Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/d16aa700194be2b1d7ed95fe99d433/negative_somatic_control_2.tnseq.vcf.gz
  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/a5/d16aa700194be2b1d7ed95fe99d433/negative_somatic_control_2.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/8f7b75d30a41387f69c388d9c2bf25/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/d16aa700194be2b1d7ed95fe99d433/negative_somatic_control_2.tnseq.vcf.gz.tbi
  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/3b/8f7b75d30a41387f69c388d9c2bf25/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/d16aa700194be2b1d7ed95fe99d433/negative_somatic_control_2.tnseq.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/d16aa700194be2b1d7ed95fe99d433/negative_somatic_control_2.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/d16aa700194be2b1d7ed95fe99d433/negative_somatic_control_2.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 Sig_18_Blood --normal_sample reference-NA12878 --max_event_count 5 -v negative_somatic_control_2.tnseq.vcf.gz --contamination negative_somatic_control_2.tnseq.contamination_data.tsv --tumor_segments negative_somatic_control_2.tnseq.segments --orientation_priors negative_somatic_control_2.tnseq.orientation_data.tsv negative_somatic_control_2.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
Received only 62 licenses out of 75 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 87 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 98 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 110 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 124 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 138 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 153 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 167 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 184 requested for sentieon:TNhaplotyper
Received only 62 licenses out of 192 requested for sentieon:TNhaplotyper
progress 5% @chr1:178000001, elapsed 0.0s, est remaining 0.9s, peak mem 414MB, user 0.1s, sys 1.8s, output queue size 35
progress 10% @chr2:43000001, elapsed 0.1s, est remaining 0.7s, peak mem 414MB, user 0.1s, sys 4.1s, output queue size 30
progress 15% @chr3:4000001, elapsed 0.1s, est remaining 0.7s, peak mem 414MB, user 0.2s, sys 6.2s, output queue size 26
progress 20% @chr3:121000001, elapsed 0.2s, est remaining 0.6s, peak mem 414MB, user 0.3s, sys 8.4s, output queue size 32
progress 25% @chr4:128000001, elapsed 0.2s, est remaining 0.6s, peak mem 414MB, user 0.4s, sys 10.6s, output queue size 29
progress 30% @chr5:105000001, elapsed 0.2s, est remaining 0.5s, peak mem 414MB, user 0.5s, sys 12.8s, output queue size 21
progress 35% @chr6:37000001, elapsed 0.3s, est remaining 0.5s, peak mem 414MB, user 0.6s, sys 15.0s, output queue size 28
progress 40% @chr7:19000001, elapsed 0.3s, est remaining 0.5s, peak mem 414MB, user 0.7s, sys 17.1s, output queue size 36
progress 45% @chr8:73000001, elapsed 0.3s, est remaining 0.4s, peak mem 414MB, user 0.8s, sys 19.3s, output queue size 28
progress 50% @chr9:37000001, elapsed 0.4s, est remaining 0.4s, peak mem 414MB, user 0.9s, sys 21.3s, output queue size 36
progress 55% @chr10:60000001, elapsed 0.4s, est remaining 0.3s, peak mem 414MB, user 1.0s, sys 23.3s, output queue size 36
progress 60% @chr12:8000001, elapsed 0.4s, est remaining 0.3s, peak mem 414MB, user 1.2s, sys 25.4s, output queue size 30
progress 65% @chr12:111000001, elapsed 0.5s, est remaining 0.3s, peak mem 414MB, user 1.3s, sys 27.5s, output queue size 38
progress 70% @chr14:89000001, elapsed 0.5s, est remaining 0.2s, peak mem 414MB, user 1.5s, sys 29.6s, output queue size 37
progress 75% @chr16:30000001, elapsed 0.6s, est remaining 0.2s, peak mem 414MB, user 1.5s, sys 31.8s, output queue size 30
progress 80% @chr18:15000001, elapsed 0.6s, est remaining 0.1s, peak mem 414MB, user 1.6s, sys 33.9s, output queue size 35
progress 85% @chr20:42000001, elapsed 0.6s, est remaining 0.1s, peak mem 414MB, user 1.8s, sys 36.0s, output queue size 36
progress 90% @chrX:38000001, elapsed 0.7s, est remaining 0.1s, peak mem 414MB, user 2.0s, sys 38.1s, output queue size 23
progress 95% @chrX:144000001, elapsed 0.7s, est remaining 0.0s, peak mem 414MB, user 2.1s, sys 40.1s, output queue size 106
progress 100% @HLA-DRB1*10:01:01:1, elapsed 0.8s, est remaining 0.0s, peak mem 414MB, user 2.2s, sys 44.1s, output queue size 703
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: 192 max 192
algo: TNfilter
license: sentieon:TNhaplotyper=62
input file size: 51111
output file size: 43431
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 513 calls 0.000 user 0.000 sys 0.010 real
"predict_filter": 171 calls 0.020 user 0.010 sys 0.008 real
advance: 3219322 calls 0.191 user 19.497 sys 22.003 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.002 sys 0.823 real
fetch_ref: 460 calls 0.000 user 0.000 sys 0.007 real
idle: 19797 calls 0.449 user 0.099 sys 3678.297 real
init: 1 calls 0.236 user 0.101 sys 0.487 real
overall: 434393088 mem 3.340 user 45.494 sys 60.191 real