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/3a/e58b16783ba41648642277a32b5739/.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-rnd-pltf-dev-nextflow-scratch-01/work/3a/e58b16783ba41648642277a32b5739/.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% @chr8:144248877, elapsed 0.0s, est remaining 0.8s, peak mem 85MB, user 0.0s, sys 0.1s, output queue size 2236
progress 10% @chr9:36903627, elapsed 0.1s, est remaining 0.7s, peak mem 91MB, user 0.0s, sys 0.3s, output queue size 4451
progress 15% @chr9:96758778, elapsed 0.1s, est remaining 0.6s, peak mem 100MB, user 0.1s, sys 0.5s, output queue size 396
progress 20% @chr9:128941445, elapsed 0.2s, est remaining 0.6s, peak mem 106MB, user 0.1s, sys 0.7s, output queue size 3017
progress 25% @chr10:14928016, elapsed 0.2s, est remaining 0.6s, peak mem 120MB, user 0.1s, sys 0.8s, output queue size 5776
progress 30% @chr10:69208600, elapsed 0.2s, est remaining 0.6s, peak mem 129MB, user 0.1s, sys 1.0s, output queue size 8162
progress 35% @chr10:100507425, elapsed 0.3s, est remaining 0.5s, peak mem 138MB, user 0.1s, sys 1.2s, output queue size 10813
progress 40% @chr11:299305, elapsed 0.3s, est remaining 0.5s, peak mem 148MB, user 0.2s, sys 1.3s, output queue size 13392
progress 45% @chr11:17995796, elapsed 0.4s, est remaining 0.5s, peak mem 154MB, user 0.2s, sys 1.5s, output queue size 15553
progress 50% @chr11:61444108, elapsed 0.4s, est remaining 0.4s, peak mem 166MB, user 0.2s, sys 1.6s, output queue size 17929
progress 55% @chr11:73234160, elapsed 0.5s, est remaining 0.4s, peak mem 172MB, user 0.3s, sys 1.7s, output queue size 20589
progress 60% @chr11:114449846, elapsed 0.5s, est remaining 0.4s, peak mem 184MB, user 0.3s, sys 1.9s, output queue size 22878
progress 65% @chr12:6465842, elapsed 0.6s, est remaining 0.3s, peak mem 192MB, user 0.3s, sys 2.0s, output queue size 25241
progress 70% @chr12:31697361, elapsed 0.6s, est remaining 0.3s, peak mem 198MB, user 0.4s, sys 2.2s, output queue size 27328
progress 75% @chr12:55971044, elapsed 0.7s, est remaining 0.2s, peak mem 207MB, user 0.4s, sys 2.3s, output queue size 29804
progress 80% @chr12:100051079, elapsed 0.8s, est remaining 0.2s, peak mem 217MB, user 0.4s, sys 2.5s, output queue size 32533
progress 85% @chr12:122996721, elapsed 1.0s, est remaining 0.2s, peak mem 222MB, user 0.5s, sys 2.7s, output queue size 35392
progress 90% @chr13:48459668, elapsed 1.1s, est remaining 0.1s, peak mem 231MB, user 0.5s, sys 2.8s, output queue size 37758
progress 95% @chr14:22633768, elapsed 1.1s, est remaining 0.1s, peak mem 241MB, user 0.5s, sys 2.9s, output queue size 40013
progress 100% @chr14:52007810, elapsed 1.2s, est remaining 0.0s, peak mem 253MB, user 0.6s, sys 3.0s, output queue size 42566
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: 22309
reads: 1001089
contig: 48642 intervals 9000010 bases
active: 98785 calls 0.002 user 0.001 sys 0.019 real
advance: 50143 calls 0.000 user 0.006 sys 0.023 real
calc: 98785 calls 0.000 user 0.007 sys 0.019 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.000 user 0.003 sys 2.255 real
fetch: 98785 calls 0.004 user 0.000 sys 0.020 real
fetch_ref: 98785 calls 0.040 user 0.018 sys 0.376 real
idle: 51 calls 0.022 user 0.032 sys 25.621 real
init: 1 calls 0.047 user 0.000 sys 0.041 real
region: 98785 calls 0.000 user 0.004 sys 0.022 real
tracker: 98785 calls 0.023 user 0.006 sys 0.095 real
overall: 269225984 mem 1.224 user 4.865 sys 3.379 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory