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/b7/51436d4951c6285276bdc45ce2a804/1029_0W2.tnseq.contamination_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/51436d4951c6285276bdc45ce2a804/1029_0W2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/3194819306f6bfa7bf45f5fbc32439/.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/b7/51436d4951c6285276bdc45ce2a804/1029_0W2.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/51436d4951c6285276bdc45ce2a804/1029_0W2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/51436d4951c6285276bdc45ce2a804/1029_0W2.tnseq.segments
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/3194819306f6bfa7bf45f5fbc32439/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/51436d4951c6285276bdc45ce2a804/1029_0W2.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 1029_0W2-T1-TDNA-1_A23KCGYLT4_1 --normal_sample 1029_0W2-N1-BDNA-1_B23KGCJLT4_1 --max_event_count 5 -v 1029_0W2.tnseq.vcf.gz --contamination 1029_0W2.tnseq.contamination_data.tsv --tumor_segments 1029_0W2.tnseq.segments --orientation_priors 1029_0W2.tnseq.orientation_data.tsv 1029_0W2.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:192000001, elapsed 0.1s, est remaining 1.7s, peak mem 505MB, user 0.3s, sys 3.6s, output queue size 161
progress 10% @chr2:106000001, elapsed 0.1s, est remaining 1.2s, peak mem 505MB, user 1.0s, sys 12.2s, output queue size 312
progress 15% @chr2:226000001, elapsed 0.2s, est remaining 0.9s, peak mem 505MB, user 1.6s, sys 19.0s, output queue size 474
progress 20% @chr4:2000001, elapsed 0.2s, est remaining 0.8s, peak mem 505MB, user 2.3s, sys 25.8s, output queue size 180
progress 25% @chr4:83000001, elapsed 0.2s, est remaining 0.7s, peak mem 505MB, user 3.1s, sys 32.2s, output queue size 341
progress 30% @chr5:62000001, elapsed 0.3s, est remaining 0.7s, peak mem 505MB, user 3.7s, sys 38.1s, output queue size 503
progress 35% @chr5:133000001, elapsed 0.3s, est remaining 0.6s, peak mem 505MB, user 4.5s, sys 43.8s, output queue size 663
progress 40% @chr7:4000001, elapsed 0.4s, est remaining 0.5s, peak mem 505MB, user 5.3s, sys 49.3s, output queue size 824
progress 45% @chr9:18000001, elapsed 0.4s, est remaining 0.5s, peak mem 505MB, user 6.0s, sys 53.1s, output queue size 987
progress 50% @chr8:34000001, elapsed 0.4s, est remaining 0.4s, peak mem 505MB, user 6.9s, sys 58.9s, output queue size 1148
progress 55% @chr10:109000001, elapsed 0.5s, est remaining 0.4s, peak mem 505MB, user 7.8s, sys 65.4s, output queue size 1309
progress 60% @chr11:87000001, elapsed 0.5s, est remaining 0.4s, peak mem 505MB, user 8.6s, sys 71.8s, output queue size 1472
progress 65% @chr13:39000001, elapsed 0.6s, est remaining 0.3s, peak mem 505MB, user 9.5s, sys 78.2s, output queue size 1633
progress 70% @chr14:21000001, elapsed 0.6s, est remaining 0.3s, peak mem 505MB, user 10.4s, sys 84.5s, output queue size 1795
progress 75% @chr16:77000001, elapsed 0.6s, est remaining 0.2s, peak mem 505MB, user 11.3s, sys 90.7s, output queue size 1957
progress 80% @chr17:33000001, elapsed 0.7s, est remaining 0.2s, peak mem 505MB, user 12.2s, sys 96.4s, output queue size 2119
progress 85% @chr20:39000001, elapsed 0.7s, est remaining 0.1s, peak mem 505MB, user 12.8s, sys 102.0s, output queue size 2281
progress 90% @chr19:44000001, elapsed 0.8s, est remaining 0.1s, peak mem 507MB, user 13.6s, sys 108.0s, output queue size 2443
progress 95% @chr4_KI270785v1_alt:1, elapsed 0.8s, est remaining 0.0s, peak mem 507MB, user 14.4s, sys 113.5s, output queue size 2714
progress 100% @HLA-C*08:01:03:1, elapsed 0.9s, est remaining 0.0s, peak mem 507MB, user 14.9s, sys 124.0s, output queue size 471
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: 3820928
output file size: 2960250
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 67869 calls 49.903 user 0.401 sys 55.462 real
"predict_filter": 22623 calls 1.723 user 0.967 sys 2.913 real
advance: 3219322 calls 1.093 user 51.774 sys 57.949 real
done: 1 calls 0.004 user 0.000 sys 0.011 real
execute: 1 calls 0.008 user 0.002 sys 1.117 real
fetch_ref: 49644 calls 0.778 user 4.645 sys 6.136 real
idle: 4145 calls 4.044 user 0.201 sys 381.591 real
init: 1 calls 0.748 user 0.063 sys 1.371 real
overall: 531910656 mem 92.137 user 133.063 sys 3.447 real