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/32/591d8c3514767f20707719a1ac2587/Sig_18_Blood.tnseq_tumor_only.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/60da8df563cbc72902c804027b9c3d/.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/32/591d8c3514767f20707719a1ac2587/Sig_18_Blood.tnseq_tumor_only.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/60da8df563cbc72902c804027b9c3d/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/591d8c3514767f20707719a1ac2587/Sig_18_Blood.tnseq_tumor_only.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/591d8c3514767f20707719a1ac2587/Sig_18_Blood.tnseq_tumor_only.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/591d8c3514767f20707719a1ac2587/Sig_18_Blood.tnseq_tumor_only.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/591d8c3514767f20707719a1ac2587/Sig_18_Blood.tnseq_tumor_only.orientation_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_Blood --max_event_count 5 -v Sig_18_Blood.tnseq_tumor_only.vcf.gz --contamination Sig_18_Blood.tnseq_tumor_only.contamination_data.tsv --tumor_segments Sig_18_Blood.tnseq_tumor_only.segments --orientation_priors Sig_18_Blood.tnseq_tumor_only.orientation_data.tsv Sig_18_Blood.tnseq_tumor_only.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:49000001, elapsed 0.1s, est remaining 1.1s, peak mem 420MB, user 0.2s, sys 2.9s, output queue size 120
progress 10% @chr2:93000001, elapsed 0.1s, est remaining 0.9s, peak mem 420MB, user 0.5s, sys 9.1s, output queue size 281
progress 15% @chr3:22000001, elapsed 0.1s, est remaining 0.7s, peak mem 420MB, user 0.9s, sys 16.4s, output queue size 420
progress 20% @chr3:162000001, elapsed 0.2s, est remaining 0.7s, peak mem 420MB, user 1.2s, sys 22.7s, output queue size 582
progress 25% @chr4:139000001, elapsed 0.2s, est remaining 0.6s, peak mem 420MB, user 1.6s, sys 29.1s, output queue size 743
progress 30% @chr5:78000001, elapsed 0.2s, est remaining 0.6s, peak mem 420MB, user 2.0s, sys 35.6s, output queue size 255
progress 35% @chr6:66000001, elapsed 0.3s, est remaining 0.5s, peak mem 420MB, user 2.5s, sys 41.4s, output queue size 416
progress 40% @chr7:77000001, elapsed 0.3s, est remaining 0.5s, peak mem 420MB, user 3.0s, sys 47.3s, output queue size 577
progress 45% @chr8:73000001, elapsed 0.4s, est remaining 0.4s, peak mem 420MB, user 3.5s, sys 53.1s, output queue size 740
progress 50% @chr9:66000001, elapsed 0.4s, est remaining 0.4s, peak mem 420MB, user 4.0s, sys 59.5s, output queue size 901
progress 55% @chr10:105000001, elapsed 0.4s, est remaining 0.3s, peak mem 420MB, user 4.3s, sys 66.0s, output queue size 1062
progress 60% @chr12:6000001, elapsed 0.5s, est remaining 0.3s, peak mem 420MB, user 4.8s, sys 71.8s, output queue size 1224
progress 65% @chr13:18000001, elapsed 0.5s, est remaining 0.3s, peak mem 420MB, user 5.3s, sys 77.3s, output queue size 1386
progress 70% @chr14:62000001, elapsed 0.5s, est remaining 0.2s, peak mem 420MB, user 5.8s, sys 83.8s, output queue size 1548
progress 75% @chr15:53000001, elapsed 0.6s, est remaining 0.2s, peak mem 420MB, user 6.2s, sys 90.3s, output queue size 1709
progress 80% @chr17:77000001, elapsed 0.6s, est remaining 0.2s, peak mem 420MB, user 6.6s, sys 96.7s, output queue size 1872
progress 85% @chr20:26000001, elapsed 0.6s, est remaining 0.1s, peak mem 420MB, user 7.1s, sys 102.8s, output queue size 2034
progress 90% @chr21:23000001, elapsed 0.7s, est remaining 0.1s, peak mem 420MB, user 7.6s, sys 108.6s, output queue size 2196
progress 95% @chrY:1000001, elapsed 0.7s, est remaining 0.0s, peak mem 420MB, user 8.1s, sys 114.7s, output queue size 2526
progress 100% @HLA-C*05:01:01:01:1, elapsed 0.8s, est remaining 0.0s, peak mem 420MB, user 8.2s, sys 129.0s, output queue size 5781
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: 57860
output file size: 46923
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 642 calls 0.002 user 0.001 sys 0.012 real
"predict_filter": 214 calls 0.030 user 0.021 sys 0.061 real
advance: 3219322 calls 0.636 user 48.019 sys 58.004 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.010 sys 0.848 real
fetch_ref: 624 calls 0.001 user 0.046 sys 0.064 real
idle: 20057 calls 0.527 user 0.561 sys 296.131 real
init: 1 calls 0.250 user 0.074 sys 0.493 real
overall: 440684544 mem 9.778 user 132.974 sys 2.438 real