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/8a/26d8ca4c41a45f2eb69d9415d7fc56/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/61ae4c293bff9a713bf18baf2c1436/.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/8a/26d8ca4c41a45f2eb69d9415d7fc56/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/26d8ca4c41a45f2eb69d9415d7fc56/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/61ae4c293bff9a713bf18baf2c1436/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/26d8ca4c41a45f2eb69d9415d7fc56/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/26d8ca4c41a45f2eb69d9415d7fc56/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/26d8ca4c41a45f2eb69d9415d7fc56/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments
==> STAGING COMPLETE (10 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample 869_VZQ-N1-BDNA-1_A23FG3YLT4_1 --max_event_count 5 -v 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz --contamination 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv --tumor_segments 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments --orientation_priors 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv 869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:109000001, elapsed 0.1s, est remaining 1.8s, peak mem 161MB, user 0.4s, sys 0.1s, output queue size 144
progress 10% @chr2:84000001, elapsed 0.1s, est remaining 1.1s, peak mem 162MB, user 1.0s, sys 0.5s, output queue size 170
progress 15% @chr2:232000001, elapsed 0.1s, est remaining 0.8s, peak mem 162MB, user 1.7s, sys 0.9s, output queue size 332
progress 20% @chr3:95000001, elapsed 0.2s, est remaining 0.7s, peak mem 162MB, user 2.3s, sys 1.2s, output queue size 352
progress 25% @chr4:141000001, elapsed 0.2s, est remaining 0.6s, peak mem 163MB, user 2.9s, sys 1.6s, output queue size 513
progress 30% @chr5:86000001, elapsed 0.2s, est remaining 0.5s, peak mem 163MB, user 3.4s, sys 1.9s, output queue size 216
progress 35% @chr6:94000001, elapsed 0.3s, est remaining 0.5s, peak mem 163MB, user 4.1s, sys 2.1s, output queue size 378
progress 40% @chr7:61000001, elapsed 0.3s, est remaining 0.4s, peak mem 164MB, user 4.7s, sys 2.4s, output queue size 539
progress 45% @chr8:65000001, elapsed 0.3s, est remaining 0.4s, peak mem 164MB, user 5.3s, sys 2.8s, output queue size 701
progress 50% @chr9:73000001, elapsed 0.3s, est remaining 0.3s, peak mem 164MB, user 6.0s, sys 3.2s, output queue size 863
progress 55% @chr10:110000001, elapsed 0.4s, est remaining 0.3s, peak mem 165MB, user 6.7s, sys 3.4s, output queue size 1024
progress 60% @chr12:4000001, elapsed 0.4s, est remaining 0.3s, peak mem 165MB, user 7.2s, sys 3.7s, output queue size 1186
progress 65% @chr13:18000001, elapsed 0.4s, est remaining 0.2s, peak mem 165MB, user 7.9s, sys 4.0s, output queue size 406
progress 70% @chr14:59000001, elapsed 0.5s, est remaining 0.2s, peak mem 165MB, user 8.5s, sys 4.3s, output queue size 567
progress 75% @chr16:29000001, elapsed 0.5s, est remaining 0.2s, peak mem 165MB, user 9.0s, sys 4.6s, output queue size 729
progress 80% @chr17:81000001, elapsed 0.5s, est remaining 0.1s, peak mem 166MB, user 9.7s, sys 4.8s, output queue size 891
progress 85% @chr20:42000001, elapsed 0.5s, est remaining 0.1s, peak mem 166MB, user 10.3s, sys 5.1s, output queue size 1053
progress 90% @chrX:44000001, elapsed 0.6s, est remaining 0.1s, peak mem 166MB, user 11.0s, sys 5.4s, output queue size 1215
progress 95% @chrY:34000001, elapsed 0.6s, est remaining 0.0s, peak mem 166MB, user 11.6s, sys 5.7s, output queue size 1383
progress 100% @HLA-B*27:05:18:1, elapsed 0.8s, est remaining 0.0s, peak mem 170MB, user 12.2s, sys 6.7s, output queue size 4801
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 48 max 48
algo: TNfilter
license: sentieon:TNhaplotyper=48
input file size: 2932586
output file size: 2079716
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 59322 calls 3.389 user 0.036 sys 4.151 real
"predict_filter": 19774 calls 1.262 user 0.095 sys 1.640 real
advance: 3219322 calls 2.220 user 2.679 sys 5.377 real
done: 1 calls 0.022 user 0.000 sys 0.033 real
execute: 1 calls 0.009 user 0.001 sys 1.069 real
fetch_ref: 49032 calls 0.694 user 0.187 sys 1.007 real
idle: 561 calls 0.287 user 0.038 sys 89.767 real
init: 1 calls 0.736 user 0.042 sys 1.395 real
overall: 178982912 mem 36.217 user 7.591 sys 3.244 real