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/6f/2cd56c4519e22647cc4de6e53722b6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/3bcd1705aeeb238b6d1a0292be9aeb/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/e4/3bcd1705aeeb238b6d1a0292be9aeb/positive_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/3bcd1705aeeb238b6d1a0292be9aeb/positive_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/3bcd1705aeeb238b6d1a0292be9aeb/positive_somatic_control_2.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/3bcd1705aeeb238b6d1a0292be9aeb/positive_somatic_control_2.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/2cd56c4519e22647cc4de6e53722b6/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/3bcd1705aeeb238b6d1a0292be9aeb/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% @chr1:115000001, elapsed 0.1s, est remaining 1.0s, peak mem 418MB, user 0.1s, sys 1.9s, output queue size 68
progress 10% @chr2:122000001, elapsed 0.1s, est remaining 0.8s, peak mem 418MB, user 0.3s, sys 6.1s, output queue size 200
progress 15% @chr3:28000001, elapsed 0.1s, est remaining 0.7s, peak mem 418MB, user 0.6s, sys 11.2s, output queue size 362
progress 20% @chr3:84000001, elapsed 0.2s, est remaining 0.7s, peak mem 418MB, user 0.9s, sys 17.0s, output queue size 494
progress 25% @chr4:115000001, elapsed 0.2s, est remaining 0.6s, peak mem 418MB, user 1.2s, sys 23.2s, output queue size 620
progress 30% @chr5:70000001, elapsed 0.2s, est remaining 0.5s, peak mem 418MB, user 1.6s, sys 29.3s, output queue size 321
progress 35% @chr6:117000001, elapsed 0.3s, est remaining 0.5s, peak mem 418MB, user 1.9s, sys 34.9s, output queue size 482
progress 40% @chr7:54000001, elapsed 0.3s, est remaining 0.5s, peak mem 418MB, user 2.4s, sys 40.7s, output queue size 643
progress 45% @chr8:66000001, elapsed 0.3s, est remaining 0.4s, peak mem 418MB, user 2.7s, sys 46.5s, output queue size 806
progress 50% @chr9:115000001, elapsed 0.4s, est remaining 0.4s, peak mem 418MB, user 3.1s, sys 51.6s, output queue size 967
progress 55% @chr10:78000001, elapsed 0.4s, est remaining 0.3s, peak mem 418MB, user 3.5s, sys 57.0s, output queue size 1128
progress 60% @chr11:131000001, elapsed 0.4s, est remaining 0.3s, peak mem 418MB, user 4.0s, sys 62.7s, output queue size 1290
progress 65% @chr12:102000001, elapsed 0.5s, est remaining 0.3s, peak mem 418MB, user 4.3s, sys 68.3s, output queue size 1452
progress 70% @chr15:67000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 4.6s, sys 73.3s, output queue size 1613
progress 75% @chr16:28000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 4.9s, sys 77.4s, output queue size 1776
progress 80% @chr18:22000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 5.2s, sys 82.2s, output queue size 1938
progress 85% @chr21:5000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 5.7s, sys 88.0s, output queue size 2100
progress 90% @chrX:99000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 6.3s, sys 94.2s, output queue size 2261
progress 95% @chr12_GL383552v1_alt:1, elapsed 0.7s, est remaining 0.0s, peak mem 418MB, user 6.5s, sys 97.5s, output queue size 243
progress 100% @HLA-DRB1*14:54:01:1, elapsed 0.8s, est remaining 0.0s, peak mem 418MB, user 6.7s, sys 111.2s, output queue size 3501
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: 192 max 192
algo: TNfilter
license: sentieon:TNhaplotyper=192
input file size: 53230
output file size: 44181
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 561 calls 0.000 user 0.000 sys 0.011 real
"predict_filter": 187 calls 0.005 user 0.005 sys 0.030 real
advance: 3219322 calls 0.503 user 45.153 sys 51.390 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.003 sys 0.810 real
fetch_ref: 476 calls 0.000 user 0.000 sys 0.015 real
idle: 20057 calls 0.602 user 0.921 sys 285.363 real
init: 1 calls 0.212 user 0.087 sys 0.440 real
overall: 439091200 mem 8.464 user 114.998 sys 2.348 real