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/d3/481df01076e99e812becfcadf45d63/869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/71514cd749d362804a30ebf6fad993/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/481df01076e99e812becfcadf45d63/869_XA6-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/d3/481df01076e99e812becfcadf45d63/869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz.stats Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/481df01076e99e812becfcadf45d63/869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/481df01076e99e812becfcadf45d63/869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/71514cd749d362804a30ebf6fad993/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/481df01076e99e812becfcadf45d63/869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz ==> STAGING COMPLETE (10 inputs) cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample 869_XA6-N1-BDNA-1_A23FG3YLT4_1 --max_event_count 5 -v 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz --contamination 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv --tumor_segments 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments --orientation_priors 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.filtered.vcf.gz This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:243000001, elapsed 0.1s, est remaining 1.4s, peak mem 496MB, user 0.4s, sys 3.2s, output queue size 161 progress 10% @chr2:180000001, elapsed 0.1s, est remaining 1.0s, peak mem 496MB, user 0.8s, sys 6.5s, output queue size 323 progress 15% @chr2:236000001, elapsed 0.2s, est remaining 1.0s, peak mem 496MB, user 1.2s, sys 9.8s, output queue size 473 progress 20% @chr4:51000001, elapsed 0.2s, est remaining 0.9s, peak mem 496MB, user 1.6s, sys 13.0s, output queue size 617 progress 25% @chr3:141000001, elapsed 0.3s, est remaining 0.8s, peak mem 496MB, user 2.0s, sys 16.7s, output queue size 765 progress 30% @chr5:120000001, elapsed 0.3s, est remaining 0.7s, peak mem 496MB, user 2.4s, sys 20.4s, output queue size 787 progress 35% @chr5:143000001, elapsed 0.3s, est remaining 0.6s, peak mem 498MB, user 2.8s, sys 24.0s, output queue size 283 progress 40% @chr8:16000001, elapsed 0.4s, est remaining 0.6s, peak mem 499MB, user 3.2s, sys 27.8s, output queue size 444 progress 45% @chr9:24000001, elapsed 0.4s, est remaining 0.5s, peak mem 499MB, user 3.6s, sys 31.8s, output queue size 606 progress 50% @chr10:38000001, elapsed 0.5s, est remaining 0.5s, peak mem 499MB, user 4.0s, sys 35.8s, output queue size 768 progress 55% @chr10:19000001, elapsed 0.5s, est remaining 0.4s, peak mem 499MB, user 4.4s, sys 39.6s, output queue size 930 progress 60% @chr11:115000001, elapsed 0.6s, est remaining 0.4s, peak mem 499MB, user 4.7s, sys 43.4s, output queue size 1092 progress 65% @chr13:112000001, elapsed 0.6s, est remaining 0.3s, peak mem 499MB, user 5.2s, sys 47.3s, output queue size 1253 progress 70% @chr13:104000001, elapsed 0.7s, est remaining 0.3s, peak mem 501MB, user 5.6s, sys 50.7s, output queue size 1415 progress 75% @chr15:81000001, elapsed 0.7s, est remaining 0.2s, peak mem 501MB, user 5.9s, sys 52.9s, output queue size 1576 progress 80% @chr19:21000001, elapsed 0.8s, est remaining 0.2s, peak mem 502MB, user 6.3s, sys 56.1s, output queue size 1738 progress 85% @chr22:10000001, elapsed 0.8s, est remaining 0.1s, peak mem 505MB, user 6.8s, sys 59.6s, output queue size 1900 progress 90% @chrX:112000001, elapsed 0.9s, est remaining 0.1s, peak mem 505MB, user 7.0s, sys 63.3s, output queue size 2062 progress 95% @chr17_GL000258v2_alt:1, elapsed 0.9s, est remaining 0.0s, peak mem 505MB, user 7.1s, sys 67.2s, output queue size 2589 progress 100% @HLA-DRB1*10:01:01:1, elapsed 1.0s, est remaining 0.0s, peak mem 507MB, user 7.6s, sys 71.4s, output queue size 5648 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: 3209417 output file size: 2244444 reads: 0 contig: 3367 intervals 3217346917 bases "learn_filter": 64587 calls 10.733 user 0.257 sys 19.240 real "predict_filter": 21529 calls 0.560 user 0.622 sys 1.854 real advance: 3219322 calls 1.407 user 30.338 sys 50.475 real done: 1 calls 0.006 user 0.008 sys 0.014 real execute: 1 calls 0.005 user 0.003 sys 1.211 real fetch_ref: 53160 calls 0.475 user 0.448 sys 5.994 real idle: 20050 calls 7.008 user 0.496 sys 448.617 real init: 1 calls 0.725 user 0.255 sys 1.466 real overall: 531918848 mem 38.657 user 75.310 sys 3.672 real