Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/0aad105789b053834c54333166eaa1/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.contamination_data.tsv
  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/6b/3e862257159852283809195e02308a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/0aad105789b053834c54333166eaa1/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/0aad105789b053834c54333166eaa1/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.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/24/0aad105789b053834c54333166eaa1/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/0aad105789b053834c54333166eaa1/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/0aad105789b053834c54333166eaa1/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/3e862257159852283809195e02308a/.command.run
==> STAGING COMPLETE (10 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1 --max_event_count 5 -v 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.vcf.gz --contamination 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.contamination_data.tsv --tumor_segments 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.segments --orientation_priors 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.orientation_data.tsv 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq_tumor_only.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
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 1 licenses out of 192 requested for sentieon:TNhaplotyper
progress 5% @chr1:160000001, elapsed 0.1s, est remaining 2.1s, peak mem 519MB, user 0.1s, sys 0.0s, output queue size 1
progress 10% @chr2:72000001, elapsed 0.2s, est remaining 1.9s, peak mem 519MB, user 0.1s, sys 0.1s, output queue size 1
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progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.7s, peak mem 519MB, user 0.3s, sys 0.1s, output queue size 1
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progress 30% @chr5:85000001, elapsed 0.6s, est remaining 1.4s, peak mem 519MB, user 0.4s, sys 0.1s, output queue size 1
progress 35% @chr6:64000001, elapsed 0.7s, est remaining 1.3s, peak mem 519MB, user 0.5s, sys 0.2s, output queue size 1
progress 40% @chr7:54000001, elapsed 0.8s, est remaining 1.2s, peak mem 519MB, user 0.6s, sys 0.2s, output queue size 1
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progress 50% @chr9:72000001, elapsed 1.0s, est remaining 1.0s, peak mem 519MB, user 0.7s, sys 0.2s, output queue size 1
progress 55% @chr10:94000001, elapsed 1.1s, est remaining 0.9s, peak mem 519MB, user 0.8s, sys 0.3s, output queue size 1
progress 60% @chr11:121000001, elapsed 1.2s, est remaining 0.8s, peak mem 519MB, user 0.9s, sys 0.3s, output queue size 1
progress 65% @chr13:14000001, elapsed 1.4s, est remaining 0.7s, peak mem 519MB, user 1.0s, sys 0.3s, output queue size 1
progress 70% @chr14:60000001, elapsed 1.5s, est remaining 0.6s, peak mem 519MB, user 1.0s, sys 0.4s, output queue size 1
progress 75% @chr16:12000001, elapsed 1.7s, est remaining 0.6s, peak mem 519MB, user 1.2s, sys 0.4s, output queue size 1
progress 80% @chr17:83000001, elapsed 1.8s, est remaining 0.4s, peak mem 519MB, user 1.2s, sys 0.5s, output queue size 1
progress 85% @chr20:21000001, elapsed 1.9s, est remaining 0.3s, peak mem 519MB, user 1.3s, sys 0.5s, output queue size 1
progress 90% @chrX:20000001, elapsed 2.0s, est remaining 0.2s, peak mem 519MB, user 1.4s, sys 0.6s, output queue size 1
progress 95% @chrY:25000001, elapsed 2.1s, est remaining 0.1s, peak mem 519MB, user 1.4s, sys 0.6s, output queue size 1
progress 100% @HLA-DRB1*16:02:01:1, elapsed 2.3s, est remaining 0.0s, peak mem 519MB, user 1.5s, sys 0.7s, output queue size 1
Received only 1 licenses out of 191 requested for sentieon:TNhaplotyper
Received only 28 licenses out of 128 requested for sentieon:TNhaplotyper
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=15
input file size: 3151668
output file size: 2296348
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 64122 calls 0.720 user 0.000 sys 0.751 real
"predict_filter": 21374 calls 0.449 user 0.011 sys 0.422 real
advance: 3219322 calls 0.169 user 0.228 sys 0.519 real
done: 1 calls 0.008 user 0.000 sys 0.012 real
execute: 1 calls 0.001 user 0.000 sys 2.262 real
fetch_ref: 50400 calls 0.164 user 0.069 sys 0.375 real
idle: 195 calls 0.020 user 0.001 sys 3897.681 real
init: 1 calls 0.650 user 0.109 sys 903.084 real
overall: 544493568 mem 4.716 user 1.288 sys 1020.385 real