Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/189fdd7848848cea301103468fcf38/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/53/189fdd7848848cea301103468fcf38/HCC1395_tumor_vs_HCC1395_BL.tnseq.segments
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/ee8b8f45d66dd2bda7583dd0638ea6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/189fdd7848848cea301103468fcf38/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/53/189fdd7848848cea301103468fcf38/HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/189fdd7848848cea301103468fcf38/HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/ee8b8f45d66dd2bda7583dd0638ea6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/189fdd7848848cea301103468fcf38/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% @chr1:180000001, elapsed 0.1s, est remaining 1.0s, peak mem 286MB, user 0.2s, sys 0.7s, output queue size 141
progress 10% @chr2:98000001, elapsed 0.1s, est remaining 0.7s, peak mem 286MB, user 0.4s, sys 2.3s, output queue size 302
progress 15% @chr3:32000001, elapsed 0.1s, est remaining 0.6s, peak mem 286MB, user 0.5s, sys 4.2s, output queue size 464
progress 20% @chr3:177000001, elapsed 0.1s, est remaining 0.6s, peak mem 286MB, user 0.7s, sys 5.9s, output queue size 626
progress 25% @chr4:147000001, elapsed 0.2s, est remaining 0.6s, peak mem 287MB, user 0.8s, sys 7.5s, output queue size 786
progress 30% @chr4:161000001, elapsed 0.3s, est remaining 0.6s, peak mem 288MB, user 0.9s, sys 7.9s, output queue size 948
progress 35% @chr6:167000001, elapsed 0.3s, est remaining 0.5s, peak mem 288MB, user 1.0s, sys 8.9s, output queue size 1109
progress 40% @chr7:99000001, elapsed 0.3s, est remaining 0.5s, peak mem 288MB, user 1.1s, sys 10.2s, output queue size 1271
progress 45% @chr5:45000001, elapsed 0.4s, est remaining 0.5s, peak mem 288MB, user 1.2s, sys 11.0s, output queue size 1433
progress 50% @chr10:6000001, elapsed 0.4s, est remaining 0.4s, peak mem 288MB, user 1.4s, sys 12.2s, output queue size 1594
progress 55% @chr11:40000001, elapsed 0.4s, est remaining 0.4s, peak mem 288MB, user 1.5s, sys 13.6s, output queue size 1755
progress 60% @chr12:48000001, elapsed 0.5s, est remaining 0.3s, peak mem 288MB, user 1.6s, sys 15.1s, output queue size 1917
progress 65% @chr13:33000001, elapsed 0.5s, est remaining 0.3s, peak mem 288MB, user 1.7s, sys 16.8s, output queue size 2047
progress 70% @chr15:18000001, elapsed 0.5s, est remaining 0.2s, peak mem 288MB, user 1.8s, sys 18.5s, output queue size 2208
progress 75% @chr16:33000001, elapsed 0.5s, est remaining 0.2s, peak mem 288MB, user 1.9s, sys 20.0s, output queue size 300
progress 80% @chr19:34000001, elapsed 0.6s, est remaining 0.1s, peak mem 288MB, user 2.0s, sys 20.9s, output queue size 462
progress 85% @chr20:49000001, elapsed 0.6s, est remaining 0.1s, peak mem 288MB, user 2.2s, sys 21.7s, output queue size 624
progress 90% @chr18:15000001, elapsed 0.7s, est remaining 0.1s, peak mem 288MB, user 2.5s, sys 22.5s, output queue size 786
progress 95% @chr21:26000001, elapsed 0.7s, est remaining 0.0s, peak mem 288MB, user 2.7s, sys 23.7s, output queue size 1046
progress 100% @HLA-DRB1*15:01:01:03:1, elapsed 1.4s, est remaining 0.0s, peak mem 288MB, user 3.0s, sys 25.8s, output queue size 31
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 128 max 128
algo: TNfilter
license: sentieon:TNhaplotyper=128
input file size: 78467
output file size: 63293
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 861 calls 0.001 user 0.000 sys 0.033 real
"predict_filter": 287 calls 0.024 user 0.007 sys 0.036 real
advance: 3219322 calls 0.529 user 10.337 sys 13.913 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.004 sys 1.390 real
fetch_ref: 768 calls 0.005 user 0.021 sys 0.215 real
idle: 19865 calls 0.462 user 0.084 sys 199.115 real
init: 1 calls 0.214 user 0.126 sys 0.502 real
overall: 302272512 mem 4.066 user 26.934 sys 3.015 real