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% @chr1:161000001, elapsed 0.1s, est remaining 2.5s, peak mem 78MB, user 0.1s, sys 3.3s, output queue size 2
progress 10% @chr2:73000001, elapsed 0.2s, est remaining 2.2s, peak mem 78MB, user 0.2s, sys 6.7s, output queue size 1
progress 15% @chr2:234000001, elapsed 0.4s, est remaining 2.0s, peak mem 78MB, user 0.4s, sys 10.1s, output queue size 4
progress 20% @chr3:152000001, elapsed 0.5s, est remaining 1.9s, peak mem 78MB, user 0.5s, sys 13.6s, output queue size 2
progress 25% @chr4:116000001, elapsed 0.6s, est remaining 1.8s, peak mem 78MB, user 0.6s, sys 17.2s, output queue size 1
progress 30% @chr5:84000001, elapsed 0.7s, est remaining 1.7s, peak mem 78MB, user 0.7s, sys 20.7s, output queue size 2
progress 35% @chr6:60000001, elapsed 0.8s, est remaining 1.5s, peak mem 78MB, user 0.9s, sys 24.2s, output queue size 5
progress 40% @chr7:55000001, elapsed 1.0s, est remaining 1.4s, peak mem 78MB, user 1.0s, sys 27.8s, output queue size 1
progress 45% @chr8:57000001, elapsed 1.1s, est remaining 1.3s, peak mem 78MB, user 1.1s, sys 31.5s, output queue size 2
progress 50% @chr9:64000001, elapsed 1.2s, est remaining 1.2s, peak mem 78MB, user 1.2s, sys 35.8s, output queue size 9
progress 55% @chr10:121000001, elapsed 1.4s, est remaining 1.2s, peak mem 78MB, user 1.3s, sys 41.2s, output queue size 18
progress 60% @chr11:87000001, elapsed 1.6s, est remaining 1.1s, peak mem 78MB, user 1.5s, sys 47.1s, output queue size 38
progress 65% @chr13:31000001, elapsed 1.8s, est remaining 1.0s, peak mem 78MB, user 1.7s, sys 53.2s, output queue size 31
progress 70% @chr14:70000001, elapsed 2.0s, est remaining 0.9s, peak mem 78MB, user 1.9s, sys 58.7s, output queue size 29
progress 75% @chr16:33000001, elapsed 2.2s, est remaining 0.7s, peak mem 78MB, user 2.1s, sys 64.3s, output queue size 30
progress 80% @chr17:31000001, elapsed 2.4s, est remaining 0.6s, peak mem 78MB, user 2.2s, sys 69.7s, output queue size 53
progress 85% @chr20:45000001, elapsed 2.5s, est remaining 0.4s, peak mem 78MB, user 2.4s, sys 75.1s, output queue size 47
progress 90% @chrX:19000001, elapsed 2.8s, est remaining 0.3s, peak mem 90MB, user 3.0s, sys 80.0s, output queue size 109
progress 95% @chrY:2000001, elapsed 3.0s, est remaining 0.2s, peak mem 105MB, user 3.4s, sys 84.7s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.4s, est remaining 0.0s, peak mem 147MB, user 4.2s, sys 93.1s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49121344
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.030 user 0.011 sys 0.047 real
VcfLineRecordHelper::sort: 26 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.438 user 20.135 sys 22.042 real
calc: 3219322 calls 0.372 user 16.255 sys 13.247 real
done: 1 calls 0.030 user 0.011 sys 0.047 real
execute: 1 calls 0.002 user 0.005 sys 3.405 real
fetch: 3219322 calls 0.260 user 16.015 sys 12.879 real
idle: 82 calls 0.002 user 0.053 sys 38.196 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 198234112 mem 4.328 user 93.690 sys 4.466 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% @chr1:161000001, elapsed 0.2s, est remaining 4.2s, peak mem 180MB, user 0.3s, sys 4.7s, output queue size 25
progress 10% @chr2:94000001, elapsed 0.4s, est remaining 3.5s, peak mem 186MB, user 0.6s, sys 9.7s, output queue size 15
progress 15% @chr2:231000001, elapsed 0.6s, est remaining 3.2s, peak mem 210MB, user 0.8s, sys 14.9s, output queue size 8
progress 20% @chr3:176000001, elapsed 0.7s, est remaining 3.0s, peak mem 225MB, user 1.0s, sys 19.9s, output queue size 9
progress 25% @chr4:94000001, elapsed 1.0s, est remaining 2.9s, peak mem 228MB, user 1.4s, sys 26.5s, output queue size 23
progress 30% @chr5:112000001, elapsed 1.2s, est remaining 2.9s, peak mem 231MB, user 1.9s, sys 33.7s, output queue size 31
progress 35% @chr6:88000001, elapsed 1.5s, est remaining 2.7s, peak mem 237MB, user 2.1s, sys 41.2s, output queue size 30
progress 40% @chr7:26000001, elapsed 1.7s, est remaining 2.6s, peak mem 246MB, user 2.5s, sys 48.3s, output queue size 29
progress 45% @chr8:18000001, elapsed 2.0s, est remaining 2.4s, peak mem 249MB, user 2.8s, sys 55.3s, output queue size 39
progress 50% @chr9:97000001, elapsed 2.2s, est remaining 2.2s, peak mem 249MB, user 3.3s, sys 61.9s, output queue size 40
progress 55% @chr10:40000001, elapsed 2.4s, est remaining 2.0s, peak mem 252MB, user 3.5s, sys 68.4s, output queue size 55
progress 60% @chr12:8000001, elapsed 2.6s, est remaining 1.7s, peak mem 252MB, user 3.9s, sys 74.4s, output queue size 50
progress 65% @chr13:29000001, elapsed 2.8s, est remaining 1.5s, peak mem 252MB, user 4.3s, sys 80.8s, output queue size 39
progress 70% @chr14:76000001, elapsed 3.0s, est remaining 1.3s, peak mem 255MB, user 4.6s, sys 87.6s, output queue size 27
progress 75% @chr15:83000001, elapsed 3.3s, est remaining 1.1s, peak mem 255MB, user 4.9s, sys 94.7s, output queue size 32
progress 80% @chr18:20000001, elapsed 3.5s, est remaining 0.9s, peak mem 255MB, user 5.3s, sys 100.8s, output queue size 54
progress 85% @chr19:26000001, elapsed 3.7s, est remaining 0.7s, peak mem 261MB, user 5.7s, sys 107.2s, output queue size 55
progress 90% @chr21:31000001, elapsed 4.1s, est remaining 0.5s, peak mem 453MB, user 8.7s, sys 112.4s, output queue size 114
progress 95% @chrY:50000001, elapsed 4.3s, est remaining 0.2s, peak mem 474MB, user 11.9s, sys 117.8s, output queue size 247
progress 100% @chr21:41000001, elapsed 5.4s, est remaining 0.0s, peak mem 486MB, user 14.6s, sys 124.7s, 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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 49121344
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.012 user 0.054 sys 0.077 real
MateInfoByVcf::load: 28282 calls 4.193 user 1.698 sys 4.473 real
MateInfoByVcf::parse_events: 28282 calls 4.110 user 1.499 sys 4.100 real
advance: 3219322 calls 1.168 user 17.972 sys 16.355 real
calc: 3219322 calls 4.421 user 46.106 sys 51.342 real
done: 1 calls 0.003 user 0.000 sys 0.005 real
exec_no_coor: 1 calls 0.000 user 0.002 sys 0.002 real
execute: 1 calls 0.000 user 0.001 sys 5.407 real
fetch: 3219323 calls 0.399 user 18.009 sys 8.147 real
find_pairEnds: 28282 calls 0.227 user 0.060 sys 0.415 real
idle: 1072 calls 0.061 user 0.146 sys 54.746 real
init: 1 calls 0.000 user 0.010 sys 0.006 real
markDup: 28282 calls 0.800 user 0.313 sys 1.686 real
vcfadvance: 28282 calls 0.010 user 0.196 sys 0.135 real
write: 3219323 calls 2.271 user 12.077 sys 18.648 real
overall: 509698048 mem 15.095 user 125.736 sys 6.424 real