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/ad/dea5656acde7cdce6c10733a54fbe7/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/90d46f1ab1346dad086d4b86eca759/positive_somatic_control_2.tnseq.segments
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/c3/90d46f1ab1346dad086d4b86eca759/positive_somatic_control_2.tnseq.orientation_data.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/90d46f1ab1346dad086d4b86eca759/positive_somatic_control_2.tnseq.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/90d46f1ab1346dad086d4b86eca759/positive_somatic_control_2.tnseq.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/90d46f1ab1346dad086d4b86eca759/positive_somatic_control_2.tnseq.vcf.gz.stats
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/dea5656acde7cdce6c10733a54fbe7/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/90d46f1ab1346dad086d4b86eca759/positive_somatic_control_2.tnseq.contamination_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 reference-NA12878 --max_event_count 5 -v positive_somatic_control_2.tnseq.vcf.gz --contamination positive_somatic_control_2.tnseq.contamination_data.tsv --tumor_segments positive_somatic_control_2.tnseq.segments --orientation_priors positive_somatic_control_2.tnseq.orientation_data.tsv positive_somatic_control_2.tnseq.filtered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:19000001, elapsed 0.0s, est remaining 0.8s, peak mem 418MB, user 0.2s, sys 1.6s, output queue size 120
progress 10% @chr1:200000001, elapsed 0.1s, est remaining 0.8s, peak mem 418MB, user 0.3s, sys 5.9s, output queue size 281
progress 15% @chr3:24000001, elapsed 0.1s, est remaining 0.7s, peak mem 418MB, user 0.5s, sys 13.5s, output queue size 437
progress 20% @chr3:122000001, elapsed 0.2s, est remaining 0.6s, peak mem 418MB, user 0.8s, sys 20.1s, output queue size 337
progress 25% @chr4:111000001, elapsed 0.2s, est remaining 0.6s, peak mem 418MB, user 1.3s, sys 26.0s, output queue size 498
progress 30% @chr5:102000001, elapsed 0.2s, est remaining 0.5s, peak mem 418MB, user 1.7s, sys 31.8s, output queue size 659
progress 35% @chr6:75000001, elapsed 0.3s, est remaining 0.5s, peak mem 418MB, user 2.0s, sys 37.2s, output queue size 820
progress 40% @chr7:54000001, elapsed 0.3s, est remaining 0.4s, peak mem 418MB, user 2.6s, sys 43.4s, output queue size 982
progress 45% @chr8:58000001, elapsed 0.3s, est remaining 0.4s, peak mem 418MB, user 3.1s, sys 49.4s, output queue size 300
progress 50% @chr9:86000001, elapsed 0.4s, est remaining 0.4s, peak mem 418MB, user 3.5s, sys 55.3s, output queue size 461
progress 55% @chr10:86000001, elapsed 0.4s, est remaining 0.3s, peak mem 418MB, user 3.9s, sys 61.0s, output queue size 622
progress 60% @chr11:115000001, elapsed 0.4s, est remaining 0.3s, peak mem 418MB, user 4.1s, sys 65.9s, output queue size 785
progress 65% @chr13:114000001, elapsed 0.5s, est remaining 0.3s, peak mem 418MB, user 4.4s, sys 71.2s, output queue size 946
progress 70% @chr14:84000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 4.8s, sys 77.3s, output queue size 1108
progress 75% @chr16:79000001, elapsed 0.5s, est remaining 0.2s, peak mem 418MB, user 5.2s, sys 83.1s, output queue size 1270
progress 80% @chr18:23000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 5.8s, sys 88.9s, output queue size 1432
progress 85% @chr20:27000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 6.4s, sys 94.4s, output queue size 1594
progress 90% @chrX:6000001, elapsed 0.6s, est remaining 0.1s, peak mem 418MB, user 7.1s, sys 100.3s, output queue size 1756
progress 95% @chr3_KI270784v1_alt:1, elapsed 0.7s, est remaining 0.0s, peak mem 418MB, user 7.5s, sys 105.8s, output queue size 2101
progress 100% @HLA-DRB1*15:03:01:01:1, elapsed 0.7s, est remaining 0.0s, peak mem 418MB, user 7.7s, sys 120.4s, output queue size 5341
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: 53227
output file size: 44186
reads: 0
contig: 3367 intervals 3217346917 bases
"learn_filter": 561 calls 0.002 user 0.000 sys 0.011 real
"predict_filter": 187 calls 0.039 user 0.011 sys 0.028 real
advance: 3219322 calls 0.503 user 44.914 sys 53.697 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.002 sys 0.804 real
fetch_ref: 476 calls 0.000 user 0.000 sys 0.017 real
idle: 20057 calls 0.569 user 0.416 sys 287.104 real
init: 1 calls 0.221 user 0.079 sys 0.443 real
overall: 439111680 mem 9.251 user 124.338 sys 2.351 real