Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/7a6fcdcc394a8b37b2755bc500d1fd/HCC1395_BL.tnseq_tumor_only.vcf.gz.stats
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/7a6fcdcc394a8b37b2755bc500d1fd/HCC1395_BL.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/4e/e281ba6d80f4e374217f454139d64f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/7a6fcdcc394a8b37b2755bc500d1fd/HCC1395_BL.tnseq_tumor_only.segments
  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/ea/7a6fcdcc394a8b37b2755bc500d1fd/HCC1395_BL.tnseq_tumor_only.contamination_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/7a6fcdcc394a8b37b2755bc500d1fd/HCC1395_BL.tnseq_tumor_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/7a6fcdcc394a8b37b2755bc500d1fd/HCC1395_BL.tnseq_tumor_only.orientation_data.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/e281ba6d80f4e374217f454139d64f/.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 HCC1395_BL --max_event_count 5 -v HCC1395_BL.tnseq_tumor_only.vcf.gz --contamination HCC1395_BL.tnseq_tumor_only.contamination_data.tsv --tumor_segments HCC1395_BL.tnseq_tumor_only.segments --orientation_priors HCC1395_BL.tnseq_tumor_only.orientation_data.tsv HCC1395_BL.tnseq_tumor_only.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:32000001, elapsed 0.1s, est remaining 1.0s, peak mem 418MB, user 0.1s, sys 2.4s, output queue size 101
progress 10% @chr1:78000001, elapsed 0.1s, est remaining 0.9s, peak mem 418MB, user 0.4s, sys 8.9s, output queue size 262
progress 15% @chr1:91000001, elapsed 0.1s, est remaining 0.7s, peak mem 418MB, user 0.9s, sys 15.6s, output queue size 393
progress 20% @chr3:170000001, elapsed 0.2s, est remaining 0.6s, peak mem 418MB, user 1.4s, sys 21.0s, output queue size 506
progress 25% @chr4:144000001, elapsed 0.2s, est remaining 0.6s, peak mem 418MB, user 1.8s, sys 26.3s, output queue size 601
progress 30% @chr5:114000001, elapsed 0.2s, est remaining 0.5s, peak mem 418MB, user 2.3s, sys 31.5s, output queue size 763
progress 35% @chr6:91000001, elapsed 0.3s, est remaining 0.5s, peak mem 418MB, user 2.8s, sys 36.6s, output queue size 923
progress 40% @chr6:34000001, elapsed 0.3s, est remaining 0.4s, peak mem 418MB, user 3.4s, sys 41.7s, output queue size 1085
progress 45% @chr8:84000001, elapsed 0.3s, est remaining 0.4s, peak mem 418MB, user 3.9s, sys 47.0s, output queue size 257
progress 50% @chr7:24000001, elapsed 0.4s, est remaining 0.4s, peak mem 418MB, user 4.3s, sys 51.9s, output queue size 418
progress 55% @chr10:128000001, elapsed 0.4s, est remaining 0.3s, peak mem 418MB, user 4.8s, sys 57.1s, output queue size 579
progress 60% @chr12:29000001, elapsed 0.4s, est remaining 0.3s, peak mem 418MB, user 5.3s, sys 62.3s, output queue size 741
progress 65% @chr13:25000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 5.7s, sys 67.6s, output queue size 903
progress 70% @chr14:91000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 6.1s, sys 72.1s, output queue size 1065
progress 75% @chr16:54000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 6.5s, sys 76.7s, output queue size 1227
progress 80% @chr19:26000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 6.8s, sys 80.5s, output queue size 1388
progress 85% @chr20:57000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 7.1s, sys 84.7s, output queue size 1551
progress 90% @chrX:45000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 7.7s, sys 89.6s, output queue size 1712
progress 95% @chr6_KB021644v2_alt:1, elapsed 0.7s, est remaining 0.0s, peak mem 418MB, user 8.1s, sys 94.4s, output queue size 2092
progress 100% @HLA-C*05:01:01:02:1, elapsed 0.7s, est remaining 0.0s, peak mem 418MB, user 8.3s, sys 104.4s, output queue size 5298
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: 192 max 192
algo: TNfilter
license: sentieon:TNhaplotyper=192
input file size: 58751
output file size: 46435
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 684 calls 0.000 user 0.000 sys 0.015 real
"predict_filter": 228 calls 0.010 user 0.000 sys 0.024 real
advance: 3219322 calls 0.531 user 41.501 sys 49.056 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.008 user 0.000 sys 0.794 real
fetch_ref: 672 calls 0.001 user 0.039 sys 0.018 real
idle: 20057 calls 0.698 user 0.879 sys 406.322 real
init: 1 calls 0.253 user 0.048 sys 1.067 real
overall: 439111680 mem 9.844 user 108.936 sys 3.143 real