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/77/af1377d933589826e521e86a718ee3/869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/af1377d933589826e521e86a718ee3/869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/af1377d933589826e521e86a718ee3/869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/efb0e8036b985dc813ea0c8d053a3c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/af1377d933589826e521e86a718ee3/869_HUS-N1-BDNA-1_A23FG3YLT4_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.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/af1377d933589826e521e86a718ee3/869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/af1377d933589826e521e86a718ee3/869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/efb0e8036b985dc813ea0c8d053a3c/.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 869_HUS-N1-BDNA-1_A23FG3YLT4_1 --max_event_count 5 -v 869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz --contamination 869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv --tumor_segments 869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments --orientation_priors 869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv 869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:156000001, elapsed 0.1s, est remaining 1.0s, peak mem 163MB, user 0.3s, sys 0.2s, output queue size 160
progress 10% @chr2:61000001, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.9s, sys 0.8s, output queue size 203
progress 15% @chr3:1, elapsed 0.1s, est remaining 0.6s, peak mem 164MB, user 1.5s, sys 1.1s, output queue size 175
progress 20% @chr3:140000001, elapsed 0.1s, est remaining 0.5s, peak mem 164MB, user 2.2s, sys 1.5s, output queue size 336
progress 25% @chr4:141000001, elapsed 0.2s, est remaining 0.5s, peak mem 164MB, user 2.9s, sys 1.9s, output queue size 497
progress 30% @chr5:109000001, elapsed 0.2s, est remaining 0.4s, peak mem 164MB, user 3.4s, sys 2.3s, output queue size 107
progress 35% @chr6:77000001, elapsed 0.2s, est remaining 0.4s, peak mem 165MB, user 4.0s, sys 2.6s, output queue size 268
progress 40% @chr7:72000001, elapsed 0.2s, est remaining 0.4s, peak mem 165MB, user 4.6s, sys 2.8s, output queue size 429
progress 45% @chr8:65000001, elapsed 0.3s, est remaining 0.3s, peak mem 165MB, user 5.2s, sys 3.0s, output queue size 590
progress 50% @chr9:71000001, elapsed 0.3s, est remaining 0.3s, peak mem 165MB, user 6.0s, sys 3.2s, output queue size 753
progress 55% @chr10:103000001, elapsed 0.3s, est remaining 0.3s, peak mem 166MB, user 6.9s, sys 3.5s, output queue size 914
progress 60% @chr12:25000001, elapsed 0.4s, est remaining 0.2s, peak mem 167MB, user 7.5s, sys 3.7s, output queue size 1075
progress 65% @chr13:32000001, elapsed 0.4s, est remaining 0.2s, peak mem 167MB, user 8.1s, sys 3.8s, output queue size 1237
progress 70% @chr14:86000001, elapsed 0.4s, est remaining 0.2s, peak mem 167MB, user 8.5s, sys 4.0s, output queue size 1398
progress 75% @chr12:3000001, elapsed 0.5s, est remaining 0.2s, peak mem 167MB, user 9.1s, sys 4.4s, output queue size 1561
progress 80% @chr18:28000001, elapsed 0.5s, est remaining 0.1s, peak mem 168MB, user 9.7s, sys 4.6s, output queue size 1723
progress 85% @chr20:29000001, elapsed 0.5s, est remaining 0.1s, peak mem 168MB, user 10.4s, sys 4.8s, output queue size 1885
progress 90% @chrX:42000001, elapsed 0.6s, est remaining 0.1s, peak mem 170MB, user 11.0s, sys 5.0s, output queue size 2047
progress 95% @chr3_GL000221v1_random:1, elapsed 0.6s, est remaining 0.0s, peak mem 170MB, user 11.6s, sys 5.2s, output queue size 2224
progress 100% @HLA-DRB1*15:03:01:02:1, elapsed 0.8s, est remaining 0.0s, peak mem 174MB, user 12.0s, sys 6.3s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 48 max 48
algo: TNfilter
license: sentieon:TNhaplotyper=48
input file size: 2985219
output file size: 2144164
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 61311 calls 3.702 user 0.022 sys 4.750 real
"predict_filter": 20437 calls 1.222 user 0.095 sys 1.881 real
advance: 3219322 calls 1.892 user 2.278 sys 5.295 real
done: 1 calls 0.018 user 0.000 sys 0.020 real
execute: 1 calls 0.010 user 0.000 sys 1.084 real
fetch_ref: 49124 calls 0.541 user 0.133 sys 1.019 real
idle: 2504 calls 1.896 user 0.081 sys 126.396 real
init: 1 calls 0.851 user 0.049 sys 2.243 real
overall: 183910400 mem 36.962 user 7.256 sys 4.131 real