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/82/82cf5de42b9d01e0cc31bdeed11a61/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/bcfcdae1f08e1ac01f352dbc227d1c/positive_somatic_control_1.tnseq.vcf.gz.stats
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/ab/bcfcdae1f08e1ac01f352dbc227d1c/positive_somatic_control_1.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/bcfcdae1f08e1ac01f352dbc227d1c/positive_somatic_control_1.tnseq.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/bcfcdae1f08e1ac01f352dbc227d1c/positive_somatic_control_1.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/bcfcdae1f08e1ac01f352dbc227d1c/positive_somatic_control_1.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/82cf5de42b9d01e0cc31bdeed11a61/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/bcfcdae1f08e1ac01f352dbc227d1c/positive_somatic_control_1.tnseq.vcf.gz.tbi
==> STAGING COMPLETE (10 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 --normal_sample reference-NA12878 --max_event_count 5 -v positive_somatic_control_1.tnseq.vcf.gz --contamination positive_somatic_control_1.tnseq.contamination_data.tsv --tumor_segments positive_somatic_control_1.tnseq.segments --orientation_priors positive_somatic_control_1.tnseq.orientation_data.tsv positive_somatic_control_1.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:112000001, elapsed 0.1s, est remaining 1.4s, peak mem 708MB, user 2.1s, sys 2.0s, output queue size 160
progress 10% @chr2:89000001, elapsed 0.1s, est remaining 1.1s, peak mem 708MB, user 6.4s, sys 3.7s, output queue size 321
progress 15% @chr3:67000001, elapsed 0.2s, est remaining 0.9s, peak mem 708MB, user 10.9s, sys 5.9s, output queue size 483
progress 20% @chr4:45000001, elapsed 0.2s, est remaining 0.8s, peak mem 709MB, user 15.2s, sys 8.7s, output queue size 644
progress 25% @chr5:46000001, elapsed 0.2s, est remaining 0.7s, peak mem 709MB, user 19.8s, sys 11.3s, output queue size 806
progress 30% @chr5:115000001, elapsed 0.3s, est remaining 0.7s, peak mem 709MB, user 23.8s, sys 13.8s, output queue size 967
progress 35% @chr6:56000001, elapsed 0.3s, est remaining 0.6s, peak mem 709MB, user 28.0s, sys 16.0s, output queue size 1128
progress 40% @chr7:127000001, elapsed 0.4s, est remaining 0.5s, peak mem 709MB, user 32.7s, sys 18.6s, output queue size 1139
progress 45% @chr8:112000001, elapsed 0.4s, est remaining 0.5s, peak mem 709MB, user 37.4s, sys 21.4s, output queue size 1301
progress 50% @chr9:5000001, elapsed 0.5s, est remaining 0.5s, peak mem 709MB, user 41.9s, sys 23.5s, output queue size 1462
progress 55% @chr9:1, elapsed 0.5s, est remaining 0.4s, peak mem 711MB, user 47.3s, sys 25.5s, output queue size 1623
progress 60% @chr11:122000001, elapsed 0.6s, est remaining 0.4s, peak mem 711MB, user 54.4s, sys 28.8s, output queue size 1785
progress 65% @chr13:16000001, elapsed 0.6s, est remaining 0.3s, peak mem 711MB, user 58.0s, sys 31.6s, output queue size 1947
progress 70% @chr16:26000001, elapsed 0.7s, est remaining 0.3s, peak mem 711MB, user 65.7s, sys 33.8s, output queue size 2108
progress 75% @chr15:25000001, elapsed 0.7s, est remaining 0.2s, peak mem 711MB, user 71.0s, sys 35.3s, output queue size 2271
progress 80% @chr20:22000001, elapsed 0.8s, est remaining 0.2s, peak mem 711MB, user 78.7s, sys 37.2s, output queue size 2433
progress 85% @chr21:5000001, elapsed 0.9s, est remaining 0.2s, peak mem 711MB, user 85.7s, sys 40.4s, output queue size 2595
progress 90% @chrX:110000001, elapsed 0.9s, est remaining 0.1s, peak mem 711MB, user 92.2s, sys 44.2s, output queue size 2756
progress 95% @chrX:1000001, elapsed 1.0s, est remaining 0.1s, peak mem 711MB, user 97.4s, sys 48.0s, output queue size 3178
progress 100% @HLA-DQA1*01:03:01:01:1, elapsed 1.1s, est remaining 0.0s, peak mem 711MB, user 105.3s, sys 62.8s, output queue size 6342
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: 20599434
output file size: 13213533
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 350658 calls 335.845 user 5.895 sys 365.595 real
"predict_filter": 116886 calls 93.459 user 3.083 sys 99.212 real
advance: 3219322 calls 0.405 user 3.391 sys 4.074 real
done: 1 calls 0.021 user 0.000 sys 0.022 real
execute: 1 calls 0.008 user 0.001 sys 2.012 real
fetch_ref: 261840 calls 3.080 user 8.656 sys 13.342 real
idle: 12599 calls 13.964 user 1.067 sys 1925.969 real
init: 1 calls 8.067 user 0.573 sys 11.133 real
overall: 750493696 mem 497.923 user 82.802 sys 13.440 real