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/86/632be7411461b3baeefb4868c11c7f/.command.sh 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/0f/d0c388585784c28bb45e081d415454/negative_somatic_control_1.tnseq.contamination_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/d0c388585784c28bb45e081d415454/negative_somatic_control_1.tnseq.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/d0c388585784c28bb45e081d415454/negative_somatic_control_1.tnseq.vcf.gz.tbi Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/632be7411461b3baeefb4868c11c7f/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/d0c388585784c28bb45e081d415454/negative_somatic_control_1.tnseq.orientation_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/d0c388585784c28bb45e081d415454/negative_somatic_control_1.tnseq.vcf.gz.stats Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/d0c388585784c28bb45e081d415454/negative_somatic_control_1.tnseq.segments ==> 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 --normal_sample reference-NA12878 --max_event_count 5 -v negative_somatic_control_1.tnseq.vcf.gz --contamination negative_somatic_control_1.tnseq.contamination_data.tsv --tumor_segments negative_somatic_control_1.tnseq.segments --orientation_priors negative_somatic_control_1.tnseq.orientation_data.tsv negative_somatic_control_1.tnseq.filtered.vcf.gz This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:154000001, elapsed 0.1s, est remaining 1.0s, peak mem 420MB, user 0.1s, sys 2.2s, output queue size 136 progress 10% @chr2:1, elapsed 0.1s, est remaining 0.9s, peak mem 420MB, user 0.3s, sys 6.3s, output queue size 237 progress 15% @chr2:231000001, elapsed 0.1s, est remaining 0.7s, peak mem 420MB, user 0.5s, sys 12.7s, output queue size 399 progress 20% @chr3:153000001, elapsed 0.2s, est remaining 0.7s, peak mem 420MB, user 0.8s, sys 18.6s, output queue size 272 progress 25% @chr4:123000001, elapsed 0.2s, est remaining 0.6s, peak mem 420MB, user 1.0s, sys 25.3s, output queue size 433 progress 30% @chr5:86000001, elapsed 0.2s, est remaining 0.5s, peak mem 420MB, user 1.4s, sys 31.4s, output queue size 594 progress 35% @chr6:122000001, elapsed 0.3s, est remaining 0.5s, peak mem 420MB, user 1.8s, sys 36.6s, output queue size 755 progress 40% @chr6:160000001, elapsed 0.3s, est remaining 0.5s, peak mem 420MB, user 2.1s, sys 41.0s, output queue size 917 progress 45% @chr7:41000001, elapsed 0.3s, est remaining 0.4s, peak mem 420MB, user 2.4s, sys 47.7s, output queue size 1079 progress 50% @chr9:93000001, elapsed 0.4s, est remaining 0.4s, peak mem 420MB, user 2.8s, sys 53.6s, output queue size 1240 progress 55% @chr9:106000001, elapsed 0.4s, est remaining 0.3s, peak mem 420MB, user 3.3s, sys 59.3s, output queue size 1401 progress 60% @chr11:128000001, elapsed 0.4s, est remaining 0.3s, peak mem 420MB, user 3.7s, sys 64.7s, output queue size 1563 progress 65% @chr12:110000001, elapsed 0.5s, est remaining 0.3s, peak mem 420MB, user 4.2s, sys 69.6s, output queue size 1725 progress 70% @chr14:70000001, elapsed 0.5s, est remaining 0.2s, peak mem 420MB, user 4.6s, sys 75.6s, output queue size 218 progress 75% @chr16:22000001, elapsed 0.5s, est remaining 0.2s, peak mem 420MB, user 5.1s, sys 81.2s, output queue size 380 progress 80% @chr18:16000001, elapsed 0.6s, est remaining 0.1s, peak mem 420MB, user 5.7s, sys 86.8s, output queue size 542 progress 85% @chr20:24000001, elapsed 0.6s, est remaining 0.1s, peak mem 420MB, user 6.1s, sys 92.3s, output queue size 704 progress 90% @chrX:45000001, elapsed 0.6s, est remaining 0.1s, peak mem 420MB, user 6.6s, sys 97.4s, output queue size 866 progress 95% @chr8_KI270810v1_alt:1, elapsed 0.7s, est remaining 0.0s, peak mem 420MB, user 6.9s, sys 102.2s, output queue size 1276 progress 100% @HLA-DQB1*02:02:01:1, elapsed 0.7s, est remaining 0.0s, peak mem 421MB, user 7.2s, sys 113.9s, output queue size 4451 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: 192 max 192 algo: TNfilter license: sentieon:TNhaplotyper=192 input file size: 46614 output file size: 40483 reads: 0 contig: 3367 intervals 3217346917 bases "learn_filter": 408 calls 0.000 user 0.000 sys 0.009 real "predict_filter": 136 calls 0.000 user 0.023 sys 0.028 real advance: 3219322 calls 0.476 user 44.581 sys 54.210 real done: 1 calls 0.000 user 0.000 sys 0.002 real execute: 1 calls 0.004 user 0.003 sys 0.795 real fetch_ref: 384 calls 0.001 user 0.044 sys 0.054 real idle: 20057 calls 0.540 user 0.780 sys 295.480 real init: 1 calls 0.215 user 0.100 sys 0.492 real overall: 442257408 mem 8.651 user 118.510 sys 2.389 real