Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/b9726253f58c8442f33c37e4ddc9af/negative_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/b9726253f58c8442f33c37e4ddc9af/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/37/a0779128b91f28b88514d2eec9c16e/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/b9726253f58c8442f33c37e4ddc9af/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/37/a0779128b91f28b88514d2eec9c16e/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/b9726253f58c8442f33c37e4ddc9af/negative_somatic_control_2.tnseq.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/b9726253f58c8442f33c37e4ddc9af/negative_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/b9726253f58c8442f33c37e4ddc9af/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% @chr1:150000001, elapsed 0.0s, est remaining 0.7s, peak mem 156MB, user 0.4s, sys 1.2s, output queue size 111
progress 10% @chr2:70000001, elapsed 0.1s, est remaining 0.6s, peak mem 156MB, user 0.9s, sys 2.3s, output queue size 272
progress 15% @chr2:224000001, elapsed 0.1s, est remaining 0.6s, peak mem 156MB, user 1.4s, sys 3.6s, output queue size 286
progress 20% @chr3:168000001, elapsed 0.1s, est remaining 0.5s, peak mem 156MB, user 1.9s, sys 5.0s, output queue size 150
progress 25% @chr4:132000001, elapsed 0.2s, est remaining 0.5s, peak mem 156MB, user 2.3s, sys 6.1s, output queue size 311
progress 30% @chr5:82000001, elapsed 0.2s, est remaining 0.5s, peak mem 156MB, user 2.8s, sys 7.2s, output queue size 473
progress 35% @chr6:81000001, elapsed 0.2s, est remaining 0.4s, peak mem 156MB, user 3.4s, sys 8.3s, output queue size 229
progress 40% @chr7:61000001, elapsed 0.3s, est remaining 0.4s, peak mem 157MB, user 3.8s, sys 9.4s, output queue size 390
progress 45% @chr8:60000001, elapsed 0.3s, est remaining 0.4s, peak mem 157MB, user 4.3s, sys 10.4s, output queue size 552
progress 50% @chr9:87000001, elapsed 0.3s, est remaining 0.3s, peak mem 157MB, user 4.8s, sys 11.5s, output queue size 714
progress 55% @chr10:81000001, elapsed 0.4s, est remaining 0.3s, peak mem 157MB, user 5.3s, sys 12.8s, output queue size 875
progress 60% @chr11:108000001, elapsed 0.4s, est remaining 0.3s, peak mem 157MB, user 5.9s, sys 14.0s, output queue size 105
progress 65% @chr13:25000001, elapsed 0.4s, est remaining 0.2s, peak mem 157MB, user 6.4s, sys 15.3s, output queue size 267
progress 70% @chr14:47000001, elapsed 0.5s, est remaining 0.2s, peak mem 157MB, user 6.9s, sys 16.6s, output queue size 429
progress 75% @chr15:99000001, elapsed 0.5s, est remaining 0.2s, peak mem 157MB, user 7.4s, sys 17.8s, output queue size 590
progress 80% @chr17:76000001, elapsed 0.5s, est remaining 0.1s, peak mem 157MB, user 7.9s, sys 18.9s, output queue size 752
progress 85% @chr20:32000001, elapsed 0.5s, est remaining 0.1s, peak mem 157MB, user 8.4s, sys 20.1s, output queue size 914
progress 90% @chrX:37000001, elapsed 0.6s, est remaining 0.1s, peak mem 158MB, user 9.1s, sys 21.3s, output queue size 1076
progress 95% @chrY:36000001, elapsed 0.6s, est remaining 0.0s, peak mem 158MB, user 9.6s, sys 22.6s, output queue size 1266
progress 100% @HLA-DQB1*03:03:02:01:1, elapsed 0.7s, est remaining 0.0s, peak mem 169MB, user 10.0s, sys 27.1s, output queue size 4662
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
signature: 00050654
features: 1f8bfbff fffa3203
extended: d19f47ab 00000018
amd bits: 2c100800 00000121
brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 64 max 64
algo: TNfilter
license: sentieon:TNhaplotyper=64
input file size: 51111
output file size: 43430
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 513 calls 0.008 user 0.000 sys 0.021 real
"predict_filter": 171 calls 0.036 user 0.004 sys 0.032 real
advance: 3219322 calls 3.090 user 10.833 sys 14.457 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.003 user 0.002 sys 0.848 real
fetch_ref: 460 calls 0.002 user 0.000 sys 0.011 real
idle: 19671 calls 0.455 user 0.227 sys 98.435 real
init: 1 calls 0.237 user 0.144 sys 0.529 real
overall: 177836032 mem 11.539 user 28.614 sys 2.374 real