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/98/e1c2a3972c64d0745e49884e28896c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/e1c2a3972c64d0745e49884e28896c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/78cff2c0816f9bd843247f460097bb/Sig_18_tissue.bam
  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/ba/78cff2c0816f9bd843247f460097bb/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% @chr1:167000001, elapsed 0.1s, est remaining 1.9s, peak mem 78MB, user 0.1s, sys 2.4s, output queue size 2
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.6s, peak mem 78MB, user 0.2s, sys 4.9s, output queue size 7
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.5s, peak mem 78MB, user 0.4s, sys 7.4s, output queue size 3
progress 20% @chr3:156000001, elapsed 0.4s, est remaining 1.4s, peak mem 78MB, user 0.6s, sys 9.9s, output queue size 11
progress 25% @chr4:113000001, elapsed 0.4s, est remaining 1.3s, peak mem 78MB, user 0.7s, sys 12.4s, output queue size 6
progress 30% @chr5:92000001, elapsed 0.5s, est remaining 1.2s, peak mem 78MB, user 0.9s, sys 15.0s, output queue size 6
progress 35% @chr6:57000001, elapsed 0.6s, est remaining 1.1s, peak mem 78MB, user 1.0s, sys 17.6s, output queue size 9
progress 40% @chr7:54000001, elapsed 0.7s, est remaining 1.1s, peak mem 78MB, user 1.1s, sys 20.1s, output queue size 6
progress 45% @chr8:55000001, elapsed 0.8s, est remaining 1.0s, peak mem 78MB, user 1.2s, sys 22.7s, output queue size 9
progress 50% @chr9:77000001, elapsed 0.9s, est remaining 0.9s, peak mem 78MB, user 1.3s, sys 25.2s, output queue size 7
progress 55% @chr10:96000001, elapsed 1.0s, est remaining 0.8s, peak mem 78MB, user 1.5s, sys 27.7s, output queue size 10
progress 60% @chr11:129000001, elapsed 1.0s, est remaining 0.7s, peak mem 78MB, user 1.6s, sys 30.2s, output queue size 5
progress 65% @chr13:6000001, elapsed 1.2s, est remaining 0.6s, peak mem 78MB, user 1.8s, sys 33.1s, output queue size 9
progress 70% @chr14:48000001, elapsed 1.3s, est remaining 0.6s, peak mem 78MB, user 2.0s, sys 38.4s, output queue size 28
progress 75% @chr16:39000001, elapsed 1.5s, est remaining 0.5s, peak mem 78MB, user 2.2s, sys 44.1s, output queue size 21
progress 80% @chr18:24000001, elapsed 1.7s, est remaining 0.4s, peak mem 78MB, user 2.3s, sys 49.8s, output queue size 22
progress 85% @chr20:5000001, elapsed 1.9s, est remaining 0.3s, peak mem 78MB, user 2.5s, sys 55.5s, output queue size 21
progress 90% @chrX:24000001, elapsed 2.1s, est remaining 0.2s, peak mem 99MB, user 3.2s, sys 60.0s, output queue size 114
progress 95% @chr21:5000001, elapsed 2.4s, est remaining 0.1s, peak mem 117MB, user 3.7s, sys 66.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.7s, est remaining 0.0s, peak mem 144MB, user 4.6s, sys 74.2s, output queue size 3664
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: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49121349
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.037 user 0.005 sys 0.046 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.519 user 16.073 sys 17.354 real
calc: 3219322 calls 0.389 user 12.266 sys 11.755 real
done: 1 calls 0.037 user 0.005 sys 0.046 real
execute: 1 calls 0.002 user 0.007 sys 2.738 real
fetch: 3219322 calls 0.279 user 12.273 sys 11.788 real
idle: 78 calls 0.002 user 0.012 sys 36.070 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 195190784 mem 4.728 user 74.868 sys 3.803 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% @chr1:138000001, elapsed 0.1s, est remaining 2.7s, peak mem 174MB, user 0.6s, sys 3.1s, output queue size 23
progress 10% @chr2:81000001, elapsed 0.2s, est remaining 2.2s, peak mem 207MB, user 1.0s, sys 6.1s, output queue size 17
progress 15% @chr3:5000001, elapsed 0.4s, est remaining 2.1s, peak mem 228MB, user 1.6s, sys 8.9s, output queue size 7
progress 20% @chr3:146000001, elapsed 0.5s, est remaining 1.9s, peak mem 234MB, user 2.1s, sys 11.9s, output queue size 9
progress 25% @chr4:105000001, elapsed 0.6s, est remaining 1.7s, peak mem 237MB, user 2.5s, sys 14.9s, output queue size 10
progress 30% @chr5:79000001, elapsed 0.7s, est remaining 1.6s, peak mem 249MB, user 3.1s, sys 17.6s, output queue size 21
progress 35% @chr6:78000001, elapsed 0.8s, est remaining 1.5s, peak mem 258MB, user 3.6s, sys 20.4s, output queue size 7
progress 40% @chr7:67000001, elapsed 0.9s, est remaining 1.4s, peak mem 261MB, user 4.3s, sys 23.3s, output queue size 9
progress 45% @chr8:68000001, elapsed 1.0s, est remaining 1.3s, peak mem 261MB, user 4.9s, sys 26.0s, output queue size 22
progress 50% @chr9:69000001, elapsed 1.1s, est remaining 1.1s, peak mem 267MB, user 5.4s, sys 29.1s, output queue size 12
progress 55% @chr10:90000001, elapsed 1.4s, est remaining 1.1s, peak mem 273MB, user 5.9s, sys 35.4s, output queue size 34
progress 60% @chr11:124000001, elapsed 1.6s, est remaining 1.1s, peak mem 273MB, user 6.4s, sys 43.4s, output queue size 37
progress 65% @chr13:21000001, elapsed 1.9s, est remaining 1.0s, peak mem 273MB, user 7.0s, sys 50.3s, output queue size 37
progress 70% @chr14:61000001, elapsed 2.1s, est remaining 0.9s, peak mem 276MB, user 7.4s, sys 57.5s, output queue size 4
progress 75% @chr16:7000001, elapsed 2.4s, est remaining 0.8s, peak mem 276MB, user 7.7s, sys 64.5s, output queue size 6
progress 80% @chr18:2000001, elapsed 2.6s, est remaining 0.6s, peak mem 276MB, user 8.1s, sys 71.4s, output queue size 6
progress 85% @chr20:16000001, elapsed 2.8s, est remaining 0.5s, peak mem 276MB, user 8.4s, sys 78.4s, output queue size 6
progress 90% @chrX:30000001, elapsed 3.2s, est remaining 0.4s, peak mem 480MB, user 11.5s, sys 83.7s, output queue size 114
progress 95% @chrY:34000001, elapsed 3.5s, est remaining 0.2s, peak mem 492MB, user 14.9s, sys 89.9s, output queue size 247
progress 100% @chr21:41000001, elapsed 4.4s, est remaining 0.0s, peak mem 498MB, user 17.8s, sys 97.4s, 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 6.12.83
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: 49121349
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.007 user 0.023 sys 0.080 real
MateInfoByVcf::load: 28282 calls 4.128 user 1.924 sys 4.863 real
MateInfoByVcf::parse_events: 28282 calls 4.054 user 1.721 sys 4.521 real
advance: 3219322 calls 1.565 user 12.624 sys 15.158 real
calc: 3219322 calls 5.953 user 34.882 sys 41.898 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.009 sys 0.000 real
execute: 1 calls 0.006 user 0.002 sys 4.496 real
fetch: 3219323 calls 0.472 user 11.221 sys 12.796 real
find_pairEnds: 28282 calls 0.230 user 0.039 sys 0.439 real
idle: 951 calls 0.051 user 0.121 sys 50.943 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 28282 calls 0.828 user 0.276 sys 1.823 real
vcfadvance: 28282 calls 0.018 user 0.132 sys 0.232 real
write: 3219323 calls 2.970 user 12.561 sys 14.337 real
overall: 522346496 mem 18.517 user 98.964 sys 5.517 real