Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5753499cdc3bcf7758184ef6165d52/negative_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5753499cdc3bcf7758184ef6165d52/negative_somatic_control_2.tnseq.contamination_data.tsv
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/f0/93085c6e3da7511381db60def05ce5/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5753499cdc3bcf7758184ef6165d52/negative_somatic_control_2.tnseq.vcf.gz.tbi
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/f0/93085c6e3da7511381db60def05ce5/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5753499cdc3bcf7758184ef6165d52/negative_somatic_control_2.tnseq.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5753499cdc3bcf7758184ef6165d52/negative_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5753499cdc3bcf7758184ef6165d52/negative_somatic_control_2.tnseq.vcf.gz.stats
==> STAGING COMPLETE (10 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample Sig_18_Blood --normal_sample reference-NA12878 --max_event_count 5 -v negative_somatic_control_2.tnseq.vcf.gz --contamination negative_somatic_control_2.tnseq.contamination_data.tsv --tumor_segments negative_somatic_control_2.tnseq.segments --orientation_priors negative_somatic_control_2.tnseq.orientation_data.tsv negative_somatic_control_2.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:192000001, elapsed 0.1s, est remaining 2.2s, peak mem 813MB, user 0.3s, sys 4.2s, output queue size 124
progress 10% @chr1:174000001, elapsed 0.2s, est remaining 2.0s, peak mem 813MB, user 0.4s, sys 12.3s, output queue size 285
progress 15% @chr2:115000001, elapsed 0.3s, est remaining 1.7s, peak mem 813MB, user 0.5s, sys 25.1s, output queue size 447
progress 20% @chr4:118000001, elapsed 0.4s, est remaining 1.5s, peak mem 813MB, user 0.8s, sys 39.1s, output queue size 608
progress 25% @chr5:137000001, elapsed 0.4s, est remaining 1.3s, peak mem 813MB, user 1.0s, sys 54.2s, output queue size 769
progress 30% @chr7:19000001, elapsed 0.5s, est remaining 1.1s, peak mem 813MB, user 1.3s, sys 69.3s, output queue size 931
progress 35% @chr3:2000001, elapsed 0.5s, est remaining 1.0s, peak mem 813MB, user 1.6s, sys 83.3s, output queue size 1092
progress 40% @chr9:2000001, elapsed 0.6s, est remaining 0.9s, peak mem 813MB, user 1.9s, sys 97.9s, output queue size 1253
progress 45% @chr9:93000001, elapsed 0.7s, est remaining 0.8s, peak mem 813MB, user 2.3s, sys 110.6s, output queue size 1308
progress 50% @chr11:23000001, elapsed 0.7s, est remaining 0.7s, peak mem 813MB, user 2.6s, sys 124.3s, output queue size 1470
progress 55% @chr12:11000001, elapsed 0.8s, est remaining 0.6s, peak mem 813MB, user 3.1s, sys 140.4s, output queue size 1631
progress 60% @chr13:113000001, elapsed 0.8s, est remaining 0.6s, peak mem 813MB, user 3.3s, sys 156.8s, output queue size 1794
progress 65% @chr12:24000001, elapsed 0.9s, est remaining 0.5s, peak mem 813MB, user 3.7s, sys 169.9s, output queue size 1956
progress 70% @chr12:98000001, elapsed 1.0s, est remaining 0.4s, peak mem 813MB, user 4.1s, sys 182.7s, output queue size 2117
progress 75% @chr18:45000001, elapsed 1.0s, est remaining 0.3s, peak mem 813MB, user 4.5s, sys 195.8s, output queue size 2280
progress 80% @chr11:110000001, elapsed 1.1s, est remaining 0.3s, peak mem 813MB, user 4.9s, sys 212.6s, output queue size 2442
progress 85% @chr17:58000001, elapsed 1.1s, est remaining 0.2s, peak mem 813MB, user 5.3s, sys 225.5s, output queue size 2604
progress 90% @chr6_KI270802v1_alt:1, elapsed 1.2s, est remaining 0.1s, peak mem 813MB, user 5.6s, sys 242.2s, output queue size 2911
progress 95% @chr22:34000001, elapsed 1.2s, est remaining 0.1s, peak mem 813MB, user 6.1s, sys 263.5s, output queue size 3269
progress 100% @HLA-DQA1*01:07:1, elapsed 1.4s, est remaining 0.0s, peak mem 813MB, user 6.4s, sys 299.6s, output queue size 6350
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: 384 max 384
algo: TNfilter
license: sentieon:TNhaplotyper=384
input file size: 51111
output file size: 43431
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 513 calls 0.000 user 0.000 sys 0.012 real
"predict_filter": 171 calls 0.029 user 0.008 sys 0.069 real
advance: 3219322 calls 0.574 user 106.267 sys 115.858 real
done: 1 calls 0.003 user 0.000 sys 0.003 real
execute: 1 calls 0.000 user 0.006 sys 1.527 real
fetch_ref: 460 calls 0.010 user 0.043 sys 0.141 real
idle: 20633 calls 0.645 user 0.705 sys 721.309 real
init: 1 calls 0.455 user 0.107 sys 0.714 real
overall: 852684800 mem 8.310 user 306.754 sys 3.482 real