Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/cbb196f619742c13c4edc71e488607/HCC1395_tumor_vs_HCC1395_BL.tnseq.orientation_data.tsv
  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/8c/cbb196f619742c13c4edc71e488607/HCC1395_tumor_vs_HCC1395_BL.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/fb262875a3360e87179755a222def4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/cbb196f619742c13c4edc71e488607/HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz.tbi
  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/8c/cbb196f619742c13c4edc71e488607/HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/cbb196f619742c13c4edc71e488607/HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/fb262875a3360e87179755a222def4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/cbb196f619742c13c4edc71e488607/HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz.stats
==> STAGING COMPLETE (10 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --max_event_count 5 -v HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz --contamination HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv --tumor_segments HCC1395_tumor_vs_HCC1395_BL.tnseq.segments --orientation_priors HCC1395_tumor_vs_HCC1395_BL.tnseq.orientation_data.tsv HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:129000001, elapsed 0.1s, est remaining 2.2s, peak mem 813MB, user 0.2s, sys 4.3s, output queue size 147
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.8s, peak mem 813MB, user 0.5s, sys 13.5s, output queue size 308
progress 15% @chr3:149000001, elapsed 0.3s, est remaining 1.6s, peak mem 813MB, user 0.8s, sys 24.2s, output queue size 470
progress 20% @chr5:59000001, elapsed 0.3s, est remaining 1.4s, peak mem 813MB, user 1.2s, sys 33.0s, output queue size 631
progress 25% @chr6:1, elapsed 0.4s, est remaining 1.3s, peak mem 813MB, user 1.4s, sys 42.4s, output queue size 793
progress 30% @chr6:139000001, elapsed 0.5s, est remaining 1.2s, peak mem 813MB, user 1.7s, sys 53.1s, output queue size 945
progress 35% @chr8:36000001, elapsed 0.6s, est remaining 1.1s, peak mem 813MB, user 1.9s, sys 64.5s, output queue size 1106
progress 40% @chr8:114000001, elapsed 0.7s, est remaining 1.0s, peak mem 813MB, user 2.1s, sys 75.7s, output queue size 1268
progress 45% @chr9:83000001, elapsed 0.8s, est remaining 1.0s, peak mem 813MB, user 2.3s, sys 86.7s, output queue size 1429
progress 50% @chr10:116000001, elapsed 0.9s, est remaining 0.9s, peak mem 813MB, user 2.6s, sys 97.4s, output queue size 1591
progress 55% @chr12:50000001, elapsed 0.9s, est remaining 0.8s, peak mem 813MB, user 2.8s, sys 107.5s, output queue size 1752
progress 60% @chr13:36000001, elapsed 1.0s, est remaining 0.7s, peak mem 813MB, user 2.9s, sys 118.0s, output queue size 1915
progress 65% @chr15:27000001, elapsed 1.1s, est remaining 0.6s, peak mem 813MB, user 3.2s, sys 126.3s, output queue size 2076
progress 70% @chr16:68000001, elapsed 1.2s, est remaining 0.5s, peak mem 813MB, user 3.6s, sys 137.5s, output queue size 2238
progress 75% @chr18:42000001, elapsed 1.2s, est remaining 0.4s, peak mem 813MB, user 3.9s, sys 151.6s, output queue size 2400
progress 80% @chr20:26000001, elapsed 1.3s, est remaining 0.3s, peak mem 813MB, user 4.2s, sys 165.5s, output queue size 2562
progress 85% @chrX:40000001, elapsed 1.4s, est remaining 0.2s, peak mem 813MB, user 4.5s, sys 179.2s, output queue size 2662
progress 90% @chrX:125000001, elapsed 1.5s, est remaining 0.2s, peak mem 813MB, user 4.9s, sys 191.2s, output queue size 2995
progress 95% @chr14:56000001, elapsed 1.5s, est remaining 0.1s, peak mem 813MB, user 5.2s, sys 200.4s, output queue size 3500
progress 100% @HLA-DRB1*14:05:01:1, elapsed 1.9s, est remaining 0.0s, peak mem 813MB, user 5.8s, sys 223.5s, output queue size 6405
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 384 max 384
algo: TNfilter
license: sentieon:TNhaplotyper=384
input file size: 71258
output file size: 60122
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 741 calls 0.006 user 0.000 sys 0.021 real
"predict_filter": 247 calls 0.025 user 0.013 sys 0.102 real
advance: 3219322 calls 0.509 user 94.128 sys 125.197 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.005 sys 2.085 real
fetch_ref: 648 calls 0.002 user 0.024 sys 0.468 real
idle: 20633 calls 0.693 user 0.278 sys 1008.309 real
init: 1 calls 0.400 user 0.119 sys 1.503 real
overall: 852627456 mem 7.691 user 229.506 sys 4.820 real