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/70/561c5b76c899c0e0cb74903b36a6f9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/3ef8e729502d74ba9fecfdd38cd140/custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/3ef8e729502d74ba9fecfdd38cd140/custom_Sig_18_tumor_normal.tnseq.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/12/3ef8e729502d74ba9fecfdd38cd140/custom_Sig_18_tumor_normal.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/3ef8e729502d74ba9fecfdd38cd140/custom_Sig_18_tumor_normal.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/3ef8e729502d74ba9fecfdd38cd140/custom_Sig_18_tumor_normal.tnseq.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/561c5b76c899c0e0cb74903b36a6f9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/3ef8e729502d74ba9fecfdd38cd140/custom_Sig_18_tumor_normal.tnseq.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_tissue --normal_sample Sig_18_Blood --max_event_count 5 -v custom_Sig_18_tumor_normal.tnseq.vcf.gz --contamination custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv --tumor_segments custom_Sig_18_tumor_normal.tnseq.segments --orientation_priors custom_Sig_18_tumor_normal.tnseq.orientation_data.tsv custom_Sig_18_tumor_normal.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:169000001, elapsed 0.1s, est remaining 2.0s, peak mem 813MB, user 0.1s, sys 2.9s, output queue size 146
progress 10% @chr3:111000001, elapsed 0.2s, est remaining 1.8s, peak mem 813MB, user 0.2s, sys 9.0s, output queue size 302
progress 15% @chr4:102000001, elapsed 0.3s, est remaining 1.7s, peak mem 813MB, user 0.3s, sys 16.0s, output queue size 464
progress 20% @chr5:66000001, elapsed 0.4s, est remaining 1.5s, peak mem 813MB, user 0.5s, sys 25.1s, output queue size 611
progress 25% @chr6:48000001, elapsed 0.5s, est remaining 1.4s, peak mem 813MB, user 0.6s, sys 34.9s, output queue size 773
progress 30% @chr7:5000001, elapsed 0.6s, est remaining 1.3s, peak mem 813MB, user 0.9s, sys 48.7s, output queue size 930
progress 35% @chr7:150000001, elapsed 0.6s, est remaining 1.2s, peak mem 813MB, user 1.2s, sys 64.3s, output queue size 1088
progress 40% @chr9:36000001, elapsed 0.7s, est remaining 1.1s, peak mem 813MB, user 1.4s, sys 76.1s, output queue size 1239
progress 45% @chr10:72000001, elapsed 0.8s, est remaining 0.9s, peak mem 813MB, user 1.7s, sys 86.4s, output queue size 1400
progress 50% @chr11:34000001, elapsed 0.8s, est remaining 0.8s, peak mem 813MB, user 2.1s, sys 97.8s, output queue size 1547
progress 55% @chr12:52000001, elapsed 0.9s, est remaining 0.7s, peak mem 813MB, user 2.6s, sys 112.4s, output queue size 1710
progress 60% @chr13:99000001, elapsed 0.9s, est remaining 0.6s, peak mem 813MB, user 3.1s, sys 127.5s, output queue size 1871
progress 65% @chr14:81000001, elapsed 1.0s, est remaining 0.5s, peak mem 813MB, user 3.9s, sys 141.2s, output queue size 2032
progress 70% @chr15:17000001, elapsed 1.1s, est remaining 0.5s, peak mem 813MB, user 4.3s, sys 155.1s, output queue size 2194
progress 75% @chr18:11000001, elapsed 1.1s, est remaining 0.4s, peak mem 813MB, user 5.0s, sys 169.1s, output queue size 2333
progress 80% @chr19:39000001, elapsed 1.2s, est remaining 0.3s, peak mem 813MB, user 5.7s, sys 187.2s, output queue size 2495
progress 85% @chrX:56000001, elapsed 1.2s, est remaining 0.2s, peak mem 813MB, user 6.2s, sys 203.7s, output queue size 2666
progress 90% @chr18:8000001, elapsed 1.3s, est remaining 0.1s, peak mem 813MB, user 6.5s, sys 217.2s, output queue size 2896
progress 95% @chrX:154000001, elapsed 1.4s, est remaining 0.1s, peak mem 813MB, user 6.7s, sys 222.1s, output queue size 3318
progress 100% @HLA-DQB1*06:09:01:1, elapsed 1.6s, est remaining 0.0s, peak mem 813MB, user 6.9s, sys 232.8s, output queue size 637
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: 95376
output file size: 77088
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 1065 calls 0.006 user 0.000 sys 0.036 real
"predict_filter": 355 calls 0.040 user 0.025 sys 0.072 real
advance: 3219322 calls 0.857 user 106.011 sys 103.633 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.011 user 0.001 sys 1.873 real
fetch_ref: 876 calls 0.000 user 0.025 sys 0.035 real
idle: 20633 calls 0.586 user 0.137 sys 747.316 real
init: 1 calls 0.428 user 0.144 sys 0.764 real
overall: 852623360 mem 8.923 user 236.833 sys 3.779 real