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/c5/ead6f921060e086639c9b63df13a9c/.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/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/ead6f921060e086639c9b63df13a9c/.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% @chr8:144255509, elapsed 0.0s, est remaining 0.8s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 379
progress 10% @chr9:36833270, elapsed 0.1s, est remaining 0.7s, peak mem 81MB, user 0.0s, sys 0.2s, output queue size 2595
progress 15% @chr9:96758778, elapsed 0.1s, est remaining 0.6s, peak mem 87MB, user 0.1s, sys 0.3s, output queue size 4376
progress 20% @chr9:128941445, elapsed 0.2s, est remaining 0.6s, peak mem 96MB, user 0.1s, sys 0.4s, output queue size 6994
progress 25% @chr10:14908408, elapsed 0.2s, est remaining 0.6s, peak mem 111MB, user 0.1s, sys 0.6s, output queue size 9748
progress 30% @chr10:69202439, elapsed 0.2s, est remaining 0.6s, peak mem 117MB, user 0.2s, sys 0.6s, output queue size 12138
progress 35% @chr10:100505361, elapsed 0.3s, est remaining 0.5s, peak mem 129MB, user 0.2s, sys 0.8s, output queue size 14790
progress 40% @chr11:314171, elapsed 0.3s, est remaining 0.5s, peak mem 141MB, user 0.3s, sys 0.9s, output queue size 17371
progress 45% @chr11:17771665, elapsed 0.4s, est remaining 0.5s, peak mem 150MB, user 0.3s, sys 1.0s, output queue size 19527
progress 50% @chr11:61419922, elapsed 0.4s, est remaining 0.4s, peak mem 156MB, user 0.3s, sys 1.2s, output queue size 21892
progress 55% @chr11:73296485, elapsed 0.5s, est remaining 0.4s, peak mem 171MB, user 0.3s, sys 1.4s, output queue size 24565
progress 60% @chr11:114444541, elapsed 0.5s, est remaining 0.3s, peak mem 183MB, user 0.4s, sys 1.5s, output queue size 26852
progress 65% @chr12:6462034, elapsed 0.5s, est remaining 0.3s, peak mem 186MB, user 0.4s, sys 1.6s, output queue size 29211
progress 70% @chr12:31697740, elapsed 0.6s, est remaining 0.3s, peak mem 192MB, user 0.4s, sys 1.7s, output queue size 31307
progress 75% @chr12:55971044, elapsed 0.6s, est remaining 0.2s, peak mem 210MB, user 0.4s, sys 1.8s, output queue size 33782
progress 80% @chr12:100047943, elapsed 0.7s, est remaining 0.2s, peak mem 216MB, user 0.4s, sys 2.0s, output queue size 36509
progress 85% @chr12:123781080, elapsed 0.7s, est remaining 0.1s, peak mem 231MB, user 0.5s, sys 2.2s, output queue size 39368
progress 90% @chr13:48429756, elapsed 0.8s, est remaining 0.1s, peak mem 240MB, user 0.5s, sys 2.4s, output queue size 1460
progress 95% @chr14:22633768, elapsed 0.9s, est remaining 0.0s, peak mem 252MB, user 0.6s, sys 2.5s, output queue size 3712
progress 100% @chr14:60468445, elapsed 0.9s, est remaining 0.0s, peak mem 258MB, user 0.6s, sys 2.7s, output queue size 6268
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 71692767
output file size: 22308
reads: 1001089
contig: 48642 intervals 9000010 bases
active: 98785 calls 0.000 user 0.003 sys 0.018 real
advance: 50143 calls 0.000 user 0.007 sys 0.021 real
calc: 98785 calls 0.006 user 0.005 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.001 sys 1.857 real
fetch: 98785 calls 0.000 user 0.000 sys 0.018 real
fetch_ref: 98785 calls 0.056 user 0.026 sys 0.354 real
idle: 39 calls 0.006 user 0.010 sys 23.949 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
region: 98785 calls 0.000 user 0.000 sys 0.022 real
tracker: 98785 calls 0.030 user 0.010 sys 0.089 real
overall: 270667776 mem 1.223 user 4.882 sys 2.973 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory