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/b6/eb604498adbde55e6662103f4527e8/1029_0I.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/7bf9e156705837a4d4c3f140b4ace3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/eb604498adbde55e6662103f4527e8/1029_0I.tnseq.vcf.gz
  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/b6/eb604498adbde55e6662103f4527e8/1029_0I.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/7bf9e156705837a4d4c3f140b4ace3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/eb604498adbde55e6662103f4527e8/1029_0I.tnseq.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/eb604498adbde55e6662103f4527e8/1029_0I.tnseq.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/eb604498adbde55e6662103f4527e8/1029_0I.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 1029_0I-T1-TDNA-1_A23KCGYLT4_1 --normal_sample 1029_0I-N1-BDNA-1_B23KGCJLT4_1 --max_event_count 5 -v 1029_0I.tnseq.vcf.gz --contamination 1029_0I.tnseq.contamination_data.tsv --tumor_segments 1029_0I.tnseq.segments --orientation_priors 1029_0I.tnseq.orientation_data.tsv 1029_0I.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 0.1s, est remaining 2.3s, peak mem 942MB, user 0.3s, sys 1.1s, output queue size 161
progress 10% @chr1:88000001, elapsed 0.2s, est remaining 1.7s, peak mem 942MB, user 1.6s, sys 10.8s, output queue size 321
progress 15% @chr3:27000001, elapsed 0.2s, est remaining 1.3s, peak mem 942MB, user 2.7s, sys 19.9s, output queue size 476
progress 20% @chr1:41000001, elapsed 0.3s, est remaining 1.1s, peak mem 942MB, user 3.8s, sys 31.3s, output queue size 633
progress 25% @chr5:90000001, elapsed 0.3s, est remaining 1.0s, peak mem 942MB, user 4.6s, sys 41.4s, output queue size 793
progress 30% @chr4:155000001, elapsed 0.4s, est remaining 0.9s, peak mem 942MB, user 5.6s, sys 50.9s, output queue size 955
progress 35% @chr6:80000001, elapsed 0.4s, est remaining 0.8s, peak mem 942MB, user 6.7s, sys 65.1s, output queue size 945
progress 40% @chr9:37000001, elapsed 0.5s, est remaining 0.7s, peak mem 942MB, user 7.6s, sys 79.0s, output queue size 1107
progress 45% @chr9:127000001, elapsed 0.5s, est remaining 0.7s, peak mem 942MB, user 8.1s, sys 90.5s, output queue size 1268
progress 50% @chr10:122000001, elapsed 0.6s, est remaining 0.6s, peak mem 942MB, user 8.9s, sys 105.1s, output queue size 1430
progress 55% @chr9:46000001, elapsed 0.7s, est remaining 0.5s, peak mem 942MB, user 9.5s, sys 117.1s, output queue size 1591
progress 60% @chr14:43000001, elapsed 0.7s, est remaining 0.5s, peak mem 942MB, user 10.1s, sys 127.1s, output queue size 1754
progress 65% @chr15:77000001, elapsed 0.8s, est remaining 0.4s, peak mem 942MB, user 10.6s, sys 137.5s, output queue size 1915
progress 70% @chr16:45000001, elapsed 0.8s, est remaining 0.4s, peak mem 942MB, user 11.2s, sys 150.2s, output queue size 2077
progress 75% @chr19:16000001, elapsed 0.9s, est remaining 0.3s, peak mem 942MB, user 12.0s, sys 161.5s, output queue size 2238
progress 80% @chr22:14000001, elapsed 0.9s, est remaining 0.2s, peak mem 942MB, user 12.9s, sys 174.3s, output queue size 2401
progress 85% @chrY:12000001, elapsed 1.0s, est remaining 0.2s, peak mem 942MB, user 13.5s, sys 185.3s, output queue size 2573
progress 90% @chr19_KI270884v1_alt:1, elapsed 1.0s, est remaining 0.1s, peak mem 942MB, user 14.3s, sys 196.9s, output queue size 3017
progress 95% @chr17:76000001, elapsed 1.1s, est remaining 0.1s, peak mem 942MB, user 14.8s, sys 213.6s, output queue size 4033
progress 100% @HLA-B*39:14:1, elapsed 1.3s, est remaining 0.0s, peak mem 942MB, user 16.3s, sys 269.1s, output queue size 6310
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: 2942516
output file size: 2443634
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 53037 calls 62.284 user 0.740 sys 76.139 real
"predict_filter": 17679 calls 1.822 user 0.957 sys 3.048 real
advance: 3219322 calls 0.952 user 102.339 sys 92.256 real
done: 1 calls 0.009 user 0.000 sys 0.012 real
execute: 1 calls 0.006 user 0.002 sys 1.556 real
fetch_ref: 35348 calls 0.987 user 1.716 sys 6.717 real
idle: 21017 calls 12.577 user 0.824 sys 1370.211 real
init: 1 calls 1.772 user 0.420 sys 2.659 real
overall: 987959296 mem 117.106 user 277.317 sys 5.322 real