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/d6/60718bae893b02cfeac743104624a0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/52929cba19d9b064778c257f6733b9/positive_somatic_control_2.tnseq.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/58/52929cba19d9b064778c257f6733b9/positive_somatic_control_2.tnseq.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/52929cba19d9b064778c257f6733b9/positive_somatic_control_2.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/52929cba19d9b064778c257f6733b9/positive_somatic_control_2.tnseq.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/52929cba19d9b064778c257f6733b9/positive_somatic_control_2.tnseq.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/60718bae893b02cfeac743104624a0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/52929cba19d9b064778c257f6733b9/positive_somatic_control_2.tnseq.contamination_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_tissue --normal_sample reference-NA12878 --max_event_count 5 -v positive_somatic_control_2.tnseq.vcf.gz --contamination positive_somatic_control_2.tnseq.contamination_data.tsv --tumor_segments positive_somatic_control_2.tnseq.segments --orientation_priors positive_somatic_control_2.tnseq.orientation_data.tsv positive_somatic_control_2.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
No more license available for sentieon:TNhaplotyper
Received only 89 licenses out of 192 requested for sentieon:TNhaplotyper
progress 5% @chr1:90000001, elapsed 0.1s, est remaining 1.2s, peak mem 418MB, user 0.1s, sys 2.4s, output queue size 71
progress 10% @chr2:118000001, elapsed 0.1s, est remaining 0.9s, peak mem 418MB, user 0.3s, sys 6.0s, output queue size 124
progress 15% @chr3:21000001, elapsed 0.1s, est remaining 0.8s, peak mem 418MB, user 0.4s, sys 9.8s, output queue size 53
progress 20% @chr3:129000001, elapsed 0.2s, est remaining 0.8s, peak mem 418MB, user 0.5s, sys 13.5s, output queue size 37
progress 25% @chr4:138000001, elapsed 0.2s, est remaining 0.7s, peak mem 418MB, user 0.5s, sys 17.1s, output queue size 42
progress 30% @chr5:62000001, elapsed 0.3s, est remaining 0.6s, peak mem 418MB, user 0.6s, sys 21.0s, output queue size 54
progress 35% @chr6:70000001, elapsed 0.3s, est remaining 0.6s, peak mem 418MB, user 0.7s, sys 24.4s, output queue size 110
progress 40% @chr6:130000001, elapsed 0.4s, est remaining 0.5s, peak mem 418MB, user 0.8s, sys 28.0s, output queue size 96
progress 45% @chr8:68000001, elapsed 0.4s, est remaining 0.5s, peak mem 418MB, user 0.9s, sys 31.3s, output queue size 34
progress 50% @chr9:33000001, elapsed 0.4s, est remaining 0.4s, peak mem 418MB, user 1.1s, sys 34.4s, output queue size 45
progress 55% @chr10:52000001, elapsed 0.5s, est remaining 0.4s, peak mem 418MB, user 1.2s, sys 37.7s, output queue size 43
progress 60% @chr12:14000001, elapsed 0.5s, est remaining 0.3s, peak mem 418MB, user 1.3s, sys 40.9s, output queue size 88
progress 65% @chr12:95000001, elapsed 0.6s, est remaining 0.3s, peak mem 418MB, user 1.4s, sys 44.3s, output queue size 95
progress 70% @chr14:85000001, elapsed 0.6s, est remaining 0.3s, peak mem 418MB, user 1.5s, sys 47.6s, output queue size 219
progress 75% @chr16:18000001, elapsed 0.6s, est remaining 0.2s, peak mem 418MB, user 1.6s, sys 50.4s, output queue size 44
progress 80% @chr16:80000001, elapsed 0.7s, est remaining 0.2s, peak mem 418MB, user 1.7s, sys 53.7s, output queue size 119
progress 85% @chr20:41000001, elapsed 0.7s, est remaining 0.1s, peak mem 418MB, user 1.9s, sys 56.9s, output queue size 75
progress 90% @chrX:37000001, elapsed 0.8s, est remaining 0.1s, peak mem 418MB, user 2.0s, sys 60.3s, output queue size 93
progress 95% @chrY:29000001, elapsed 0.8s, est remaining 0.0s, peak mem 418MB, user 2.1s, sys 63.8s, output queue size 252
progress 100% @HLA-A*02:259:1, elapsed 0.9s, est remaining 0.0s, peak mem 418MB, user 2.2s, sys 70.4s, output queue size 2174
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=89
input file size: 53230
output file size: 44181
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 561 calls 0.003 user 0.001 sys 0.016 real
"predict_filter": 187 calls 0.000 user 0.000 sys 0.010 real
advance: 3219322 calls 0.283 user 31.854 sys 33.325 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.003 sys 0.911 real
fetch_ref: 476 calls 0.000 user 0.002 sys 0.012 real
idle: 13357 calls 0.358 user 0.775 sys 5261.877 real
init: 1 calls 0.461 user 0.184 sys 60.959 real
overall: 439111680 mem 3.711 user 73.998 sys 120.196 real