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/fe/2ce26107936dee87ff0468f8522a26/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/b0a4002342a30599908379d4072c3d/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/de/b0a4002342a30599908379d4072c3d/positive_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/b0a4002342a30599908379d4072c3d/positive_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/b0a4002342a30599908379d4072c3d/positive_somatic_control_2.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/b0a4002342a30599908379d4072c3d/positive_somatic_control_2.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/2ce26107936dee87ff0468f8522a26/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/b0a4002342a30599908379d4072c3d/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% @chr1:92000001, elapsed 0.1s, est remaining 1.5s, peak mem 414MB, user 0.1s, sys 0.1s, output queue size 74
progress 10% @chr1:98000001, elapsed 0.1s, est remaining 1.3s, peak mem 415MB, user 0.2s, sys 0.7s, output queue size 236
progress 15% @chr1:245000001, elapsed 0.2s, est remaining 1.1s, peak mem 417MB, user 0.5s, sys 3.9s, output queue size 397
progress 20% @chr4:67000001, elapsed 0.2s, est remaining 0.9s, peak mem 417MB, user 0.7s, sys 7.9s, output queue size 559
progress 25% @chr2:5000001, elapsed 0.3s, est remaining 0.8s, peak mem 417MB, user 0.8s, sys 11.8s, output queue size 555
progress 30% @chr3:59000001, elapsed 0.3s, est remaining 0.7s, peak mem 418MB, user 0.9s, sys 13.3s, output queue size 716
progress 35% @chr7:4000001, elapsed 0.4s, est remaining 0.7s, peak mem 418MB, user 1.1s, sys 15.8s, output queue size 877
progress 40% @chr8:29000001, elapsed 0.4s, est remaining 0.6s, peak mem 418MB, user 1.2s, sys 18.9s, output queue size 1039
progress 45% @chr5:124000001, elapsed 0.5s, est remaining 0.6s, peak mem 418MB, user 1.4s, sys 22.2s, output queue size 1042
progress 50% @chr9:35000001, elapsed 0.5s, est remaining 0.5s, peak mem 418MB, user 1.6s, sys 25.9s, output queue size 731
progress 55% @chr11:35000001, elapsed 0.5s, est remaining 0.4s, peak mem 418MB, user 1.7s, sys 29.9s, output queue size 893
progress 60% @chr5:126000001, elapsed 0.6s, est remaining 0.4s, peak mem 418MB, user 1.9s, sys 34.1s, output queue size 1055
progress 65% @chr13:92000001, elapsed 0.6s, est remaining 0.3s, peak mem 418MB, user 2.2s, sys 38.3s, output queue size 1216
progress 70% @chr13:95000001, elapsed 0.7s, est remaining 0.3s, peak mem 418MB, user 2.5s, sys 43.0s, output queue size 1378
progress 75% @chr15:88000001, elapsed 0.7s, est remaining 0.2s, peak mem 418MB, user 2.8s, sys 47.8s, output queue size 1540
progress 80% @chr19:12000001, elapsed 0.7s, est remaining 0.2s, peak mem 418MB, user 3.1s, sys 52.5s, output queue size 1701
progress 85% @chr22:21000001, elapsed 0.8s, est remaining 0.1s, peak mem 418MB, user 3.4s, sys 56.8s, output queue size 1863
progress 90% @chrX:54000001, elapsed 0.8s, est remaining 0.1s, peak mem 418MB, user 3.7s, sys 61.8s, output queue size 2025
progress 95% @chrY:44000001, elapsed 0.8s, est remaining 0.0s, peak mem 418MB, user 4.0s, sys 66.9s, output queue size 2385
progress 100% @HLA-C*08:112:1, elapsed 0.9s, est remaining 0.0s, peak mem 418MB, user 4.2s, sys 76.7s, output queue size 5611
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: 53230
output file size: 44181
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 561 calls 0.001 user 0.000 sys 0.016 real
"predict_filter": 187 calls 0.028 user 0.014 sys 0.030 real
advance: 3219322 calls 0.543 user 30.938 sys 46.038 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.000 user 0.004 sys 1.020 real
fetch_ref: 476 calls 0.000 user 0.003 sys 0.111 real
idle: 20057 calls 0.764 user 0.223 sys 365.098 real
init: 1 calls 0.219 user 0.220 sys 0.772 real
overall: 439078912 mem 5.651 user 80.021 sys 2.879 real