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/fd/c20ecf6211d4517906f80aa4036628/.command.sh
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/59/86cef9424036291ebb9bf155f3502e/negative_somatic_control_1.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/86cef9424036291ebb9bf155f3502e/negative_somatic_control_1.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/86cef9424036291ebb9bf155f3502e/negative_somatic_control_1.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/c20ecf6211d4517906f80aa4036628/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/86cef9424036291ebb9bf155f3502e/negative_somatic_control_1.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/86cef9424036291ebb9bf155f3502e/negative_somatic_control_1.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/86cef9424036291ebb9bf155f3502e/negative_somatic_control_1.tnseq.segments
==> STAGING COMPLETE (10 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --max_event_count 5 -v negative_somatic_control_1.tnseq.vcf.gz --contamination negative_somatic_control_1.tnseq.contamination_data.tsv --tumor_segments negative_somatic_control_1.tnseq.segments --orientation_priors negative_somatic_control_1.tnseq.orientation_data.tsv negative_somatic_control_1.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:182000001, elapsed 0.0s, est remaining 0.7s, peak mem 220MB, user 0.3s, sys 1.4s, output queue size 138
progress 10% @chr2:113000001, elapsed 0.1s, est remaining 0.6s, peak mem 220MB, user 0.5s, sys 2.8s, output queue size 253
progress 15% @chr3:14000001, elapsed 0.1s, est remaining 0.6s, peak mem 220MB, user 0.8s, sys 4.7s, output queue size 415
progress 20% @chr3:179000001, elapsed 0.1s, est remaining 0.5s, peak mem 220MB, user 1.1s, sys 6.6s, output queue size 334
progress 25% @chr4:13000001, elapsed 0.2s, est remaining 0.5s, peak mem 220MB, user 1.4s, sys 8.6s, output queue size 494
progress 30% @chr5:139000001, elapsed 0.2s, est remaining 0.4s, peak mem 220MB, user 1.6s, sys 10.3s, output queue size 656
progress 35% @chr5:85000001, elapsed 0.2s, est remaining 0.4s, peak mem 220MB, user 1.9s, sys 11.9s, output queue size 817
progress 40% @chr6:168000001, elapsed 0.3s, est remaining 0.4s, peak mem 220MB, user 2.3s, sys 14.0s, output queue size 978
progress 45% @chr8:81000001, elapsed 0.3s, est remaining 0.3s, peak mem 220MB, user 2.6s, sys 15.5s, output queue size 1139
progress 50% @chr9:115000001, elapsed 0.3s, est remaining 0.3s, peak mem 220MB, user 2.8s, sys 17.1s, output queue size 1301
progress 55% @chr10:93000001, elapsed 0.3s, est remaining 0.3s, peak mem 220MB, user 3.1s, sys 19.2s, output queue size 1463
progress 60% @chr9:24000001, elapsed 0.4s, est remaining 0.3s, peak mem 220MB, user 3.5s, sys 21.1s, output queue size 1625
progress 65% @chr13:24000001, elapsed 0.4s, est remaining 0.2s, peak mem 220MB, user 3.8s, sys 23.0s, output queue size 1787
progress 70% @chr14:88000001, elapsed 0.4s, est remaining 0.2s, peak mem 220MB, user 4.2s, sys 24.8s, output queue size 1949
progress 75% @chr16:11000001, elapsed 0.5s, est remaining 0.2s, peak mem 220MB, user 4.5s, sys 26.7s, output queue size 2110
progress 80% @chr17:79000001, elapsed 0.5s, est remaining 0.1s, peak mem 220MB, user 4.8s, sys 28.7s, output queue size 2272
progress 85% @chr20:17000001, elapsed 0.5s, est remaining 0.1s, peak mem 220MB, user 5.0s, sys 30.5s, output queue size 2435
progress 90% @chrX:41000001, elapsed 0.6s, est remaining 0.1s, peak mem 221MB, user 5.5s, sys 32.3s, output queue size 2596
progress 95% @chr16_KI270728v1_random:1, elapsed 0.6s, est remaining 0.0s, peak mem 222MB, user 5.8s, sys 34.0s, output queue size 2825
progress 100% @HLA-DQA1*05:01:01:01:1, elapsed 0.7s, est remaining 0.0s, peak mem 223MB, user 6.1s, sys 40.8s, output queue size 3199
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 46614
output file size: 40482
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 408 calls 0.000 user 0.000 sys 0.017 real
"predict_filter": 136 calls 0.017 user 0.004 sys 0.019 real
advance: 3219322 calls 0.622 user 14.275 sys 17.946 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
execute: 1 calls 0.004 user 0.003 sys 0.850 real
fetch_ref: 384 calls 0.008 user 0.068 sys 0.336 real
idle: 19769 calls 0.442 user 0.525 sys 138.902 real
init: 1 calls 0.228 user 0.098 sys 0.406 real
overall: 233984000 mem 7.503 user 43.496 sys 2.291 real