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/e0/d6a50c4f8abd7719297b2263d7d543/.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/fa/46e2ef121a4af62d8ca8901bffbe1c/negative_somatic_control_1.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/46e2ef121a4af62d8ca8901bffbe1c/negative_somatic_control_1.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/46e2ef121a4af62d8ca8901bffbe1c/negative_somatic_control_1.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/d6a50c4f8abd7719297b2263d7d543/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/46e2ef121a4af62d8ca8901bffbe1c/negative_somatic_control_1.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/46e2ef121a4af62d8ca8901bffbe1c/negative_somatic_control_1.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/46e2ef121a4af62d8ca8901bffbe1c/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% @chr1:52000001, elapsed 0.1s, est remaining 1.7s, peak mem 810MB, user 0.1s, sys 2.8s, output queue size 136
progress 10% @chr3:165000001, elapsed 0.2s, est remaining 1.6s, peak mem 810MB, user 0.2s, sys 9.8s, output queue size 297
progress 15% @chr4:103000001, elapsed 0.3s, est remaining 1.6s, peak mem 810MB, user 0.4s, sys 25.7s, output queue size 459
progress 20% @chr4:134000001, elapsed 0.4s, est remaining 1.4s, peak mem 810MB, user 0.6s, sys 42.7s, output queue size 620
progress 25% @chr6:3000001, elapsed 0.4s, est remaining 1.3s, peak mem 810MB, user 0.8s, sys 58.1s, output queue size 782
progress 30% @chr6:72000001, elapsed 0.5s, est remaining 1.2s, peak mem 810MB, user 1.0s, sys 73.7s, output queue size 942
progress 35% @chr7:23000001, elapsed 0.6s, est remaining 1.1s, peak mem 810MB, user 1.2s, sys 89.2s, output queue size 1055
progress 40% @chr8:122000001, elapsed 0.7s, est remaining 1.0s, peak mem 810MB, user 1.6s, sys 107.0s, output queue size 1217
progress 45% @chr9:76000001, elapsed 0.8s, est remaining 0.9s, peak mem 810MB, user 2.0s, sys 124.0s, output queue size 1378
progress 50% @chr11:52000001, elapsed 0.9s, est remaining 0.9s, peak mem 810MB, user 2.2s, sys 140.3s, output queue size 1540
progress 55% @chr11:102000001, elapsed 0.9s, est remaining 0.8s, peak mem 810MB, user 2.5s, sys 156.1s, output queue size 1702
progress 60% @chr1:198000001, elapsed 1.0s, est remaining 0.7s, peak mem 810MB, user 2.7s, sys 172.4s, output queue size 1864
progress 65% @chr14:60000001, elapsed 1.1s, est remaining 0.6s, peak mem 810MB, user 2.9s, sys 185.5s, output queue size 2025
progress 70% @chr17:29000001, elapsed 1.2s, est remaining 0.5s, peak mem 810MB, user 3.4s, sys 199.4s, output queue size 2187
progress 75% @chr13:60000001, elapsed 1.3s, est remaining 0.4s, peak mem 810MB, user 3.7s, sys 212.9s, output queue size 2349
progress 80% @chrX:13000001, elapsed 1.4s, est remaining 0.3s, peak mem 810MB, user 4.0s, sys 225.4s, output queue size 2511
progress 85% @chr20:34000001, elapsed 1.4s, est remaining 0.3s, peak mem 810MB, user 4.4s, sys 238.1s, output queue size 2695
progress 90% @chrX:122000001, elapsed 1.5s, est remaining 0.2s, peak mem 810MB, user 4.9s, sys 248.6s, output queue size 3046
progress 95% @chrX:112000001, elapsed 1.5s, est remaining 0.1s, peak mem 810MB, user 5.4s, sys 261.3s, output queue size 3484
progress 100% @HLA-DQA1*05:01:01:02:1, elapsed 1.7s, est remaining 0.0s, peak mem 810MB, user 5.8s, sys 282.5s, output queue size 1636
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000a06d1
features: bfebfbff 7ffefbff
extended: f3bfb7ef fb417ffe
amd bits: 2c100800 00000121
brand: Intel(R) Xeon(R) 6975P-C
threads: 384 max 384
algo: TNfilter
license: sentieon:TNhaplotyper=384
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 0.003 user 0.013 sys 0.076 real
advance: 3219322 calls 0.349 user 115.572 sys 141.075 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.007 user 0.005 sys 1.857 real
fetch_ref: 384 calls 0.008 user 0.040 sys 0.494 real
idle: 20633 calls 0.828 user 0.571 sys 984.753 real
init: 1 calls 0.365 user 0.073 sys 1.434 real
overall: 849543168 mem 7.587 user 291.748 sys 4.524 real