Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/c876e54e7a246e35bf044b7d1e6dc3/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta 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/12/bf6cfdbbfb9f5eec8e32276ba4e2cf/negative_somatic_control_1.tnseq.contamination_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/bf6cfdbbfb9f5eec8e32276ba4e2cf/negative_somatic_control_1.tnseq.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/bf6cfdbbfb9f5eec8e32276ba4e2cf/negative_somatic_control_1.tnseq.vcf.gz.tbi Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/c876e54e7a246e35bf044b7d1e6dc3/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/bf6cfdbbfb9f5eec8e32276ba4e2cf/negative_somatic_control_1.tnseq.orientation_data.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/bf6cfdbbfb9f5eec8e32276ba4e2cf/negative_somatic_control_1.tnseq.vcf.gz.stats Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/bf6cfdbbfb9f5eec8e32276ba4e2cf/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% @chr1:221000001, elapsed 0.0s, est remaining 0.9s, peak mem 423MB, user 0.2s, sys 2.1s, output queue size 116 progress 10% @chr2:101000001, elapsed 0.1s, est remaining 0.8s, peak mem 423MB, user 0.6s, sys 7.7s, output queue size 266 progress 15% @chr2:225000001, elapsed 0.1s, est remaining 0.7s, peak mem 423MB, user 1.1s, sys 13.6s, output queue size 388 progress 20% @chr3:164000001, elapsed 0.2s, est remaining 0.6s, peak mem 423MB, user 1.6s, sys 19.4s, output queue size 550 progress 25% @chr3:182000001, elapsed 0.2s, est remaining 0.6s, peak mem 423MB, user 2.1s, sys 25.0s, output queue size 535 progress 30% @chr4:174000001, elapsed 0.2s, est remaining 0.5s, peak mem 423MB, user 2.6s, sys 30.7s, output queue size 696 progress 35% @chr6:101000001, elapsed 0.3s, est remaining 0.5s, peak mem 423MB, user 3.2s, sys 36.4s, output queue size 857 progress 40% @chr7:66000001, elapsed 0.3s, est remaining 0.4s, peak mem 423MB, user 3.7s, sys 42.4s, output queue size 1019 progress 45% @chr7:39000001, elapsed 0.3s, est remaining 0.4s, peak mem 423MB, user 4.2s, sys 47.8s, output queue size 228 progress 50% @chr9:88000001, elapsed 0.4s, est remaining 0.4s, peak mem 423MB, user 4.9s, sys 52.8s, output queue size 389 progress 55% @chr9:73000001, elapsed 0.4s, est remaining 0.3s, peak mem 423MB, user 5.5s, sys 58.2s, output queue size 550 progress 60% @chr10:20000001, elapsed 0.4s, est remaining 0.3s, peak mem 423MB, user 6.0s, sys 64.1s, output queue size 712 progress 65% @chr12:26000001, elapsed 0.5s, est remaining 0.3s, peak mem 423MB, user 6.5s, sys 69.3s, output queue size 874 progress 70% @chr14:105000001, elapsed 0.5s, est remaining 0.2s, peak mem 423MB, user 7.1s, sys 74.7s, output queue size 1036 progress 75% @chr16:38000001, elapsed 0.5s, est remaining 0.2s, peak mem 423MB, user 7.8s, sys 80.2s, output queue size 1197 progress 80% @chr17:80000001, elapsed 0.6s, est remaining 0.1s, peak mem 423MB, user 8.2s, sys 85.7s, output queue size 1360 progress 85% @chr20:61000001, elapsed 0.6s, est remaining 0.1s, peak mem 423MB, user 8.6s, sys 90.6s, output queue size 1521 progress 90% @chrX:76000001, elapsed 0.6s, est remaining 0.1s, peak mem 423MB, user 9.0s, sys 94.9s, output queue size 1684 progress 95% @chr4_KI270785v1_alt:1, elapsed 0.7s, est remaining 0.0s, peak mem 423MB, user 9.6s, sys 99.8s, output queue size 1991 progress 100% @HLA-DQB1*05:03:01:02:1, elapsed 0.8s, est remaining 0.0s, peak mem 423MB, user 10.0s, sys 107.2s, output queue size 5269 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 0.001 user 0.023 sys 0.031 real advance: 3219322 calls 1.112 user 43.621 sys 53.067 real done: 1 calls 0.000 user 0.000 sys 0.002 real execute: 1 calls 0.002 user 0.002 sys 0.831 real fetch_ref: 384 calls 0.002 user 0.040 sys 0.092 real idle: 20057 calls 0.514 user 0.493 sys 294.395 real init: 1 calls 0.215 user 0.112 sys 0.464 real overall: 443817984 mem 11.497 user 111.284 sys 2.445 real