Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/cc498edcbd177a65a4d9715be2db1a/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.vcf.gz.tbi
  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/67/c73c1ad003f0119b8c398018a38289/.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/43/cc498edcbd177a65a4d9715be2db1a/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/cc498edcbd177a65a4d9715be2db1a/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/cc498edcbd177a65a4d9715be2db1a/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/c73c1ad003f0119b8c398018a38289/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/cc498edcbd177a65a4d9715be2db1a/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/cc498edcbd177a65a4d9715be2db1a/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.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 1136_5WB-N1-BDNA-1_B23KFG5LT4_1 --max_event_count 5 -v 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.vcf.gz --contamination 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.contamination_data.tsv --tumor_segments 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.segments --orientation_priors 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.orientation_data.tsv 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:194000001, elapsed 0.0s, est remaining 0.7s, peak mem 206MB, user 0.4s, sys 0.5s, output queue size 161
progress 10% @chr2:99000001, elapsed 0.1s, est remaining 0.6s, peak mem 207MB, user 0.7s, sys 1.1s, output queue size 316
progress 15% @chr3:2000001, elapsed 0.1s, est remaining 0.5s, peak mem 208MB, user 1.0s, sys 1.8s, output queue size 454
progress 20% @chr3:190000001, elapsed 0.1s, est remaining 0.5s, peak mem 209MB, user 1.3s, sys 2.5s, output queue size 615
progress 25% @chr4:90000001, elapsed 0.1s, est remaining 0.4s, peak mem 209MB, user 1.6s, sys 3.2s, output queue size 621
progress 30% @chr5:103000001, elapsed 0.2s, est remaining 0.4s, peak mem 209MB, user 1.9s, sys 3.8s, output queue size 783
progress 35% @chr6:99000001, elapsed 0.2s, est remaining 0.4s, peak mem 210MB, user 2.3s, sys 4.4s, output queue size 944
progress 40% @chr7:80000001, elapsed 0.2s, est remaining 0.3s, peak mem 211MB, user 2.8s, sys 5.0s, output queue size 1105
progress 45% @chr7:156000001, elapsed 0.2s, est remaining 0.3s, peak mem 211MB, user 3.1s, sys 5.7s, output queue size 1267
progress 50% @chr9:105000001, elapsed 0.3s, est remaining 0.3s, peak mem 211MB, user 3.4s, sys 6.4s, output queue size 1429
progress 55% @chr10:115000001, elapsed 0.3s, est remaining 0.2s, peak mem 211MB, user 3.7s, sys 6.9s, output queue size 1590
progress 60% @chr12:14000001, elapsed 0.3s, est remaining 0.2s, peak mem 211MB, user 4.0s, sys 7.5s, output queue size 1752
progress 65% @chr12:53000001, elapsed 0.3s, est remaining 0.2s, peak mem 212MB, user 4.3s, sys 8.1s, output queue size 481
progress 70% @chr14:95000001, elapsed 0.4s, est remaining 0.2s, peak mem 212MB, user 4.5s, sys 8.8s, output queue size 643
progress 75% @chr15:89000001, elapsed 0.4s, est remaining 0.1s, peak mem 214MB, user 4.8s, sys 9.4s, output queue size 804
progress 80% @chr18:37000001, elapsed 0.4s, est remaining 0.1s, peak mem 214MB, user 5.1s, sys 9.9s, output queue size 966
progress 85% @chr20:45000001, elapsed 0.4s, est remaining 0.1s, peak mem 215MB, user 5.4s, sys 10.4s, output queue size 1129
progress 90% @chrX:55000001, elapsed 0.5s, est remaining 0.1s, peak mem 215MB, user 5.8s, sys 10.9s, output queue size 1290
progress 95% @chrY:44000001, elapsed 0.5s, est remaining 0.0s, peak mem 215MB, user 6.2s, sys 11.3s, output queue size 1542
progress 100% @HLA-DQA1*01:03:01:01:1, elapsed 0.6s, est remaining 0.0s, peak mem 219MB, user 6.5s, sys 12.5s, output queue size 4876
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: 64 max 64
algo: TNfilter
license: sentieon:TNhaplotyper=64
input file size: 2770121
output file size: 2021296
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 59400 calls 1.598 user 0.058 sys 3.394 real
"predict_filter": 19800 calls 0.542 user 0.136 sys 1.145 real
advance: 3219322 calls 0.867 user 4.933 sys 10.041 real
done: 1 calls 0.012 user 0.000 sys 0.016 real
execute: 1 calls 0.000 user 0.010 sys 0.718 real
fetch_ref: 45732 calls 0.159 user 0.077 sys 0.665 real
idle: 13699 calls 2.912 user 0.204 sys 111.460 real
init: 1 calls 0.545 user 0.017 sys 1.023 real
overall: 230772736 mem 20.398 user 13.926 sys 2.649 real