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/df/180aa541742c609b42646afa2d33e5/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/dd771d49bb2ef4fecfd8375f12e4af/positive_somatic_control_2.tnseq.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/de/dd771d49bb2ef4fecfd8375f12e4af/positive_somatic_control_2.tnseq.orientation_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/dd771d49bb2ef4fecfd8375f12e4af/positive_somatic_control_2.tnseq.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/dd771d49bb2ef4fecfd8375f12e4af/positive_somatic_control_2.tnseq.vcf.gz.tbi Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/dd771d49bb2ef4fecfd8375f12e4af/positive_somatic_control_2.tnseq.vcf.gz.stats Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/180aa541742c609b42646afa2d33e5/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/dd771d49bb2ef4fecfd8375f12e4af/positive_somatic_control_2.tnseq.contamination_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 reference-NA12878 --max_event_count 5 -v positive_somatic_control_2.tnseq.vcf.gz --contamination positive_somatic_control_2.tnseq.contamination_data.tsv --tumor_segments positive_somatic_control_2.tnseq.segments --orientation_priors positive_somatic_control_2.tnseq.orientation_data.tsv positive_somatic_control_2.tnseq.filtered.vcf.gz This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:198000001, elapsed 0.1s, est remaining 1.7s, peak mem 810MB, user 0.1s, sys 2.7s, output queue size 118 progress 10% @chr3:159000001, elapsed 0.2s, est remaining 1.8s, peak mem 810MB, user 0.1s, sys 11.8s, output queue size 256 progress 15% @chr4:103000001, elapsed 0.3s, est remaining 1.4s, peak mem 810MB, user 0.4s, sys 27.5s, output queue size 418 progress 20% @chr2:23000001, elapsed 0.3s, est remaining 1.2s, peak mem 810MB, user 0.7s, sys 44.6s, output queue size 579 progress 25% @chr5:1000001, elapsed 0.4s, est remaining 1.1s, peak mem 810MB, user 1.1s, sys 60.2s, output queue size 656 progress 30% @chr6:13000001, elapsed 0.4s, est remaining 1.0s, peak mem 810MB, user 1.6s, sys 68.8s, output queue size 817 progress 35% @chr2:227000001, elapsed 0.5s, est remaining 0.9s, peak mem 810MB, user 2.1s, sys 81.4s, output queue size 979 progress 40% @chr8:49000001, elapsed 0.5s, est remaining 0.8s, peak mem 810MB, user 2.7s, sys 96.8s, output queue size 1140 progress 45% @chr9:116000001, elapsed 0.6s, est remaining 0.7s, peak mem 810MB, user 3.1s, sys 108.4s, output queue size 1302 progress 50% @chr11:77000001, elapsed 0.7s, est remaining 0.7s, peak mem 810MB, user 3.7s, sys 120.9s, output queue size 1464 progress 55% @chr9:29000001, elapsed 0.7s, est remaining 0.6s, peak mem 810MB, user 4.4s, sys 135.9s, output queue size 1625 progress 60% @chr13:55000001, elapsed 0.8s, est remaining 0.5s, peak mem 810MB, user 4.9s, sys 149.2s, output queue size 1787 progress 65% @chr10:48000001, elapsed 0.8s, est remaining 0.4s, peak mem 810MB, user 5.5s, sys 161.7s, output queue size 1949 progress 70% @chr16:44000001, elapsed 0.9s, est remaining 0.4s, peak mem 810MB, user 6.1s, sys 175.4s, output queue size 2110 progress 75% @chr18:55000001, elapsed 0.9s, est remaining 0.3s, peak mem 810MB, user 6.5s, sys 189.3s, output queue size 2273 progress 80% @chr20:58000001, elapsed 1.0s, est remaining 0.3s, peak mem 810MB, user 7.1s, sys 205.5s, output queue size 2434 progress 85% @chr13:91000001, elapsed 1.1s, est remaining 0.2s, peak mem 810MB, user 7.6s, sys 223.2s, output queue size 2602 progress 90% @chrX:138000001, elapsed 1.2s, est remaining 0.1s, peak mem 810MB, user 8.1s, sys 240.7s, output queue size 2941 progress 95% @chrX:57000001, elapsed 1.2s, est remaining 0.1s, peak mem 810MB, user 8.4s, sys 256.8s, output queue size 3343 progress 100% @HLA-DRB1*10:01:01:1, elapsed 1.7s, est remaining 0.0s, peak mem 810MB, user 9.3s, sys 323.7s, output queue size 6343 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.88 cpu vendor: GenuineIntel signature: 000a06d1 features: 1f8bfbff fffab20b extended: f1bf27eb 1b407f7e amd bits: 2c100800 00000121 brand: Intel(R) Xeon(R) 6975P-C threads: 384 max 384 algo: TNfilter license: sentieon:TNhaplotyper=384 input file size: 53230 output file size: 44178 reads: 0 contig: 3367 intervals 3217346917 bases "learn_filter": 561 calls 0.003 user 0.000 sys 0.010 real "predict_filter": 187 calls 0.024 user 0.001 sys 0.028 real advance: 3219322 calls 0.559 user 111.230 sys 125.554 real done: 1 calls 0.001 user 0.000 sys 0.002 real execute: 1 calls 0.005 user 0.005 sys 1.824 real fetch_ref: 476 calls 0.001 user 0.048 sys 2.041 real idle: 20633 calls 0.655 user 4.536 sys 721.017 real init: 1 calls 0.366 user 0.098 sys 0.630 real overall: 849498112 mem 11.692 user 352.135 sys 4.309 real