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/b2/b8bce9b156df479e79d6843df2cfee/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/4d3ebe9948686a29f4969120b79632/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/37/4d3ebe9948686a29f4969120b79632/positive_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/4d3ebe9948686a29f4969120b79632/positive_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/4d3ebe9948686a29f4969120b79632/positive_somatic_control_2.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/4d3ebe9948686a29f4969120b79632/positive_somatic_control_2.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/b8bce9b156df479e79d6843df2cfee/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/4d3ebe9948686a29f4969120b79632/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% @chr1:175000001, elapsed 0.1s, est remaining 2.0s, peak mem 810MB, user 0.2s, sys 2.6s, output queue size 142
progress 10% @chr3:142000001, elapsed 0.2s, est remaining 1.7s, peak mem 810MB, user 0.3s, sys 9.7s, output queue size 303
progress 15% @chr1:231000001, elapsed 0.3s, est remaining 1.6s, peak mem 810MB, user 0.4s, sys 22.0s, output queue size 465
progress 20% @chr4:166000001, elapsed 0.3s, est remaining 1.3s, peak mem 810MB, user 0.7s, sys 43.5s, output queue size 627
progress 25% @chr4:147000001, elapsed 0.4s, est remaining 1.2s, peak mem 810MB, user 1.0s, sys 61.8s, output queue size 788
progress 30% @chr6:149000001, elapsed 0.5s, est remaining 1.1s, peak mem 810MB, user 1.4s, sys 75.0s, output queue size 950
progress 35% @chr7:75000001, elapsed 0.5s, est remaining 1.0s, peak mem 810MB, user 1.9s, sys 89.1s, output queue size 866
progress 40% @chr8:127000001, elapsed 0.6s, est remaining 0.9s, peak mem 810MB, user 2.4s, sys 102.6s, output queue size 1028
progress 45% @chr9:117000001, elapsed 0.6s, est remaining 0.8s, peak mem 810MB, user 2.8s, sys 116.1s, output queue size 1189
progress 50% @chr11:18000001, elapsed 0.7s, est remaining 0.7s, peak mem 810MB, user 3.2s, sys 130.2s, output queue size 1350
progress 55% @chr12:9000001, elapsed 0.7s, est remaining 0.6s, peak mem 810MB, user 3.8s, sys 147.5s, output queue size 1512
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progress 65% @chr2:232000001, elapsed 0.9s, est remaining 0.5s, peak mem 810MB, user 4.8s, sys 188.8s, output queue size 1835
progress 70% @chr13:113000001, elapsed 0.9s, est remaining 0.4s, peak mem 810MB, user 5.2s, sys 205.4s, output queue size 1996
progress 75% @chr18:48000001, elapsed 1.0s, est remaining 0.3s, peak mem 810MB, user 5.6s, sys 217.7s, output queue size 2158
progress 80% @chr17:51000001, elapsed 1.0s, est remaining 0.3s, peak mem 810MB, user 5.9s, sys 231.1s, output queue size 2319
progress 85% @chrX:103000001, elapsed 1.1s, est remaining 0.2s, peak mem 810MB, user 6.3s, sys 245.0s, output queue size 2483
progress 90% @chr16:50000001, elapsed 1.2s, est remaining 0.1s, peak mem 810MB, user 6.6s, sys 260.4s, output queue size 2786
progress 95% @chrX:155000001, elapsed 1.2s, est remaining 0.1s, peak mem 810MB, user 6.9s, sys 279.5s, output queue size 3236
progress 100% @HLA-C*07:66:1, elapsed 1.3s, est remaining 0.0s, peak mem 810MB, user 7.2s, sys 318.7s, output queue size 6230
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: 384 max 384
algo: TNfilter
license: sentieon:TNhaplotyper=384
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 0.007 user 0.009 sys 0.022 real
advance: 3219322 calls 0.350 user 111.017 sys 116.490 real
done: 1 calls 0.003 user 0.000 sys 0.003 real
execute: 1 calls 0.003 user 0.003 sys 1.448 real
fetch_ref: 476 calls 0.000 user 0.082 sys 0.989 real
idle: 20633 calls 0.632 user 0.885 sys 696.444 real
init: 1 calls 0.371 user 0.143 sys 0.666 real
overall: 849534976 mem 8.857 user 328.836 sys 3.351 real