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/a4/de733e5ef56492921bf5a3fe6bc2fc/1029_16G.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/c1baf4d0c8dcf9acfb799cdef2b22a/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/de733e5ef56492921bf5a3fe6bc2fc/1029_16G.tnseq.vcf.gz.tbi
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/a4/de733e5ef56492921bf5a3fe6bc2fc/1029_16G.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/de733e5ef56492921bf5a3fe6bc2fc/1029_16G.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/c1baf4d0c8dcf9acfb799cdef2b22a/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/de733e5ef56492921bf5a3fe6bc2fc/1029_16G.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/de733e5ef56492921bf5a3fe6bc2fc/1029_16G.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 1029_16G-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_16G-N1-BDNA-1_B23KGCJLT4_1 --max_event_count 5 -v 1029_16G.tnseq.vcf.gz --contamination 1029_16G.tnseq.contamination_data.tsv --tumor_segments 1029_16G.tnseq.segments --orientation_priors 1029_16G.tnseq.orientation_data.tsv 1029_16G.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:56000001, elapsed 0.1s, est remaining 1.3s, peak mem 478MB, user 0.4s, sys 2.3s, output queue size 156
progress 10% @chr2:59000001, elapsed 0.1s, est remaining 0.9s, peak mem 478MB, user 1.1s, sys 8.3s, output queue size 272
progress 15% @chr3:11000001, elapsed 0.1s, est remaining 0.7s, peak mem 478MB, user 1.8s, sys 13.5s, output queue size 434
progress 20% @chr3:152000001, elapsed 0.2s, est remaining 0.7s, peak mem 478MB, user 2.4s, sys 15.7s, output queue size 100
progress 25% @chr4:33000001, elapsed 0.2s, est remaining 0.6s, peak mem 478MB, user 3.2s, sys 20.4s, output queue size 262
progress 30% @chr5:39000001, elapsed 0.2s, est remaining 0.6s, peak mem 478MB, user 4.0s, sys 26.0s, output queue size 424
progress 35% @chr7:61000001, elapsed 0.3s, est remaining 0.5s, peak mem 478MB, user 4.8s, sys 29.7s, output queue size 584
progress 40% @chr6:153000001, elapsed 0.3s, est remaining 0.5s, peak mem 478MB, user 5.6s, sys 32.7s, output queue size 746
progress 45% @chr8:43000001, elapsed 0.3s, est remaining 0.4s, peak mem 478MB, user 6.5s, sys 37.8s, output queue size 908
progress 50% @chr9:89000001, elapsed 0.4s, est remaining 0.4s, peak mem 478MB, user 7.4s, sys 43.1s, output queue size 1069
progress 55% @chr10:112000001, elapsed 0.4s, est remaining 0.3s, peak mem 478MB, user 8.3s, sys 48.3s, output queue size 1230
progress 60% @chr11:87000001, elapsed 0.4s, est remaining 0.3s, peak mem 478MB, user 9.2s, sys 53.5s, output queue size 1392
progress 65% @chr13:74000001, elapsed 0.5s, est remaining 0.3s, peak mem 478MB, user 9.9s, sys 58.6s, output queue size 1554
progress 70% @chr15:55000001, elapsed 0.5s, est remaining 0.2s, peak mem 478MB, user 10.9s, sys 60.6s, output queue size 1715
progress 75% @chr14:83000001, elapsed 0.5s, est remaining 0.2s, peak mem 478MB, user 11.8s, sys 65.2s, output queue size 1878
progress 80% @chr17:61000001, elapsed 0.6s, est remaining 0.1s, peak mem 478MB, user 12.7s, sys 70.3s, output queue size 2040
progress 85% @chr20:34000001, elapsed 0.6s, est remaining 0.1s, peak mem 478MB, user 13.7s, sys 75.4s, output queue size 2202
progress 90% @chrX:50000001, elapsed 0.6s, est remaining 0.1s, peak mem 478MB, user 14.6s, sys 80.8s, output queue size 2364
progress 95% @chrY:22000001, elapsed 0.7s, est remaining 0.0s, peak mem 478MB, user 15.5s, sys 85.7s, output queue size 2716
progress 100% @HLA-B*54:01:01:1, elapsed 0.8s, est remaining 0.0s, peak mem 478MB, user 16.1s, sys 96.3s, output queue size 3577
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000a06d1
features: bfebfbff 7ffefbff
extended: f3bfb7ef fb417ffe
amd bits: 2c100800 00000121
brand: Intel(R) Xeon(R) 6975P-C
threads: 192 max 192
algo: TNfilter
license: sentieon:TNhaplotyper=192
input file size: 2016845
output file size: 1828235
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 36804 calls 1.865 user 0.045 sys 4.464 real
"predict_filter": 12268 calls 0.998 user 0.361 sys 1.360 real
advance: 3219322 calls 1.240 user 39.013 sys 44.801 real
done: 1 calls 0.007 user 0.000 sys 0.009 real
execute: 1 calls 0.001 user 0.001 sys 0.893 real
fetch_ref: 22040 calls 0.259 user 0.384 sys 1.241 real
idle: 20054 calls 8.788 user 1.068 sys 654.908 real
init: 1 calls 0.967 user 0.534 sys 2.461 real
overall: 502001664 mem 36.847 user 101.057 sys 4.420 real