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/5f/4f2c84d696b86c0519c44ba2fe5d4c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/e583d96ce2eeb2c9b22a29fb5c0245/positive_somatic_control_1.tnseq.vcf.gz.stats
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/b8/e583d96ce2eeb2c9b22a29fb5c0245/positive_somatic_control_1.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/e583d96ce2eeb2c9b22a29fb5c0245/positive_somatic_control_1.tnseq.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/e583d96ce2eeb2c9b22a29fb5c0245/positive_somatic_control_1.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/e583d96ce2eeb2c9b22a29fb5c0245/positive_somatic_control_1.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/4f2c84d696b86c0519c44ba2fe5d4c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/e583d96ce2eeb2c9b22a29fb5c0245/positive_somatic_control_1.tnseq.vcf.gz.tbi
==> STAGING COMPLETE (10 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta --algo TNfilter --tumor_sample HCC1395_tumor --normal_sample reference-NA12878 --max_event_count 5 -v positive_somatic_control_1.tnseq.vcf.gz --contamination positive_somatic_control_1.tnseq.contamination_data.tsv --tumor_segments positive_somatic_control_1.tnseq.segments --orientation_priors positive_somatic_control_1.tnseq.orientation_data.tsv positive_somatic_control_1.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:166000001, elapsed 0.0s, est remaining 0.6s, peak mem 94MB, user 0.2s, sys 0.5s, output queue size 33
progress 10% @chr2:75000001, elapsed 0.1s, est remaining 0.6s, peak mem 94MB, user 0.4s, sys 1.1s, output queue size 83
progress 15% @chr2:235000001, elapsed 0.1s, est remaining 0.5s, peak mem 94MB, user 0.7s, sys 1.5s, output queue size 73
progress 20% @chr3:156000001, elapsed 0.1s, est remaining 0.5s, peak mem 95MB, user 1.0s, sys 2.0s, output queue size 234
progress 25% @chr4:127000001, elapsed 0.2s, est remaining 0.5s, peak mem 95MB, user 1.3s, sys 2.6s, output queue size 17
progress 30% @chr5:87000001, elapsed 0.2s, est remaining 0.4s, peak mem 95MB, user 1.5s, sys 3.1s, output queue size 179
progress 35% @chr6:65000001, elapsed 0.2s, est remaining 0.4s, peak mem 95MB, user 1.7s, sys 3.7s, output queue size 89
progress 40% @chr7:58000001, elapsed 0.2s, est remaining 0.4s, peak mem 95MB, user 2.0s, sys 4.3s, output queue size 90
progress 45% @chr8:57000001, elapsed 0.3s, est remaining 0.3s, peak mem 95MB, user 2.2s, sys 4.8s, output queue size 130
progress 50% @chr9:76000001, elapsed 0.3s, est remaining 0.3s, peak mem 95MB, user 2.5s, sys 5.4s, output queue size 153
progress 55% @chr10:104000001, elapsed 0.3s, est remaining 0.3s, peak mem 95MB, user 2.8s, sys 5.9s, output queue size 314
progress 60% @chr11:123000001, elapsed 0.4s, est remaining 0.3s, peak mem 95MB, user 3.0s, sys 6.4s, output queue size 65
progress 65% @chr13:17000001, elapsed 0.4s, est remaining 0.2s, peak mem 95MB, user 3.3s, sys 6.9s, output queue size 227
progress 70% @chr14:61000001, elapsed 0.4s, est remaining 0.2s, peak mem 95MB, user 3.7s, sys 7.4s, output queue size 209
progress 75% @chr16:10000001, elapsed 0.5s, est remaining 0.2s, peak mem 95MB, user 4.0s, sys 7.8s, output queue size 88
progress 80% @chr18:2000001, elapsed 0.5s, est remaining 0.1s, peak mem 95MB, user 4.4s, sys 8.3s, output queue size 250
progress 85% @chr20:20000001, elapsed 0.5s, est remaining 0.1s, peak mem 95MB, user 4.7s, sys 8.7s, output queue size 77
progress 90% @chr22:28000001, elapsed 0.6s, est remaining 0.1s, peak mem 97MB, user 5.2s, sys 9.2s, output queue size 239
progress 95% @chrY:31000001, elapsed 0.6s, est remaining 0.0s, peak mem 97MB, user 5.5s, sys 9.8s, output queue size 191
progress 100% @HLA-DRB1*08:03:02:1, elapsed 0.7s, est remaining 0.0s, peak mem 104MB, user 5.8s, sys 11.2s, output queue size 2633
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
signature: 00050654
features: 1f8bfbff fffa3203
extended: d19f47ab 00000018
amd bits: 2c100800 00000121
brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 32 max 32
algo: TNfilter
license: sentieon:TNhaplotyper=32
input file size: 50711
output file size: 43805
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 513 calls 0.021 user 0.000 sys 0.024 real
"predict_filter": 171 calls 0.000 user 0.000 sys 0.015 real
advance: 3219322 calls 2.040 user 4.588 sys 7.766 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.002 sys 0.766 real
fetch_ref: 448 calls 0.002 user 0.001 sys 0.008 real
idle: 15061 calls 0.313 user 0.078 sys 43.136 real
init: 1 calls 0.194 user 0.063 sys 0.383 real
overall: 110043136 mem 7.290 user 12.221 sys 2.154 real