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/93/0d8349b5a5fbc22468290854a5adba/Sig_18_Blood.tnseq_tumor_only.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/191dc6da61430acecf5fe32d1342ed/.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/93/0d8349b5a5fbc22468290854a5adba/Sig_18_Blood.tnseq_tumor_only.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/191dc6da61430acecf5fe32d1342ed/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/0d8349b5a5fbc22468290854a5adba/Sig_18_Blood.tnseq_tumor_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/0d8349b5a5fbc22468290854a5adba/Sig_18_Blood.tnseq_tumor_only.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/0d8349b5a5fbc22468290854a5adba/Sig_18_Blood.tnseq_tumor_only.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/0d8349b5a5fbc22468290854a5adba/Sig_18_Blood.tnseq_tumor_only.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 --max_event_count 5 -v Sig_18_Blood.tnseq_tumor_only.vcf.gz --contamination Sig_18_Blood.tnseq_tumor_only.contamination_data.tsv --tumor_segments Sig_18_Blood.tnseq_tumor_only.segments --orientation_priors Sig_18_Blood.tnseq_tumor_only.orientation_data.tsv Sig_18_Blood.tnseq_tumor_only.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr3:1, elapsed 0.1s, est remaining 2.2s, peak mem 807MB, user 0.1s, sys 3.7s, output queue size 147
progress 10% @chr3:104000001, elapsed 0.2s, est remaining 2.1s, peak mem 807MB, user 0.2s, sys 14.3s, output queue size 308
progress 15% @chr2:39000001, elapsed 0.3s, est remaining 1.9s, peak mem 807MB, user 0.4s, sys 30.1s, output queue size 470
progress 20% @chr4:127000001, elapsed 0.4s, est remaining 1.7s, peak mem 807MB, user 0.6s, sys 45.6s, output queue size 631
progress 25% @chr5:112000001, elapsed 0.5s, est remaining 1.6s, peak mem 807MB, user 0.8s, sys 60.5s, output queue size 719
progress 30% @chr6:112000001, elapsed 0.6s, est remaining 1.4s, peak mem 807MB, user 1.1s, sys 76.2s, output queue size 880
progress 35% @chr7:84000001, elapsed 0.7s, est remaining 1.3s, peak mem 807MB, user 1.3s, sys 92.1s, output queue size 1041
progress 40% @chr8:124000001, elapsed 0.8s, est remaining 1.2s, peak mem 807MB, user 1.5s, sys 105.5s, output queue size 1176
progress 45% @chr9:125000001, elapsed 0.9s, est remaining 1.1s, peak mem 807MB, user 1.8s, sys 120.2s, output queue size 1337
progress 50% @chr10:86000001, elapsed 1.0s, est remaining 1.0s, peak mem 807MB, user 1.9s, sys 134.0s, output queue size 1499
progress 55% @chr12:126000001, elapsed 1.1s, est remaining 0.9s, peak mem 807MB, user 2.2s, sys 147.9s, output queue size 1661
progress 60% @chr13:51000001, elapsed 1.2s, est remaining 0.8s, peak mem 807MB, user 2.3s, sys 162.3s, output queue size 1823
progress 65% @chr13:104000001, elapsed 1.3s, est remaining 0.7s, peak mem 807MB, user 2.5s, sys 176.6s, output queue size 1984
progress 70% @chr8:74000001, elapsed 1.4s, est remaining 0.6s, peak mem 807MB, user 2.8s, sys 189.8s, output queue size 2147
progress 75% @chr17:80000001, elapsed 1.4s, est remaining 0.5s, peak mem 807MB, user 3.2s, sys 202.9s, output queue size 2308
progress 80% @chrX:26000001, elapsed 1.5s, est remaining 0.4s, peak mem 807MB, user 3.5s, sys 216.5s, output queue size 2455
progress 85% @chrX:90000001, elapsed 1.6s, est remaining 0.3s, peak mem 807MB, user 3.8s, sys 231.4s, output queue size 2624
progress 90% @chr16_GL383556v1_alt:1, elapsed 1.7s, est remaining 0.2s, peak mem 807MB, user 4.1s, sys 247.6s, output queue size 3029
progress 95% @chrX:152000001, elapsed 1.8s, est remaining 0.1s, peak mem 807MB, user 4.4s, sys 263.2s, output queue size 3825
progress 100% @HLA-DRB1*15:01:01:04:1, elapsed 1.9s, est remaining 0.0s, peak mem 807MB, user 4.7s, sys 275.2s, output queue size 587
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 384 max 384
algo: TNfilter
license: sentieon:TNhaplotyper=384
input file size: 57860
output file size: 46927
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 642 calls 0.000 user 0.000 sys 0.014 real
"predict_filter": 214 calls 0.003 user 0.013 sys 0.029 real
advance: 3219322 calls 0.467 user 129.597 sys 171.248 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.006 sys 2.169 real
fetch_ref: 624 calls 0.000 user 0.040 sys 0.423 real
idle: 20633 calls 0.720 user 0.535 sys 853.905 real
init: 1 calls 0.368 user 0.159 sys 0.819 real
overall: 846409728 mem 6.277 user 284.987 sys 4.480 real