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/0f/44ef01985c4c18a2b72187f331b11d/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/23b1bdbe83d64ae69726161a3d2482/positive_somatic_control_2.tnseq.segments
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/32/23b1bdbe83d64ae69726161a3d2482/positive_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/23b1bdbe83d64ae69726161a3d2482/positive_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/23b1bdbe83d64ae69726161a3d2482/positive_somatic_control_2.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/23b1bdbe83d64ae69726161a3d2482/positive_somatic_control_2.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/44ef01985c4c18a2b72187f331b11d/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/23b1bdbe83d64ae69726161a3d2482/positive_somatic_control_2.tnseq.contamination_data.tsv
==> 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_tissue --normal_sample reference-NA12878 --max_event_count 5 -v positive_somatic_control_2.tnseq.vcf.gz --contamination positive_somatic_control_2.tnseq.contamination_data.tsv --tumor_segments positive_somatic_control_2.tnseq.segments --orientation_priors positive_somatic_control_2.tnseq.orientation_data.tsv positive_somatic_control_2.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:189000001, elapsed 0.1s, est remaining 1.0s, peak mem 219MB, user 0.5s, sys 2.2s, output queue size 94
progress 10% @chr2:41000001, elapsed 0.1s, est remaining 0.8s, peak mem 219MB, user 0.9s, sys 5.0s, output queue size 184
progress 15% @chr2:232000001, elapsed 0.1s, est remaining 0.7s, peak mem 219MB, user 1.2s, sys 7.5s, output queue size 159
progress 20% @chr3:177000001, elapsed 0.2s, est remaining 0.7s, peak mem 219MB, user 1.6s, sys 10.3s, output queue size 321
progress 25% @chr4:99000001, elapsed 0.2s, est remaining 0.6s, peak mem 219MB, user 2.0s, sys 13.0s, output queue size 483
progress 30% @chr4:186000001, elapsed 0.2s, est remaining 0.6s, peak mem 220MB, user 2.7s, sys 15.5s, output queue size 644
progress 35% @chr6:104000001, elapsed 0.3s, est remaining 0.5s, peak mem 220MB, user 3.0s, sys 17.5s, output queue size 805
progress 40% @chr7:49000001, elapsed 0.3s, est remaining 0.5s, peak mem 220MB, user 3.4s, sys 20.2s, output queue size 966
progress 45% @chr8:99000001, elapsed 0.4s, est remaining 0.5s, peak mem 220MB, user 3.7s, sys 22.8s, output queue size 1128
progress 50% @chr9:108000001, elapsed 0.4s, est remaining 0.4s, peak mem 220MB, user 4.0s, sys 25.6s, output queue size 1290
progress 55% @chr10:96000001, elapsed 0.5s, est remaining 0.4s, peak mem 220MB, user 4.4s, sys 28.1s, output queue size 1451
progress 60% @chr11:108000001, elapsed 0.5s, est remaining 0.3s, peak mem 220MB, user 4.7s, sys 30.4s, output queue size 1613
progress 65% @chr13:30000001, elapsed 0.5s, est remaining 0.3s, peak mem 220MB, user 5.0s, sys 33.1s, output queue size 1775
progress 70% @chr14:79000001, elapsed 0.6s, est remaining 0.2s, peak mem 220MB, user 5.4s, sys 35.7s, output queue size 1937
progress 75% @chr16:35000001, elapsed 0.6s, est remaining 0.2s, peak mem 220MB, user 5.9s, sys 38.3s, output queue size 2098
progress 80% @chr18:6000001, elapsed 0.7s, est remaining 0.2s, peak mem 220MB, user 6.3s, sys 41.0s, output queue size 2260
progress 85% @chr20:19000001, elapsed 0.7s, est remaining 0.1s, peak mem 220MB, user 6.6s, sys 43.8s, output queue size 2423
progress 90% @chrX:23000001, elapsed 0.7s, est remaining 0.1s, peak mem 220MB, user 7.1s, sys 46.5s, output queue size 2584
progress 95% @chrY:3000001, elapsed 0.8s, est remaining 0.0s, peak mem 220MB, user 7.5s, sys 49.2s, output queue size 2813
progress 100% @HLA-DRB1*16:02:01:1, elapsed 0.9s, est remaining 0.0s, peak mem 220MB, user 7.8s, sys 59.4s, output queue size 1356
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 00050657
features: bfebfbff 7ffefbff
extended: d39ff7eb 00000818
amd bits: 2c100800 00000121
brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 96 max 96
algo: TNfilter
license: sentieon:TNhaplotyper=96
input file size: 53230
output file size: 44181
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 561 calls 0.004 user 0.001 sys 0.022 real
"predict_filter": 187 calls 0.039 user 0.001 sys 0.037 real
advance: 3219322 calls 0.645 user 22.814 sys 26.911 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.002 user 0.001 sys 1.011 real
fetch_ref: 476 calls 0.000 user 0.012 sys 0.015 real
idle: 19769 calls 0.470 user 0.245 sys 132.295 real
init: 1 calls 0.209 user 0.075 sys 0.355 real
overall: 231624704 mem 9.461 user 61.739 sys 2.383 real