Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/87e9754245d8b7808f8909de654c35/HCC1395_BL.tnseq_tumor_only.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/87e9754245d8b7808f8909de654c35/HCC1395_BL.tnseq_tumor_only.vcf.gz.stats
  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/0e/53e6db24353197f436c3867be02635/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/87e9754245d8b7808f8909de654c35/HCC1395_BL.tnseq_tumor_only.segments
  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/8c/87e9754245d8b7808f8909de654c35/HCC1395_BL.tnseq_tumor_only.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/87e9754245d8b7808f8909de654c35/HCC1395_BL.tnseq_tumor_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/87e9754245d8b7808f8909de654c35/HCC1395_BL.tnseq_tumor_only.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/53e6db24353197f436c3867be02635/.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_BL --max_event_count 5 -v HCC1395_BL.tnseq_tumor_only.vcf.gz --contamination HCC1395_BL.tnseq_tumor_only.contamination_data.tsv --tumor_segments HCC1395_BL.tnseq_tumor_only.segments --orientation_priors HCC1395_BL.tnseq_tumor_only.orientation_data.tsv HCC1395_BL.tnseq_tumor_only.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:150000001, elapsed 0.1s, est remaining 2.0s, peak mem 810MB, user 0.1s, sys 4.5s, output queue size 150
progress 10% @chr3:134000001, elapsed 0.2s, est remaining 1.8s, peak mem 810MB, user 0.2s, sys 13.5s, output queue size 275
progress 15% @chr4:92000001, elapsed 0.3s, est remaining 1.4s, peak mem 810MB, user 0.4s, sys 24.6s, output queue size 437
progress 20% @chr5:63000001, elapsed 0.3s, est remaining 1.3s, peak mem 810MB, user 0.7s, sys 37.5s, output queue size 598
progress 25% @chr5:120000001, elapsed 0.4s, est remaining 1.1s, peak mem 810MB, user 1.1s, sys 50.6s, output queue size 760
progress 30% @chr6:73000001, elapsed 0.4s, est remaining 1.0s, peak mem 810MB, user 1.6s, sys 63.4s, output queue size 921
progress 35% @chr7:59000001, elapsed 0.5s, est remaining 0.9s, peak mem 810MB, user 2.0s, sys 81.2s, output queue size 1082
progress 40% @chr6:111000001, elapsed 0.5s, est remaining 0.8s, peak mem 810MB, user 2.4s, sys 100.6s, output queue size 1244
progress 45% @chr10:27000001, elapsed 0.6s, est remaining 0.7s, peak mem 810MB, user 2.6s, sys 114.5s, output queue size 1405
progress 50% @chr11:40000001, elapsed 0.6s, est remaining 0.6s, peak mem 810MB, user 2.9s, sys 128.0s, output queue size 1566
progress 55% @chr12:19000001, elapsed 0.7s, est remaining 0.6s, peak mem 810MB, user 3.5s, sys 139.3s, output queue size 1728
progress 60% @chr12:65000001, elapsed 0.7s, est remaining 0.5s, peak mem 810MB, user 3.8s, sys 152.7s, output queue size 1890
progress 65% @chr11:133000001, elapsed 0.8s, est remaining 0.4s, peak mem 810MB, user 4.1s, sys 166.4s, output queue size 2052
progress 70% @chr16:51000001, elapsed 0.8s, est remaining 0.4s, peak mem 810MB, user 4.6s, sys 181.9s, output queue size 2213
progress 75% @chr12:106000001, elapsed 0.9s, est remaining 0.3s, peak mem 810MB, user 4.9s, sys 197.0s, output queue size 2375
progress 80% @chr20:3000001, elapsed 0.9s, est remaining 0.2s, peak mem 810MB, user 5.4s, sys 211.4s, output queue size 2538
progress 85% @chrX:123000001, elapsed 1.0s, est remaining 0.2s, peak mem 810MB, user 5.8s, sys 228.3s, output queue size 2700
progress 90% @chrY:14000001, elapsed 1.1s, est remaining 0.1s, peak mem 810MB, user 6.4s, sys 247.9s, output queue size 3065
progress 95% @chr22:24000001, elapsed 1.1s, est remaining 0.1s, peak mem 810MB, user 6.8s, sys 279.9s, output queue size 3576
progress 100% @HLA-DRB1*08:03:02:1, elapsed 1.2s, est remaining 0.0s, peak mem 810MB, user 7.2s, sys 331.0s, output queue size 413
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: 51811
output file size: 43436
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 540 calls 0.001 user 0.000 sys 0.010 real
"predict_filter": 180 calls 0.000 user 0.014 sys 0.035 real
advance: 3219322 calls 0.308 user 107.883 sys 113.650 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.007 user 0.007 sys 1.319 real
fetch_ref: 528 calls 0.000 user 0.055 sys 0.176 real
idle: 20633 calls 0.666 user 0.881 sys 729.783 real
init: 1 calls 0.396 user 0.178 sys 0.743 real
overall: 849502208 mem 9.051 user 341.781 sys 3.412 real