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/a2/03957a4be40918e81b47c8e15700d2/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/1fc3986f90e0651a2b41539d937775/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/04/1fc3986f90e0651a2b41539d937775/positive_somatic_control_1.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/1fc3986f90e0651a2b41539d937775/positive_somatic_control_1.tnseq.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/1fc3986f90e0651a2b41539d937775/positive_somatic_control_1.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/1fc3986f90e0651a2b41539d937775/positive_somatic_control_1.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/03957a4be40918e81b47c8e15700d2/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/1fc3986f90e0651a2b41539d937775/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% @chr2:35000001, elapsed 0.1s, est remaining 1.0s, peak mem 417MB, user 0.2s, sys 2.2s, output queue size 131
progress 10% @chr2:196000001, elapsed 0.1s, est remaining 0.8s, peak mem 417MB, user 0.5s, sys 6.6s, output queue size 289
progress 15% @chr3:5000001, elapsed 0.1s, est remaining 0.7s, peak mem 417MB, user 1.0s, sys 12.2s, output queue size 438
progress 20% @chr4:6000001, elapsed 0.2s, est remaining 0.7s, peak mem 417MB, user 1.6s, sys 17.6s, output queue size 600
progress 25% @chr5:2000001, elapsed 0.2s, est remaining 0.6s, peak mem 417MB, user 2.4s, sys 23.0s, output queue size 710
progress 30% @chr5:105000001, elapsed 0.2s, est remaining 0.5s, peak mem 417MB, user 3.0s, sys 28.1s, output queue size 872
progress 35% @chr5:33000001, elapsed 0.3s, est remaining 0.5s, peak mem 417MB, user 3.5s, sys 33.0s, output queue size 1032
progress 40% @chr8:14000001, elapsed 0.3s, est remaining 0.4s, peak mem 417MB, user 4.1s, sys 37.6s, output queue size 1120
progress 45% @chr8:68000001, elapsed 0.3s, est remaining 0.4s, peak mem 417MB, user 4.7s, sys 42.6s, output queue size 1282
progress 50% @chr9:102000001, elapsed 0.4s, est remaining 0.4s, peak mem 417MB, user 5.0s, sys 47.3s, output queue size 1443
progress 55% @chr11:62000001, elapsed 0.4s, est remaining 0.3s, peak mem 417MB, user 5.4s, sys 52.3s, output queue size 1604
progress 60% @chr12:74000001, elapsed 0.4s, est remaining 0.3s, peak mem 417MB, user 5.8s, sys 57.2s, output queue size 1765
progress 65% @chr13:24000001, elapsed 0.5s, est remaining 0.2s, peak mem 417MB, user 6.2s, sys 61.9s, output queue size 1928
progress 70% @chr15:10000001, elapsed 0.5s, est remaining 0.2s, peak mem 417MB, user 6.6s, sys 66.4s, output queue size 2090
progress 75% @chr16:60000001, elapsed 0.5s, est remaining 0.2s, peak mem 417MB, user 7.0s, sys 71.2s, output queue size 421
progress 80% @chr18:79000001, elapsed 0.6s, est remaining 0.1s, peak mem 417MB, user 7.6s, sys 75.9s, output queue size 583
progress 85% @chrX:48000001, elapsed 0.6s, est remaining 0.1s, peak mem 417MB, user 8.0s, sys 80.4s, output queue size 744
progress 90% @chrX:97000001, elapsed 0.6s, est remaining 0.1s, peak mem 417MB, user 8.2s, sys 83.3s, output queue size 907
progress 95% @chrX:32000001, elapsed 0.7s, est remaining 0.0s, peak mem 417MB, user 8.7s, sys 88.0s, output queue size 1210
progress 100% @HLA-C*03:46:1, elapsed 0.8s, est remaining 0.0s, peak mem 417MB, user 8.8s, sys 96.1s, output queue size 4492
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 50707
output file size: 43804
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 513 calls 0.003 user 0.000 sys 0.011 real
"predict_filter": 171 calls 0.019 user 0.011 sys 0.019 real
advance: 3219322 calls 1.021 user 38.380 sys 47.398 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.004 sys 0.824 real
fetch_ref: 448 calls 0.001 user 0.021 sys 0.013 real
idle: 20057 calls 0.518 user 0.533 sys 291.583 real
init: 1 calls 0.219 user 0.108 sys 0.472 real
overall: 437538816 mem 10.129 user 99.894 sys 2.385 real