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/02/52115ccfcc733d7e01be37c2040bc8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/817a27ebe38d4d648920ad357cb247/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/2e/817a27ebe38d4d648920ad357cb247/positive_somatic_control_1.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/817a27ebe38d4d648920ad357cb247/positive_somatic_control_1.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/817a27ebe38d4d648920ad357cb247/positive_somatic_control_1.tnseq.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/817a27ebe38d4d648920ad357cb247/positive_somatic_control_1.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/52115ccfcc733d7e01be37c2040bc8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/817a27ebe38d4d648920ad357cb247/positive_somatic_control_1.tnseq.vcf.gz.tbi
==> 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% @chr2:132000001, elapsed 0.1s, est remaining 2.2s, peak mem 810MB, user 0.1s, sys 4.9s, output queue size 153
progress 10% @chr3:143000001, elapsed 0.2s, est remaining 2.1s, peak mem 810MB, user 0.3s, sys 17.2s, output queue size 314
progress 15% @chr4:37000001, elapsed 0.3s, est remaining 1.7s, peak mem 810MB, user 0.7s, sys 30.8s, output queue size 476
progress 20% @chr4:125000001, elapsed 0.4s, est remaining 1.5s, peak mem 810MB, user 1.0s, sys 41.2s, output queue size 638
progress 25% @chr5:141000001, elapsed 0.4s, est remaining 1.3s, peak mem 810MB, user 1.4s, sys 51.3s, output queue size 798
progress 30% @chr6:115000001, elapsed 0.5s, est remaining 1.2s, peak mem 810MB, user 1.6s, sys 63.3s, output queue size 959
progress 35% @chr8:87000001, elapsed 0.6s, est remaining 1.1s, peak mem 810MB, user 1.8s, sys 70.7s, output queue size 1121
progress 40% @chr2:189000001, elapsed 0.7s, est remaining 1.0s, peak mem 810MB, user 2.1s, sys 77.9s, output queue size 1283
progress 45% @chr7:130000001, elapsed 0.8s, est remaining 1.0s, peak mem 810MB, user 2.5s, sys 81.6s, output queue size 1444
progress 50% @chr8:31000001, elapsed 0.9s, est remaining 0.9s, peak mem 810MB, user 2.7s, sys 87.9s, output queue size 1607
progress 55% @chr12:104000001, elapsed 1.0s, est remaining 0.8s, peak mem 810MB, user 3.0s, sys 97.0s, output queue size 1768
progress 60% @chr13:76000001, elapsed 1.1s, est remaining 0.7s, peak mem 810MB, user 3.4s, sys 108.0s, output queue size 1931
progress 65% @chr14:83000001, elapsed 1.1s, est remaining 0.6s, peak mem 810MB, user 3.9s, sys 118.8s, output queue size 2082
progress 70% @chr14:79000001, elapsed 1.2s, est remaining 0.5s, peak mem 810MB, user 4.2s, sys 130.7s, output queue size 2243
progress 75% @chr15:71000001, elapsed 1.2s, est remaining 0.4s, peak mem 810MB, user 4.5s, sys 140.2s, output queue size 2365
progress 80% @chr22:16000001, elapsed 1.3s, est remaining 0.3s, peak mem 810MB, user 4.8s, sys 146.9s, output queue size 2528
progress 85% @chrX:90000001, elapsed 1.4s, est remaining 0.2s, peak mem 810MB, user 5.3s, sys 156.1s, output queue size 2694
progress 90% @chr16_KI270728v1_random:1000001, elapsed 1.4s, est remaining 0.2s, peak mem 810MB, user 5.7s, sys 169.2s, output queue size 3042
progress 95% @chr20:7000001, elapsed 1.4s, est remaining 0.1s, peak mem 810MB, user 6.1s, sys 181.3s, output queue size 3474
progress 100% @HLA-C*15:05:02:1, elapsed 1.6s, est remaining 0.0s, peak mem 810MB, user 6.3s, sys 195.2s, output queue size 3465
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: 43806
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 513 calls 0.000 user 0.000 sys 0.011 real
"predict_filter": 171 calls 0.035 user 0.027 sys 0.078 real
advance: 3219322 calls 0.538 user 75.491 sys 82.605 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.000 user 0.010 sys 1.701 real
fetch_ref: 448 calls 0.000 user 0.057 sys 0.082 real
idle: 20633 calls 0.684 user 0.496 sys 746.718 real
init: 1 calls 0.373 user 0.166 sys 0.769 real
overall: 849481728 mem 8.173 user 203.179 sys 3.731 real