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/ca/2c2983ea639e6c5bfe68c74babe33d/.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/48/d6d264afd0123ae8eae2821740f21e/negative_somatic_control_1.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/d6d264afd0123ae8eae2821740f21e/negative_somatic_control_1.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/d6d264afd0123ae8eae2821740f21e/negative_somatic_control_1.tnseq.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/2c2983ea639e6c5bfe68c74babe33d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/d6d264afd0123ae8eae2821740f21e/negative_somatic_control_1.tnseq.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/d6d264afd0123ae8eae2821740f21e/negative_somatic_control_1.tnseq.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/d6d264afd0123ae8eae2821740f21e/negative_somatic_control_1.tnseq.segments
==> STAGING COMPLETE (10 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --max_event_count 5 -v negative_somatic_control_1.tnseq.vcf.gz --contamination negative_somatic_control_1.tnseq.contamination_data.tsv --tumor_segments negative_somatic_control_1.tnseq.segments --orientation_priors negative_somatic_control_1.tnseq.orientation_data.tsv negative_somatic_control_1.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:221000001, elapsed 0.1s, est remaining 1.1s, peak mem 417MB, user 0.3s, sys 2.3s, output queue size 129
progress 10% @chr2:118000001, elapsed 0.1s, est remaining 0.9s, peak mem 417MB, user 0.4s, sys 6.6s, output queue size 265
progress 15% @chr3:59000001, elapsed 0.1s, est remaining 0.8s, peak mem 417MB, user 0.6s, sys 10.8s, output queue size 347
progress 20% @chr3:183000001, elapsed 0.2s, est remaining 0.7s, peak mem 417MB, user 0.8s, sys 16.3s, output queue size 509
progress 25% @chr4:41000001, elapsed 0.2s, est remaining 0.7s, peak mem 417MB, user 1.0s, sys 22.3s, output queue size 670
progress 30% @chr4:127000001, elapsed 0.3s, est remaining 0.6s, peak mem 417MB, user 1.3s, sys 28.3s, output queue size 832
progress 35% @chr6:90000001, elapsed 0.3s, est remaining 0.6s, peak mem 417MB, user 1.7s, sys 34.0s, output queue size 992
progress 40% @chr7:36000001, elapsed 0.3s, est remaining 0.5s, peak mem 417MB, user 2.0s, sys 39.6s, output queue size 1154
progress 45% @chr8:106000001, elapsed 0.4s, est remaining 0.5s, peak mem 417MB, user 2.3s, sys 44.3s, output queue size 1316
progress 50% @chr10:38000001, elapsed 0.4s, est remaining 0.4s, peak mem 417MB, user 2.6s, sys 49.1s, output queue size 1477
progress 55% @chr7:98000001, elapsed 0.5s, est remaining 0.4s, peak mem 417MB, user 2.9s, sys 54.1s, output queue size 1639
progress 60% @chr11:77000001, elapsed 0.5s, est remaining 0.3s, peak mem 417MB, user 3.3s, sys 59.4s, output queue size 1800
progress 65% @chr13:103000001, elapsed 0.6s, est remaining 0.3s, peak mem 417MB, user 3.6s, sys 65.4s, output queue size 1962
progress 70% @chr15:56000001, elapsed 0.6s, est remaining 0.2s, peak mem 417MB, user 3.9s, sys 71.4s, output queue size 287
progress 75% @chr16:59000001, elapsed 0.6s, est remaining 0.2s, peak mem 417MB, user 4.3s, sys 76.4s, output queue size 449
progress 80% @chr18:70000001, elapsed 0.7s, est remaining 0.2s, peak mem 417MB, user 4.6s, sys 82.0s, output queue size 611
progress 85% @chr22:24000001, elapsed 0.7s, est remaining 0.1s, peak mem 417MB, user 5.1s, sys 87.6s, output queue size 772
progress 90% @chrX:52000001, elapsed 0.8s, est remaining 0.1s, peak mem 417MB, user 5.6s, sys 93.6s, output queue size 935
progress 95% @chrY:17000001, elapsed 0.8s, est remaining 0.0s, peak mem 417MB, user 6.0s, sys 99.5s, output queue size 1282
progress 100% @HLA-DRB1*12:17:1, elapsed 0.9s, est remaining 0.0s, peak mem 418MB, user 6.3s, sys 113.4s, output queue size 4520
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 192 max 192
algo: TNfilter
license: sentieon:TNhaplotyper=192
input file size: 46618
output file size: 40485
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 408 calls 0.000 user 0.000 sys 0.009 real
"predict_filter": 136 calls 0.000 user 0.021 sys 0.035 real
advance: 3219322 calls 0.760 user 44.345 sys 53.426 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.002 sys 0.970 real
fetch_ref: 384 calls 0.004 user 0.075 sys 0.142 real
idle: 20057 calls 0.517 user 0.347 sys 292.684 real
init: 1 calls 0.241 user 0.085 sys 0.473 real
overall: 439115776 mem 7.783 user 117.559 sys 2.513 real