Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/fed4742c35391f5141f867a0fb2676/HCC1395_BL.tnseq_tumor_only.vcf.gz.tbi Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/fed4742c35391f5141f867a0fb2676/HCC1395_BL.tnseq_tumor_only.vcf.gz.stats 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/d0/ea382ebf958c77beeac19e7d7aa5b1/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/fed4742c35391f5141f867a0fb2676/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/33/fed4742c35391f5141f867a0fb2676/HCC1395_BL.tnseq_tumor_only.contamination_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/fed4742c35391f5141f867a0fb2676/HCC1395_BL.tnseq_tumor_only.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/fed4742c35391f5141f867a0fb2676/HCC1395_BL.tnseq_tumor_only.orientation_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/ea382ebf958c77beeac19e7d7aa5b1/.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% @chr1:190000001, elapsed 0.1s, est remaining 1.1s, peak mem 420MB, user 0.3s, sys 2.1s, output queue size 160 progress 10% @chr2:159000001, elapsed 0.1s, est remaining 1.0s, peak mem 420MB, user 0.5s, sys 5.2s, output queue size 321 progress 15% @chr2:218000001, elapsed 0.2s, est remaining 0.9s, peak mem 420MB, user 0.7s, sys 8.0s, output queue size 467 progress 20% @chr3:109000001, elapsed 0.2s, est remaining 0.8s, peak mem 420MB, user 1.0s, sys 10.8s, output queue size 544 progress 25% @chr4:31000001, elapsed 0.2s, est remaining 0.7s, peak mem 420MB, user 1.3s, sys 13.9s, output queue size 705 progress 30% @chr5:167000001, elapsed 0.3s, est remaining 0.7s, peak mem 420MB, user 1.5s, sys 16.7s, output queue size 867 progress 35% @chr6:150000001, elapsed 0.3s, est remaining 0.6s, peak mem 420MB, user 1.7s, sys 19.6s, output queue size 1028 progress 40% @chr7:130000001, elapsed 0.4s, est remaining 0.6s, peak mem 420MB, user 1.9s, sys 22.5s, output queue size 1009 progress 45% @chr8:38000001, elapsed 0.4s, est remaining 0.5s, peak mem 420MB, user 2.1s, sys 25.7s, output queue size 1171 progress 50% @chr9:38000001, elapsed 0.5s, est remaining 0.5s, peak mem 420MB, user 2.3s, sys 29.3s, output queue size 1332 progress 55% @chr11:84000001, elapsed 0.5s, est remaining 0.4s, peak mem 420MB, user 2.4s, sys 32.7s, output queue size 1493 progress 60% @chr12:93000001, elapsed 0.6s, est remaining 0.4s, peak mem 420MB, user 2.6s, sys 36.1s, output queue size 590 progress 65% @chr12:66000001, elapsed 0.6s, est remaining 0.3s, peak mem 420MB, user 2.9s, sys 39.2s, output queue size 751 progress 70% @chr15:87000001, elapsed 0.7s, est remaining 0.3s, peak mem 420MB, user 3.1s, sys 42.1s, output queue size 913 progress 75% @chr17:45000001, elapsed 0.7s, est remaining 0.2s, peak mem 420MB, user 3.4s, sys 45.0s, output queue size 1074 progress 80% @chr19:41000001, elapsed 0.7s, est remaining 0.2s, peak mem 420MB, user 3.7s, sys 48.4s, output queue size 1236 progress 85% @chr18:44000001, elapsed 0.8s, est remaining 0.1s, peak mem 420MB, user 4.0s, sys 52.7s, output queue size 1398 progress 90% @chrX:123000001, elapsed 0.8s, est remaining 0.1s, peak mem 420MB, user 4.3s, sys 56.8s, output queue size 1560 progress 95% @chr13_KI270840v1_alt:1, elapsed 0.8s, est remaining 0.0s, peak mem 420MB, user 4.5s, sys 61.2s, output queue size 1985 progress 100% @HLA-DQA1*01:10:1, elapsed 0.9s, est remaining 0.0s, peak mem 420MB, user 4.8s, sys 67.2s, output queue size 5146 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.83 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: 51811 output file size: 43437 reads: 0 contig: 3367 intervals 3217346917 bases "learn_filter": 540 calls 0.000 user 0.000 sys 0.010 real "predict_filter": 180 calls 0.001 user 0.006 sys 0.038 real advance: 3219322 calls 0.573 user 29.689 sys 62.421 real done: 1 calls 0.000 user 0.000 sys 0.002 real execute: 1 calls 0.001 user 0.001 sys 0.993 real fetch_ref: 528 calls 0.001 user 0.028 sys 0.137 real idle: 20057 calls 0.526 user 0.333 sys 314.168 real init: 1 calls 0.214 user 0.117 sys 0.586 real overall: 440651776 mem 6.160 user 70.104 sys 2.669 real