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/7e/ad109e72016badb0d6a82b7094a238/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/920dc830638321c2f996bdc03493ee/custom_Sig_18_tumor_normal.tnseq.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/920dc830638321c2f996bdc03493ee/custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv
  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/4d/920dc830638321c2f996bdc03493ee/custom_Sig_18_tumor_normal.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/920dc830638321c2f996bdc03493ee/custom_Sig_18_tumor_normal.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/920dc830638321c2f996bdc03493ee/custom_Sig_18_tumor_normal.tnseq.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/ad109e72016badb0d6a82b7094a238/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/920dc830638321c2f996bdc03493ee/custom_Sig_18_tumor_normal.tnseq.orientation_data.tsv
==> STAGING COMPLETE (10 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample Sig_18_tissue --normal_sample Sig_18_Blood --max_event_count 5 -v custom_Sig_18_tumor_normal.tnseq.vcf.gz --contamination custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv --tumor_segments custom_Sig_18_tumor_normal.tnseq.segments --orientation_priors custom_Sig_18_tumor_normal.tnseq.orientation_data.tsv custom_Sig_18_tumor_normal.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:69000001, elapsed 0.1s, est remaining 1.9s, peak mem 813MB, user 0.1s, sys 3.5s, output queue size 130
progress 10% @chr3:157000001, elapsed 0.2s, est remaining 1.7s, peak mem 813MB, user 0.2s, sys 12.0s, output queue size 291
progress 15% @chr4:57000001, elapsed 0.3s, est remaining 1.4s, peak mem 813MB, user 0.5s, sys 27.7s, output queue size 453
progress 20% @chr1:191000001, elapsed 0.3s, est remaining 1.2s, peak mem 813MB, user 0.8s, sys 44.0s, output queue size 615
progress 25% @chr6:4000001, elapsed 0.4s, est remaining 1.1s, peak mem 813MB, user 1.1s, sys 59.5s, output queue size 776
progress 30% @chr6:166000001, elapsed 0.4s, est remaining 0.9s, peak mem 813MB, user 1.6s, sys 72.5s, output queue size 937
progress 35% @chr5:14000001, elapsed 0.4s, est remaining 0.8s, peak mem 813MB, user 2.1s, sys 85.6s, output queue size 1098
progress 40% @chr8:77000001, elapsed 0.5s, est remaining 0.7s, peak mem 813MB, user 2.5s, sys 96.7s, output queue size 1260
progress 45% @chr9:109000001, elapsed 0.5s, est remaining 0.7s, peak mem 813MB, user 2.9s, sys 107.6s, output queue size 1421
progress 50% @chr10:130000001, elapsed 0.6s, est remaining 0.6s, peak mem 813MB, user 3.4s, sys 120.1s, output queue size 1583
progress 55% @chr3:8000001, elapsed 0.6s, est remaining 0.5s, peak mem 813MB, user 3.8s, sys 133.5s, output queue size 1745
progress 60% @chr13:70000001, elapsed 0.7s, est remaining 0.5s, peak mem 813MB, user 4.2s, sys 143.2s, output queue size 1689
progress 65% @chr15:45000001, elapsed 0.7s, est remaining 0.4s, peak mem 813MB, user 4.8s, sys 154.5s, output queue size 1850
progress 70% @chr17:26000001, elapsed 0.8s, est remaining 0.3s, peak mem 813MB, user 5.2s, sys 165.4s, output queue size 2012
progress 75% @chr12:3000001, elapsed 0.9s, est remaining 0.3s, peak mem 813MB, user 5.7s, sys 176.8s, output queue size 2173
progress 80% @chr16:80000001, elapsed 0.9s, est remaining 0.2s, peak mem 813MB, user 6.2s, sys 188.5s, output queue size 2336
progress 85% @chr17:61000001, elapsed 0.9s, est remaining 0.2s, peak mem 813MB, user 6.7s, sys 201.5s, output queue size 2500
progress 90% @chr3:17000001, elapsed 1.0s, est remaining 0.1s, peak mem 813MB, user 7.1s, sys 218.7s, output queue size 2877
progress 95% @chr2:184000001, elapsed 1.1s, est remaining 0.1s, peak mem 813MB, user 7.5s, sys 242.7s, output queue size 3456
progress 100% @HLA-DQA1*01:01:02:1, elapsed 1.2s, est remaining 0.0s, peak mem 813MB, user 8.0s, sys 286.7s, output queue size 6244
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: 95376
output file size: 77088
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 1065 calls 0.005 user 0.000 sys 0.030 real
"predict_filter": 355 calls 0.010 user 0.012 sys 0.033 real
advance: 3219322 calls 0.419 user 108.763 sys 96.253 real
done: 1 calls 0.001 user 0.000 sys 0.003 real
execute: 1 calls 0.002 user 0.002 sys 1.439 real
fetch_ref: 876 calls 0.007 user 0.071 sys 0.055 real
idle: 20633 calls 0.729 user 1.343 sys 852.114 real
init: 1 calls 0.352 user 0.118 sys 1.080 real
overall: 852623360 mem 9.946 user 293.972 sys 3.605 real