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/c8/abbcfee41306aae7e91e76cf922f2a/.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/ba/8ad9e44c089d73bc20bbf9db2e5de0/negative_somatic_control_1.tnseq.contamination_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/8ad9e44c089d73bc20bbf9db2e5de0/negative_somatic_control_1.tnseq.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/8ad9e44c089d73bc20bbf9db2e5de0/negative_somatic_control_1.tnseq.vcf.gz.tbi Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/abbcfee41306aae7e91e76cf922f2a/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/8ad9e44c089d73bc20bbf9db2e5de0/negative_somatic_control_1.tnseq.orientation_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/8ad9e44c089d73bc20bbf9db2e5de0/negative_somatic_control_1.tnseq.vcf.gz.stats Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/8ad9e44c089d73bc20bbf9db2e5de0/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% @chr1:202000001, elapsed 0.1s, est remaining 1.0s, peak mem 174MB, user 0.3s, sys 1.6s, output queue size 143 progress 10% @chr2:121000001, elapsed 0.1s, est remaining 0.8s, peak mem 174MB, user 0.6s, sys 3.5s, output queue size 214 progress 15% @chr3:29000001, elapsed 0.1s, est remaining 0.8s, peak mem 174MB, user 1.0s, sys 5.1s, output queue size 376 progress 20% @chr3:184000001, elapsed 0.2s, est remaining 0.7s, peak mem 174MB, user 1.5s, sys 6.8s, output queue size 538 progress 25% @chr4:137000001, elapsed 0.2s, est remaining 0.7s, peak mem 174MB, user 1.9s, sys 8.5s, output queue size 698 progress 30% @chr5:113000001, elapsed 0.3s, est remaining 0.6s, peak mem 174MB, user 2.4s, sys 10.1s, output queue size 600 progress 35% @chr6:80000001, elapsed 0.3s, est remaining 0.6s, peak mem 174MB, user 2.8s, sys 11.5s, output queue size 761 progress 40% @chr7:65000001, elapsed 0.3s, est remaining 0.5s, peak mem 174MB, user 3.2s, sys 13.0s, output queue size 922 progress 45% @chr8:99000001, elapsed 0.4s, est remaining 0.5s, peak mem 174MB, user 3.7s, sys 14.5s, output queue size 339 progress 50% @chr9:7000001, elapsed 0.4s, est remaining 0.4s, peak mem 174MB, user 4.1s, sys 16.1s, output queue size 501 progress 55% @chr10:124000001, elapsed 0.5s, est remaining 0.4s, peak mem 175MB, user 4.5s, sys 17.8s, output queue size 662 progress 60% @chr11:34000001, elapsed 0.5s, est remaining 0.3s, peak mem 175MB, user 4.9s, sys 19.5s, output queue size 824 progress 65% @chr13:49000001, elapsed 0.6s, est remaining 0.3s, peak mem 175MB, user 5.3s, sys 21.1s, output queue size 986 progress 70% @chr14:59000001, elapsed 0.6s, est remaining 0.3s, peak mem 175MB, user 5.8s, sys 22.7s, output queue size 1148 progress 75% @chr16:5000001, elapsed 0.6s, est remaining 0.2s, peak mem 175MB, user 6.1s, sys 24.5s, output queue size 1309 progress 80% @chr18:47000001, elapsed 0.7s, est remaining 0.2s, peak mem 175MB, user 6.5s, sys 26.0s, output queue size 1471 progress 85% @chr19:21000001, elapsed 0.7s, est remaining 0.1s, peak mem 175MB, user 6.9s, sys 27.7s, output queue size 207 progress 90% @chrX:56000001, elapsed 0.8s, est remaining 0.1s, peak mem 175MB, user 7.3s, sys 29.3s, output queue size 369 progress 95% @chrX:146000001, elapsed 0.8s, est remaining 0.0s, peak mem 175MB, user 7.7s, sys 30.8s, output queue size 611 progress 100% @HLA-DRB1*07:01:01:01:1, elapsed 1.0s, est remaining 0.0s, peak mem 182MB, user 8.1s, sys 34.8s, output queue size 3955 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.83 cpu vendor: GenuineIntel signature: 00050657 features: 1f8bfbff fffa320b extended: d19f47ab 00000018 amd bits: 2c100800 00000121 brand: Intel(R) Xeon(R) Platinum 8223CL CPU @ 3.00GHz threads: 72 max 72 algo: TNfilter license: sentieon:TNhaplotyper=72 input file size: 46614 output file size: 40482 reads: 0 contig: 3367 intervals 3217346917 bases "learn_filter": 408 calls 0.005 user 0.000 sys 0.019 real "predict_filter": 136 calls 0.007 user 0.012 sys 0.028 real advance: 3219322 calls 2.916 user 14.785 sys 23.307 real done: 1 calls 0.000 user 0.000 sys 0.002 real execute: 1 calls 0.005 user 0.005 sys 1.100 real fetch_ref: 384 calls 0.011 user 0.033 sys 0.092 real idle: 19697 calls 0.489 user 0.239 sys 109.336 real init: 1 calls 0.204 user 0.116 sys 0.501 real overall: 191184896 mem 9.536 user 36.523 sys 2.611 real