 0.009 sys 23.178 real
init: 1 calls 0.040 user 0.000 sys 0.042 real
region: 98785 calls 0.000 user 0.011 sys 0.018 real
tracker: 98785 calls 0.031 user 0.014 sys 0.083 real
overall: 286445568 mem 1.180 user 6.030 sys 2.985 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory