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/e5/cbd6979db222c55795d2b7da47e75c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/2932f225af687dffb1922b570e6657/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/46/2932f225af687dffb1922b570e6657/positive_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/2932f225af687dffb1922b570e6657/positive_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/2932f225af687dffb1922b570e6657/positive_somatic_control_2.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/2932f225af687dffb1922b570e6657/positive_somatic_control_2.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/cbd6979db222c55795d2b7da47e75c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/2932f225af687dffb1922b570e6657/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% @chr1:193000001, elapsed 0.1s, est remaining 1.1s, peak mem 285MB, user 0.1s, sys 3.2s, output queue size 131
progress 10% @chr2:89000001, elapsed 0.1s, est remaining 0.9s, peak mem 285MB, user 0.3s, sys 7.5s, output queue size 259
progress 15% @chr3:54000001, elapsed 0.1s, est remaining 0.8s, peak mem 285MB, user 0.4s, sys 11.4s, output queue size 156
progress 20% @chr3:131000001, elapsed 0.2s, est remaining 0.7s, peak mem 285MB, user 0.5s, sys 15.6s, output queue size 318
progress 25% @chr4:110000001, elapsed 0.2s, est remaining 0.6s, peak mem 285MB, user 0.6s, sys 19.6s, output queue size 479
progress 30% @chr5:153000001, elapsed 0.3s, est remaining 0.6s, peak mem 285MB, user 0.7s, sys 23.5s, output queue size 640
progress 35% @chr6:85000001, elapsed 0.3s, est remaining 0.6s, peak mem 285MB, user 0.9s, sys 27.1s, output queue size 477
progress 40% @chr7:72000001, elapsed 0.3s, est remaining 0.5s, peak mem 285MB, user 1.1s, sys 30.6s, output queue size 638
progress 45% @chr8:66000001, elapsed 0.4s, est remaining 0.5s, peak mem 285MB, user 1.3s, sys 34.3s, output queue size 801
progress 50% @chr9:80000001, elapsed 0.4s, est remaining 0.4s, peak mem 285MB, user 1.4s, sys 38.5s, output queue size 962
progress 55% @chr10:80000001, elapsed 0.5s, est remaining 0.4s, peak mem 285MB, user 1.5s, sys 42.9s, output queue size 248
progress 60% @chr12:26000001, elapsed 0.5s, est remaining 0.3s, peak mem 285MB, user 1.6s, sys 47.0s, output queue size 410
progress 65% @chr12:81000001, elapsed 0.5s, est remaining 0.3s, peak mem 285MB, user 1.7s, sys 50.7s, output queue size 572
progress 70% @chr14:12000001, elapsed 0.6s, est remaining 0.2s, peak mem 285MB, user 1.8s, sys 53.8s, output queue size 733
progress 75% @chr15:85000001, elapsed 0.6s, est remaining 0.2s, peak mem 285MB, user 1.9s, sys 58.1s, output queue size 896
progress 80% @chr18:52000001, elapsed 0.7s, est remaining 0.2s, peak mem 285MB, user 2.0s, sys 62.6s, output queue size 1057
progress 85% @chr20:32000001, elapsed 0.7s, est remaining 0.1s, peak mem 285MB, user 2.1s, sys 67.0s, output queue size 1220
progress 90% @chrX:87000001, elapsed 0.7s, est remaining 0.1s, peak mem 286MB, user 2.3s, sys 71.2s, output queue size 1381
progress 95% @chrY:28000001, elapsed 0.8s, est remaining 0.0s, peak mem 286MB, user 2.4s, sys 75.6s, output queue size 1688
progress 100% @HLA-B*08:79:1, elapsed 0.9s, est remaining 0.0s, peak mem 286MB, user 2.5s, sys 81.4s, output queue size 4967
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: 128 max 128
algo: TNfilter
license: sentieon:TNhaplotyper=128
input file size: 53230
output file size: 44182
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 561 calls 0.000 user 0.000 sys 0.011 real
"predict_filter": 187 calls 0.010 user 0.001 sys 0.013 real
advance: 3219322 calls 0.473 user 36.580 sys 42.485 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.002 sys 0.916 real
fetch_ref: 476 calls 0.008 user 0.013 sys 0.013 real
idle: 19865 calls 0.499 user 0.185 sys 179.641 real
init: 1 calls 0.176 user 0.064 sys 0.382 real
overall: 301420544 mem 3.753 user 84.272 sys 2.355 real