Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/5610d5f6c4d9adfd28ac3c3f1c54f6/negative_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/5610d5f6c4d9adfd28ac3c3f1c54f6/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/a9/31fd18260713c3b8c603ef67850e21/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/5610d5f6c4d9adfd28ac3c3f1c54f6/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/a9/31fd18260713c3b8c603ef67850e21/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/5610d5f6c4d9adfd28ac3c3f1c54f6/negative_somatic_control_2.tnseq.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/5610d5f6c4d9adfd28ac3c3f1c54f6/negative_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/5610d5f6c4d9adfd28ac3c3f1c54f6/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% @chr1:212000001, elapsed 0.0s, est remaining 0.8s, peak mem 418MB, user 0.1s, sys 1.5s, output queue size 90
progress 10% @chr1:222000001, elapsed 0.1s, est remaining 0.7s, peak mem 418MB, user 0.3s, sys 7.4s, output queue size 249
progress 15% @chr3:8000001, elapsed 0.1s, est remaining 0.6s, peak mem 418MB, user 0.5s, sys 12.2s, output queue size 324
progress 20% @chr3:139000001, elapsed 0.1s, est remaining 0.6s, peak mem 418MB, user 0.7s, sys 17.3s, output queue size 486
progress 25% @chr4:152000001, elapsed 0.2s, est remaining 0.5s, peak mem 418MB, user 0.9s, sys 22.2s, output queue size 647
progress 30% @chr5:77000001, elapsed 0.2s, est remaining 0.5s, peak mem 418MB, user 1.0s, sys 26.7s, output queue size 808
progress 35% @chr6:64000001, elapsed 0.2s, est remaining 0.4s, peak mem 418MB, user 1.1s, sys 32.2s, output queue size 969
progress 40% @chr7:104000001, elapsed 0.3s, est remaining 0.4s, peak mem 418MB, user 1.3s, sys 37.3s, output queue size 1130
progress 45% @chr8:47000001, elapsed 0.3s, est remaining 0.4s, peak mem 418MB, user 1.5s, sys 42.5s, output queue size 1292
progress 50% @chr9:121000001, elapsed 0.3s, est remaining 0.3s, peak mem 418MB, user 1.6s, sys 47.6s, output queue size 1454
progress 55% @chr10:114000001, elapsed 0.4s, est remaining 0.3s, peak mem 418MB, user 1.8s, sys 52.7s, output queue size 1615
progress 60% @chr12:5000001, elapsed 0.4s, est remaining 0.3s, peak mem 418MB, user 2.0s, sys 58.2s, output queue size 1777
progress 65% @chr13:41000001, elapsed 0.4s, est remaining 0.2s, peak mem 418MB, user 2.1s, sys 63.2s, output queue size 1938
progress 70% @chr15:34000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 2.3s, sys 67.7s, output queue size 2101
progress 75% @chr16:6000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 2.5s, sys 72.2s, output queue size 2263
progress 80% @chr18:16000001, elapsed 0.5s, est remaining 0.1s, peak mem 418MB, user 2.7s, sys 77.1s, output queue size 2425
progress 85% @chr20:43000001, elapsed 0.5s, est remaining 0.1s, peak mem 418MB, user 2.9s, sys 82.2s, output queue size 2586
progress 90% @chr21:5000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 3.0s, sys 86.6s, output queue size 2748
progress 95% @chr21:25000001, elapsed 0.6s, est remaining 0.0s, peak mem 418MB, user 3.4s, sys 91.3s, output queue size 2921
progress 100% @HLA-DQB1*03:03:02:01:1, elapsed 0.7s, est remaining 0.0s, peak mem 418MB, user 3.5s, sys 106.7s, output queue size 6334
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000c06f2
features: bfebfbff 7ffefbff
extended: f3bfb7ef fb417ffe
amd bits: 2c100800 00000121
brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 192 max 192
algo: TNfilter
license: sentieon:TNhaplotyper=192
input file size: 51111
output file size: 43431
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 513 calls 0.007 user 0.001 sys 0.011 real
"predict_filter": 171 calls 0.012 user 0.025 sys 0.055 real
advance: 3219322 calls 0.345 user 30.720 sys 33.364 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.004 sys 0.765 real
fetch_ref: 460 calls 0.006 user 0.087 sys 0.210 real
idle: 20057 calls 0.612 user 0.351 sys 441.358 real
init: 1 calls 0.197 user 0.075 sys 1.270 real
overall: 439160832 mem 4.877 user 111.072 sys 3.151 real