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/a1/560470717ee1d02e81f587dcea9a63/Sig_18_Blood.tnseq_tumor_only.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/26fa874afbfaa53b4bf0df516f3e3e/.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/a1/560470717ee1d02e81f587dcea9a63/Sig_18_Blood.tnseq_tumor_only.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/26fa874afbfaa53b4bf0df516f3e3e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/560470717ee1d02e81f587dcea9a63/Sig_18_Blood.tnseq_tumor_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/560470717ee1d02e81f587dcea9a63/Sig_18_Blood.tnseq_tumor_only.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/560470717ee1d02e81f587dcea9a63/Sig_18_Blood.tnseq_tumor_only.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/560470717ee1d02e81f587dcea9a63/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% @chr1:245000001, elapsed 0.1s, est remaining 1.4s, peak mem 816MB, user 0.1s, sys 1.0s, output queue size 161
progress 10% @chr2:182000001, elapsed 0.2s, est remaining 1.7s, peak mem 816MB, user 0.3s, sys 4.1s, output queue size 306
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progress 25% @chr6:32000001, elapsed 0.4s, est remaining 1.1s, peak mem 816MB, user 1.0s, sys 24.1s, output queue size 786
progress 30% @chr7:21000001, elapsed 0.4s, est remaining 0.9s, peak mem 816MB, user 1.5s, sys 32.8s, output queue size 947
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progress 50% @chr10:131000001, elapsed 0.6s, est remaining 0.6s, peak mem 816MB, user 3.4s, sys 74.8s, output queue size 1592
progress 55% @chr12:25000001, elapsed 0.6s, est remaining 0.5s, peak mem 816MB, user 3.8s, sys 84.4s, output queue size 1755
progress 60% @chr3:182000001, elapsed 0.7s, est remaining 0.5s, peak mem 816MB, user 4.2s, sys 98.2s, output queue size 1917
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progress 70% @chr15:101000001, elapsed 0.8s, est remaining 0.4s, peak mem 816MB, user 4.9s, sys 128.6s, output queue size 2240
progress 75% @chr18:77000001, elapsed 0.9s, est remaining 0.3s, peak mem 816MB, user 5.3s, sys 144.6s, output queue size 1779
progress 80% @chr18:14000001, elapsed 0.9s, est remaining 0.2s, peak mem 816MB, user 5.8s, sys 160.6s, output queue size 1941
progress 85% @chrX:84000001, elapsed 1.0s, est remaining 0.2s, peak mem 816MB, user 6.3s, sys 176.9s, output queue size 2106
progress 90% @chrY:7000001, elapsed 1.0s, est remaining 0.1s, peak mem 816MB, user 6.7s, sys 197.8s, output queue size 2395
progress 95% @chrX:100000001, elapsed 1.1s, est remaining 0.1s, peak mem 816MB, user 7.2s, sys 221.5s, output queue size 2822
progress 100% @HLA-C*03:46:1, elapsed 1.2s, est remaining 0.0s, peak mem 816MB, user 7.6s, sys 260.6s, output queue size 5849
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 0.005 user 0.001 sys 0.018 real
"predict_filter": 214 calls 0.011 user 0.040 sys 0.175 real
advance: 3219322 calls 0.363 user 96.765 sys 97.675 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.012 sys 1.313 real
fetch_ref: 624 calls 0.009 user 0.100 sys 0.428 real
idle: 20752 calls 1.754 user 2.232 sys 1225.448 real
init: 1 calls 0.878 user 0.466 sys 2.024 real
overall: 855838720 mem 11.189 user 270.681 sys 4.583 real