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/97/5ef4b52db21b5ef0db2b036565a242/.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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr1_69091-70008.bed.gz
  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/GATKBundle/dbsnp_146.hg38.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/5ef4b52db21b5ef0db2b036565a242/.command.run
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr1_69091-70008.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:18376800, elapsed 0.1s, est remaining 1.0s, peak mem 82MB, user 0.1s, sys 0.1s, output queue size 2255
progress 10% @chr1:37794183, elapsed 0.1s, est remaining 1.1s, peak mem 91MB, user 0.1s, sys 0.2s, output queue size 2325
progress 15% @chr1:65405870, elapsed 0.2s, est remaining 1.0s, peak mem 105MB, user 0.2s, sys 0.3s, output queue size 5052
progress 20% @chr1:113837590, elapsed 0.3s, est remaining 1.0s, peak mem 115MB, user 0.2s, sys 0.5s, output queue size 7810
progress 25% @chr1:155266729, elapsed 0.3s, est remaining 0.9s, peak mem 126MB, user 0.2s, sys 0.6s, output queue size 10179
progress 30% @chr1:179102287, elapsed 0.4s, est remaining 0.9s, peak mem 129MB, user 0.2s, sys 0.7s, output queue size 12633
progress 35% @chr1:209801240, elapsed 0.4s, est remaining 0.8s, peak mem 142MB, user 0.2s, sys 0.9s, output queue size 15058
progress 40% @chr1:247037449, elapsed 0.5s, est remaining 0.7s, peak mem 151MB, user 0.3s, sys 1.0s, output queue size 17466
progress 45% @chr2:32607455, elapsed 0.6s, est remaining 0.7s, peak mem 160MB, user 0.3s, sys 1.1s, output queue size 19756
progress 50% @chr2:74461275, elapsed 0.6s, est remaining 0.6s, peak mem 168MB, user 0.3s, sys 1.2s, output queue size 22241
progress 55% @chr2:112659204, elapsed 0.7s, est remaining 0.6s, peak mem 181MB, user 0.4s, sys 1.3s, output queue size 2032
progress 60% @chr2:170993780, elapsed 0.7s, est remaining 0.5s, peak mem 187MB, user 0.4s, sys 1.5s, output queue size 4728
progress 65% @chr2:202765446, elapsed 0.8s, est remaining 0.4s, peak mem 198MB, user 0.4s, sys 1.6s, output queue size 6999
progress 70% @chr2:233772261, elapsed 0.9s, est remaining 0.4s, peak mem 211MB, user 0.5s, sys 1.7s, output queue size 9479
progress 75% @chr3:25623515, elapsed 0.9s, est remaining 0.3s, peak mem 219MB, user 0.5s, sys 1.8s, output queue size 11702
progress 80% @chr3:49804181, elapsed 1.0s, est remaining 0.2s, peak mem 226MB, user 0.6s, sys 2.0s, output queue size 14179
progress 85% @chr3:101859272, elapsed 1.0s, est remaining 0.2s, peak mem 235MB, user 0.6s, sys 2.2s, output queue size 16815
progress 90% @chr3:140404558, elapsed 1.1s, est remaining 0.1s, peak mem 249MB, user 0.6s, sys 2.4s, output queue size 19414
progress 95% @chr3:187741772, elapsed 1.1s, est remaining 0.1s, peak mem 255MB, user 0.6s, sys 2.6s, output queue size 21818
progress 100% @chr4:9980592, elapsed 1.2s, est remaining 0.0s, peak mem 268MB, user 0.7s, sys 2.7s, output queue size 24053
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: 22306
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.001 sys 0.019 real
advance: 51084 calls 0.005 user 0.001 sys 0.025 real
calc: 100735 calls 0.000 user 0.010 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.004 sys 2.136 real
fetch: 100735 calls 0.009 user 0.001 sys 0.019 real
fetch_ref: 100735 calls 0.032 user 0.037 sys 0.360 real
idle: 39 calls 0.004 user 0.011 sys 24.104 real
init: 1 calls 0.029 user 0.011 sys 0.041 real
region: 100735 calls 0.000 user 0.002 sys 0.021 real
tracker: 100735 calls 0.014 user 0.002 sys 0.093 real
overall: 281821184 mem 1.097 user 4.292 sys 3.257 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory