Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/ce054e2e6ed4fc742bcbcfa387a720/HCC1395_tumor_vs_HCC1395_BL.tnseq.orientation_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/38/ce054e2e6ed4fc742bcbcfa387a720/HCC1395_tumor_vs_HCC1395_BL.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/cb3af164d0ef2105fbd64289cfd4a2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/ce054e2e6ed4fc742bcbcfa387a720/HCC1395_tumor_vs_HCC1395_BL.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/38/ce054e2e6ed4fc742bcbcfa387a720/HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/ce054e2e6ed4fc742bcbcfa387a720/HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/cb3af164d0ef2105fbd64289cfd4a2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/ce054e2e6ed4fc742bcbcfa387a720/HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz.stats
==> STAGING COMPLETE (10 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --max_event_count 5 -v HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz --contamination HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv --tumor_segments HCC1395_tumor_vs_HCC1395_BL.tnseq.segments --orientation_priors HCC1395_tumor_vs_HCC1395_BL.tnseq.orientation_data.tsv HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:173000001, elapsed 0.1s, est remaining 2.4s, peak mem 810MB, user 0.1s, sys 8.1s, output queue size 132
progress 10% @chr3:137000001, elapsed 0.2s, est remaining 1.8s, peak mem 810MB, user 0.2s, sys 19.3s, output queue size 293
progress 15% @chr1:215000001, elapsed 0.3s, est remaining 1.5s, peak mem 810MB, user 0.4s, sys 30.8s, output queue size 455
progress 20% @chr1:161000001, elapsed 0.3s, est remaining 1.2s, peak mem 810MB, user 0.8s, sys 41.0s, output queue size 616
progress 25% @chr6:1000001, elapsed 0.4s, est remaining 1.1s, peak mem 810MB, user 1.1s, sys 50.5s, output queue size 777
progress 30% @chr1:198000001, elapsed 0.4s, est remaining 1.0s, peak mem 810MB, user 1.5s, sys 68.3s, output queue size 938
progress 35% @chr7:107000001, elapsed 0.5s, est remaining 0.9s, peak mem 810MB, user 1.9s, sys 84.0s, output queue size 1100
progress 40% @chr5:14000001, elapsed 0.5s, est remaining 0.8s, peak mem 810MB, user 2.4s, sys 100.1s, output queue size 1261
progress 45% @chr9:13000001, elapsed 0.6s, est remaining 0.7s, peak mem 810MB, user 2.7s, sys 113.8s, output queue size 1186
progress 50% @chr11:65000001, elapsed 0.7s, est remaining 0.7s, peak mem 810MB, user 3.1s, sys 124.3s, output queue size 1347
progress 55% @chr12:1000001, elapsed 0.7s, est remaining 0.6s, peak mem 810MB, user 3.5s, sys 137.6s, output queue size 1509
progress 60% @chr13:50000001, elapsed 0.8s, est remaining 0.5s, peak mem 810MB, user 4.1s, sys 150.7s, output queue size 1672
progress 65% @chr14:78000001, elapsed 0.8s, est remaining 0.4s, peak mem 810MB, user 4.6s, sys 167.3s, output queue size 1832
progress 70% @chr16:52000001, elapsed 0.9s, est remaining 0.4s, peak mem 810MB, user 5.0s, sys 185.7s, output queue size 1994
progress 75% @chr18:14000001, elapsed 0.9s, est remaining 0.3s, peak mem 810MB, user 5.6s, sys 206.2s, output queue size 2155
progress 80% @chr2:114000001, elapsed 1.0s, est remaining 0.2s, peak mem 810MB, user 5.9s, sys 222.7s, output queue size 2319
progress 85% @chrX:44000001, elapsed 1.0s, est remaining 0.2s, peak mem 810MB, user 6.3s, sys 237.2s, output queue size 2481
progress 90% @chr20:1000001, elapsed 1.1s, est remaining 0.1s, peak mem 810MB, user 6.8s, sys 259.3s, output queue size 2758
progress 95% @chr19_KI270930v1_alt:1, elapsed 1.2s, est remaining 0.1s, peak mem 810MB, user 7.1s, sys 283.2s, output queue size 3152
progress 100% @HLA-DRB1*07:01:01:01:1, elapsed 1.3s, est remaining 0.0s, peak mem 813MB, user 7.4s, sys 333.0s, output queue size 6227
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: 71258
output file size: 60122
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 741 calls 0.025 user 0.014 sys 0.045 real
"predict_filter": 247 calls 0.020 user 0.047 sys 0.216 real
advance: 3219322 calls 0.316 user 110.598 sys 113.082 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.007 user 0.006 sys 1.426 real
fetch_ref: 648 calls 0.002 user 0.122 sys 0.423 real
idle: 20635 calls 1.748 user 2.805 sys 1030.001 real
init: 1 calls 0.464 user 0.452 sys 1.380 real
overall: 852619264 mem 10.347 user 346.119 sys 4.318 real