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/1b/d604a8a223f9ab5dd385f9c1f9d5bf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/f5fb1a39bf82ac689dbac10556d5e1/positive_somatic_control_1.tnseq.vcf.gz.stats
  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/0d/f5fb1a39bf82ac689dbac10556d5e1/positive_somatic_control_1.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/f5fb1a39bf82ac689dbac10556d5e1/positive_somatic_control_1.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/f5fb1a39bf82ac689dbac10556d5e1/positive_somatic_control_1.tnseq.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/f5fb1a39bf82ac689dbac10556d5e1/positive_somatic_control_1.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/f5fb1a39bf82ac689dbac10556d5e1/positive_somatic_control_1.tnseq.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/d604a8a223f9ab5dd385f9c1f9d5bf/.command.run
==> 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 reference-NA12878 --max_event_count 5 -v positive_somatic_control_1.tnseq.vcf.gz --contamination positive_somatic_control_1.tnseq.contamination_data.tsv --tumor_segments positive_somatic_control_1.tnseq.segments --orientation_priors positive_somatic_control_1.tnseq.orientation_data.tsv positive_somatic_control_1.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:63000001, elapsed 0.1s, est remaining 2.0s, peak mem 813MB, user 0.1s, sys 4.1s, output queue size 127
progress 10% @chr2:203000001, elapsed 0.2s, est remaining 1.9s, peak mem 813MB, user 0.3s, sys 13.1s, output queue size 281
progress 15% @chr3:166000001, elapsed 0.3s, est remaining 1.7s, peak mem 813MB, user 0.4s, sys 22.7s, output queue size 443
progress 20% @chr5:24000001, elapsed 0.4s, est remaining 1.6s, peak mem 813MB, user 0.5s, sys 31.9s, output queue size 604
progress 25% @chr5:159000001, elapsed 0.5s, est remaining 1.5s, peak mem 813MB, user 0.7s, sys 41.6s, output queue size 764
progress 30% @chr6:52000001, elapsed 0.6s, est remaining 1.4s, peak mem 813MB, user 1.0s, sys 52.9s, output queue size 925
progress 35% @chr7:38000001, elapsed 0.7s, est remaining 1.3s, peak mem 816MB, user 1.1s, sys 64.7s, output queue size 1084
progress 40% @chr8:80000001, elapsed 0.8s, est remaining 1.2s, peak mem 816MB, user 1.4s, sys 77.9s, output queue size 1246
progress 45% @chr9:59000001, elapsed 0.9s, est remaining 1.1s, peak mem 816MB, user 1.6s, sys 90.7s, output queue size 1408
progress 50% @chr11:4000001, elapsed 1.0s, est remaining 1.0s, peak mem 816MB, user 1.9s, sys 105.3s, output queue size 1569
progress 55% @chr11:123000001, elapsed 1.1s, est remaining 0.9s, peak mem 816MB, user 2.2s, sys 121.2s, output queue size 1730
progress 60% @chr13:24000001, elapsed 1.1s, est remaining 0.8s, peak mem 816MB, user 2.5s, sys 135.0s, output queue size 1892
progress 65% @chr12:67000001, elapsed 1.2s, est remaining 0.6s, peak mem 816MB, user 2.9s, sys 144.7s, output queue size 2055
progress 70% @chr17:24000001, elapsed 1.3s, est remaining 0.5s, peak mem 816MB, user 3.1s, sys 155.7s, output queue size 2217
progress 75% @chr19:11000001, elapsed 1.3s, est remaining 0.4s, peak mem 816MB, user 3.5s, sys 166.9s, output queue size 2378
progress 80% @chr21:15000001, elapsed 1.4s, est remaining 0.3s, peak mem 816MB, user 3.9s, sys 180.4s, output queue size 2538
progress 85% @chrX:127000001, elapsed 1.4s, est remaining 0.3s, peak mem 816MB, user 4.1s, sys 194.4s, output queue size 2672
progress 90% @chrY:42000001, elapsed 1.5s, est remaining 0.2s, peak mem 816MB, user 4.4s, sys 208.3s, output queue size 3144
progress 95% @chr2:161000001, elapsed 1.6s, est remaining 0.1s, peak mem 816MB, user 4.7s, sys 229.0s, output queue size 4293
progress 100% @HLA-DQA1*01:03:01:02:1, elapsed 1.7s, est remaining 0.0s, peak mem 816MB, user 5.0s, sys 254.9s, output queue size 465
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: 384 max 384
algo: TNfilter
license: sentieon:TNhaplotyper=384
input file size: 50711
output file size: 43803
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 513 calls 0.001 user 0.000 sys 0.011 real
"predict_filter": 171 calls 0.005 user 0.020 sys 0.050 real
advance: 3219322 calls 0.432 user 106.637 sys 113.103 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.009 user 0.009 sys 1.741 real
fetch_ref: 448 calls 0.001 user 0.058 sys 0.581 real
idle: 20632 calls 0.595 user 6.360 sys 739.580 real
init: 1 calls 0.370 user 0.126 sys 0.665 real
overall: 855773184 mem 6.754 user 303.566 sys 4.182 real