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/fa/6b0c44616a5447e5ddb355a63f75c7/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/f2a55958088cbec0241125151fbb08/custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/f2a55958088cbec0241125151fbb08/custom_Sig_18_tumor_normal.tnseq.vcf.gz.tbi
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/65/f2a55958088cbec0241125151fbb08/custom_Sig_18_tumor_normal.tnseq.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/f2a55958088cbec0241125151fbb08/custom_Sig_18_tumor_normal.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/f2a55958088cbec0241125151fbb08/custom_Sig_18_tumor_normal.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/6b0c44616a5447e5ddb355a63f75c7/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/f2a55958088cbec0241125151fbb08/custom_Sig_18_tumor_normal.tnseq.orientation_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 Sig_18_Blood --max_event_count 5 -v custom_Sig_18_tumor_normal.tnseq.vcf.gz --contamination custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv --tumor_segments custom_Sig_18_tumor_normal.tnseq.segments --orientation_priors custom_Sig_18_tumor_normal.tnseq.orientation_data.tsv custom_Sig_18_tumor_normal.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr3:25000001, elapsed 0.1s, est remaining 1.6s, peak mem 816MB, user 0.2s, sys 2.2s, output queue size 136
progress 10% @chr1:215000001, elapsed 0.2s, est remaining 1.5s, peak mem 816MB, user 0.3s, sys 10.9s, output queue size 297
progress 15% @chr4:76000001, elapsed 0.2s, est remaining 1.3s, peak mem 816MB, user 0.6s, sys 25.0s, output queue size 459
progress 20% @chr2:162000001, elapsed 0.3s, est remaining 1.1s, peak mem 816MB, user 1.0s, sys 40.5s, output queue size 620
progress 25% @chr1:208000001, elapsed 0.3s, est remaining 1.0s, peak mem 816MB, user 1.5s, sys 54.2s, output queue size 782
progress 30% @chr5:30000001, elapsed 0.4s, est remaining 0.9s, peak mem 816MB, user 2.0s, sys 68.5s, output queue size 943
progress 35% @chr7:75000001, elapsed 0.4s, est remaining 0.8s, peak mem 816MB, user 2.6s, sys 82.4s, output queue size 1104
progress 40% @chr6:38000001, elapsed 0.5s, est remaining 0.7s, peak mem 816MB, user 2.9s, sys 92.9s, output queue size 1265
progress 45% @chr7:141000001, elapsed 0.5s, est remaining 0.7s, peak mem 816MB, user 3.2s, sys 102.6s, output queue size 1252
progress 50% @chr8:142000001, elapsed 0.6s, est remaining 0.6s, peak mem 816MB, user 3.6s, sys 113.5s, output queue size 1413
progress 55% @chr10:83000001, elapsed 0.6s, est remaining 0.5s, peak mem 816MB, user 4.2s, sys 124.7s, output queue size 1575
progress 60% @chr12:91000001, elapsed 0.7s, est remaining 0.5s, peak mem 816MB, user 4.7s, sys 138.6s, output queue size 1737
progress 65% @chr14:101000001, elapsed 0.8s, est remaining 0.4s, peak mem 816MB, user 5.1s, sys 154.0s, output queue size 1899
progress 70% @chr14:79000001, elapsed 0.8s, est remaining 0.3s, peak mem 816MB, user 5.6s, sys 168.8s, output queue size 2060
progress 75% @chr13:95000001, elapsed 0.9s, est remaining 0.3s, peak mem 816MB, user 6.0s, sys 183.1s, output queue size 2222
progress 80% @chr15:92000001, elapsed 0.9s, est remaining 0.2s, peak mem 816MB, user 6.6s, sys 198.0s, output queue size 2385
progress 85% @chrX:37000001, elapsed 1.0s, est remaining 0.2s, peak mem 816MB, user 7.0s, sys 213.5s, output queue size 2559
progress 90% @chrY:51000001, elapsed 1.0s, est remaining 0.1s, peak mem 816MB, user 7.8s, sys 232.8s, output queue size 2862
progress 95% @chr19_KI270885v1_alt:1, elapsed 1.1s, est remaining 0.1s, peak mem 816MB, user 8.3s, sys 257.6s, output queue size 3196
progress 100% @HLA-C*08:36N:1, elapsed 1.3s, est remaining 0.0s, peak mem 816MB, user 8.7s, sys 285.6s, output queue size 6293
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: 384 max 384
algo: TNfilter
license: sentieon:TNhaplotyper=384
input file size: 95376
output file size: 77089
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 1065 calls 0.009 user 0.000 sys 0.027 real
"predict_filter": 355 calls 0.015 user 0.064 sys 0.208 real
advance: 3219322 calls 0.515 user 106.396 sys 112.275 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.003 sys 1.541 real
fetch_ref: 876 calls 0.016 user 0.089 sys 0.373 real
idle: 20633 calls 0.570 user 2.465 sys 734.237 real
init: 1 calls 0.403 user 0.122 sys 0.715 real
overall: 855830528 mem 10.636 user 298.107 sys 3.364 real