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/f7/7df0dd603900a4e96831ac49153a79/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/1a5691192d592cd50482399cb824f1/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/7df0dd603900a4e96831ac49153a79/.command.run
  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/9f/1a5691192d592cd50482399cb824f1/Sig_18_tissue.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_tissue.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Sig_18_tissue.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.1s, sys 1.5s, output queue size 15
progress 10% @chr2:52000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.2s, sys 3.2s, output queue size 21
progress 15% @chr2:234000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.3s, sys 4.9s, output queue size 18
progress 20% @chr3:152000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.4s, sys 6.5s, output queue size 1
progress 25% @chr4:116000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.6s, sys 8.2s, output queue size 23
progress 30% @chr5:86000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.8s, sys 9.8s, output queue size 22
progress 35% @chr6:66000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 11.5s, output queue size 23
progress 40% @chr7:56000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.0s, sys 13.1s, output queue size 21
progress 45% @chr8:58000001, elapsed 0.5s, est remaining 0.6s, peak mem 81MB, user 1.2s, sys 14.7s, output queue size 24
progress 50% @chr9:74000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.3s, sys 16.4s, output queue size 15
progress 55% @chr10:69000001, elapsed 0.6s, est remaining 0.5s, peak mem 81MB, user 1.5s, sys 18.0s, output queue size 26
progress 60% @chr11:122000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 19.6s, output queue size 23
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.8s, sys 21.3s, output queue size 2
progress 70% @chr14:61000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.9s, sys 23.0s, output queue size 2
progress 75% @chr16:13000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 2.0s, sys 24.6s, output queue size 2
progress 80% @chr18:1, elapsed 0.9s, est remaining 0.2s, peak mem 81MB, user 2.2s, sys 26.2s, output queue size 2
progress 85% @chr20:24000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.3s, sys 27.9s, output queue size 8
progress 90% @chrX:29000001, elapsed 1.1s, est remaining 0.1s, peak mem 117MB, user 2.9s, sys 29.6s, output queue size 114
progress 95% @chrY:35000001, elapsed 1.2s, est remaining 0.1s, peak mem 147MB, user 3.1s, sys 31.9s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.4s, est remaining 0.0s, peak mem 162MB, user 3.8s, sys 34.1s, output queue size 3664
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: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49121342
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.020 user 0.019 sys 0.052 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.468 user 6.743 sys 8.224 real
calc: 3219322 calls 0.261 user 5.519 sys 6.188 real
done: 1 calls 0.020 user 0.019 sys 0.052 real
execute: 1 calls 0.003 user 0.001 sys 1.414 real
fetch: 3219322 calls 0.366 user 5.114 sys 6.148 real
idle: 84 calls 0.002 user 0.009 sys 36.024 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 220356608 mem 3.941 user 34.804 sys 2.476 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_tissue.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Sig_18_tissue.md.score --metrics Sig_18_tissue.md.metrics Sig_18_tissue.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:155000001, elapsed 0.1s, est remaining 2.1s, peak mem 186MB, user 0.4s, sys 2.5s, output queue size 6
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 1.8s, peak mem 213MB, user 0.6s, sys 4.9s, output queue size 2
progress 15% @chr2:231000001, elapsed 0.3s, est remaining 1.6s, peak mem 240MB, user 0.8s, sys 7.3s, output queue size 4
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.4s, peak mem 258MB, user 1.0s, sys 9.6s, output queue size 1
progress 25% @chr4:113000001, elapsed 0.4s, est remaining 1.3s, peak mem 261MB, user 1.1s, sys 12.0s, output queue size 2
progress 30% @chr5:63000001, elapsed 0.5s, est remaining 1.2s, peak mem 267MB, user 1.3s, sys 14.3s, output queue size 23
progress 35% @chr6:65000001, elapsed 0.6s, est remaining 1.1s, peak mem 267MB, user 1.6s, sys 16.7s, output queue size 26
progress 40% @chr7:55000001, elapsed 0.7s, est remaining 1.0s, peak mem 267MB, user 1.8s, sys 19.0s, output queue size 22
progress 45% @chr8:56000001, elapsed 0.8s, est remaining 0.9s, peak mem 273MB, user 1.9s, sys 21.4s, output queue size 15
progress 50% @chr9:73000001, elapsed 0.9s, est remaining 0.9s, peak mem 273MB, user 2.1s, sys 23.8s, output queue size 12
progress 55% @chr10:88000001, elapsed 1.0s, est remaining 0.8s, peak mem 273MB, user 2.3s, sys 26.8s, output queue size 7
progress 60% @chr11:113000001, elapsed 1.1s, est remaining 0.8s, peak mem 273MB, user 2.7s, sys 31.6s, output queue size 10
progress 65% @chr13:4000001, elapsed 1.3s, est remaining 0.7s, peak mem 273MB, user 3.1s, sys 37.4s, output queue size 11
progress 70% @chr14:55000001, elapsed 1.6s, est remaining 0.7s, peak mem 276MB, user 3.5s, sys 43.4s, output queue size 13
progress 75% @chr16:36000001, elapsed 1.8s, est remaining 0.6s, peak mem 276MB, user 3.9s, sys 49.7s, output queue size 11
progress 80% @chr17:75000001, elapsed 2.0s, est remaining 0.5s, peak mem 276MB, user 4.2s, sys 56.0s, output queue size 18
progress 85% @chr20:28000001, elapsed 2.2s, est remaining 0.4s, peak mem 279MB, user 4.6s, sys 62.7s, output queue size 6
progress 90% @chrX:34000001, elapsed 2.6s, est remaining 0.3s, peak mem 486MB, user 7.9s, sys 67.4s, output queue size 114
progress 95% @chrY:29000001, elapsed 2.8s, est remaining 0.1s, peak mem 501MB, user 11.6s, sys 73.7s, output queue size 240
progress 100% @chr21:41000001, elapsed 3.8s, est remaining 0.0s, peak mem 507MB, user 14.2s, sys 80.8s, output queue size 3664
library Sig_18_tissue:
chimeric_paired 1886
duped 84376
duped_chimeric_paired 8
duped_paired 84374
duped_unpaired 2
optical_dup 3799
paired 999968
reads 1001834
secondary_supplementary 1858
unmapped 8
unpaired 4
optical dup clusters 3695, maxdup 3, total optical dup pairs 3799
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: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 49121342
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.003 user 0.019 sys 0.068 real
MateInfoByVcf::load: 28282 calls 4.491 user 1.343 sys 4.494 real
MateInfoByVcf::parse_events: 28282 calls 4.434 user 1.214 sys 4.196 real
advance: 3219322 calls 1.367 user 10.336 sys 12.312 real
calc: 3219322 calls 4.391 user 29.607 sys 34.906 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.005 sys 0.002 real
execute: 1 calls 0.002 user 0.004 sys 3.825 real
fetch: 3219323 calls 0.469 user 9.254 sys 9.848 real
find_pairEnds: 28282 calls 0.233 user 0.049 sys 0.414 real
idle: 957 calls 0.026 user 0.116 sys 50.797 real
init: 1 calls 0.000 user 0.010 sys 0.006 real
markDup: 28282 calls 0.772 user 0.245 sys 1.693 real
vcfadvance: 28282 calls 0.016 user 0.081 sys 0.192 real
write: 3219323 calls 2.429 user 9.428 sys 12.394 real
overall: 531677184 mem 14.685 user 82.548 sys 4.850 real