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/dd/c95e892c33a0d6c4ac504340d3b06c/.command.sh
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/02/a73da0a024810ee00e61665d77d3a2/negative_somatic_control_1.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/a73da0a024810ee00e61665d77d3a2/negative_somatic_control_1.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/a73da0a024810ee00e61665d77d3a2/negative_somatic_control_1.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/c95e892c33a0d6c4ac504340d3b06c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/a73da0a024810ee00e61665d77d3a2/negative_somatic_control_1.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/a73da0a024810ee00e61665d77d3a2/negative_somatic_control_1.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/a73da0a024810ee00e61665d77d3a2/negative_somatic_control_1.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 HCC1395_BL --normal_sample reference-NA12878 --max_event_count 5 -v negative_somatic_control_1.tnseq.vcf.gz --contamination negative_somatic_control_1.tnseq.contamination_data.tsv --tumor_segments negative_somatic_control_1.tnseq.segments --orientation_priors negative_somatic_control_1.tnseq.orientation_data.tsv negative_somatic_control_1.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:194000001, elapsed 0.1s, est remaining 1.9s, peak mem 822MB, user 0.2s, sys 3.1s, output queue size 134
progress 10% @chr3:141000001, elapsed 0.2s, est remaining 1.8s, peak mem 822MB, user 0.2s, sys 9.9s, output queue size 297
progress 15% @chr1:167000001, elapsed 0.3s, est remaining 1.6s, peak mem 822MB, user 0.4s, sys 27.3s, output queue size 458
progress 20% @chr4:166000001, elapsed 0.3s, est remaining 1.3s, peak mem 822MB, user 0.7s, sys 43.3s, output queue size 619
progress 25% @chr5:135000001, elapsed 0.4s, est remaining 1.2s, peak mem 822MB, user 0.9s, sys 56.4s, output queue size 781
progress 30% @chr1:195000001, elapsed 0.4s, est remaining 1.0s, peak mem 822MB, user 1.1s, sys 77.0s, output queue size 942
progress 35% @chr6:86000001, elapsed 0.5s, est remaining 0.9s, peak mem 822MB, user 1.6s, sys 92.0s, output queue size 1103
progress 40% @chr6:67000001, elapsed 0.6s, est remaining 0.8s, peak mem 822MB, user 1.7s, sys 103.3s, output queue size 1265
progress 45% @chr10:30000001, elapsed 0.6s, est remaining 0.8s, peak mem 822MB, user 2.0s, sys 116.7s, output queue size 1426
progress 50% @chr10:122000001, elapsed 0.7s, est remaining 0.7s, peak mem 822MB, user 2.4s, sys 133.0s, output queue size 1587
progress 55% @chr11:84000001, elapsed 0.7s, est remaining 0.6s, peak mem 822MB, user 2.7s, sys 150.6s, output queue size 1749
progress 60% @chr13:30000001, elapsed 0.8s, est remaining 0.5s, peak mem 822MB, user 3.1s, sys 170.8s, output queue size 1911
progress 65% @chr11:124000001, elapsed 0.8s, est remaining 0.5s, peak mem 822MB, user 3.5s, sys 192.1s, output queue size 2073
progress 70% @chr14:68000001, elapsed 0.9s, est remaining 0.4s, peak mem 822MB, user 3.8s, sys 213.8s, output queue size 2234
progress 75% @chr17:49000001, elapsed 1.0s, est remaining 0.3s, peak mem 822MB, user 4.2s, sys 233.6s, output queue size 499
progress 80% @chr20:47000001, elapsed 1.0s, est remaining 0.3s, peak mem 822MB, user 4.5s, sys 253.3s, output queue size 662
progress 85% @chr17:39000001, elapsed 1.1s, est remaining 0.2s, peak mem 822MB, user 4.9s, sys 273.5s, output queue size 824
progress 90% @chr18:35000001, elapsed 1.1s, est remaining 0.1s, peak mem 822MB, user 5.1s, sys 294.9s, output queue size 1076
progress 95% @chrY:1000001, elapsed 1.2s, est remaining 0.1s, peak mem 822MB, user 5.3s, sys 319.9s, output queue size 1432
progress 100% @HLA-B*51:42:1, elapsed 1.3s, est remaining 0.0s, peak mem 822MB, user 5.6s, sys 375.1s, output queue size 4571
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: 384 max 384
algo: TNfilter
license: sentieon:TNhaplotyper=384
input file size: 46614
output file size: 40483
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 408 calls 0.000 user 0.000 sys 0.009 real
"predict_filter": 136 calls 0.010 user 0.007 sys 0.040 real
advance: 3219322 calls 0.256 user 116.118 sys 118.163 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.000 user 0.014 sys 1.430 real
fetch_ref: 384 calls 0.001 user 0.073 sys 0.061 real
idle: 20633 calls 0.673 user 1.217 sys 723.274 real
init: 1 calls 0.396 user 0.121 sys 0.734 real
overall: 862064640 mem 7.506 user 383.903 sys 3.454 real