cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0001104.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0001104.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 3.8s, est remaining 71.9s, peak mem 2288MB, user 85.7s, sys 5.6s, output queue size 160
progress 10% @chr2:89000001, elapsed 6.3s, est remaining 56.3s, peak mem 2572MB, user 175.2s, sys 7.8s, output queue size 47
progress 15% @chr2:27000001, elapsed 8.9s, est remaining 50.4s, peak mem 4093MB, user 245.6s, sys 9.4s, output queue size 208
progress 20% @chr3:156000001, elapsed 11.8s, est remaining 47.1s, peak mem 6131MB, user 319.1s, sys 10.4s, output queue size 364
progress 25% @chr4:108000001, elapsed 13.7s, est remaining 41.2s, peak mem 7755MB, user 394.3s, sys 11.6s, output queue size 525
progress 30% @chr5:107000001, elapsed 15.4s, est remaining 35.9s, peak mem 8700MB, user 439.8s, sys 12.5s, output queue size 686
progress 35% @chr6:79000001, elapsed 18.1s, est remaining 33.6s, peak mem 10539MB, user 506.5s, sys 13.5s, output queue size 848
progress 40% @chr7:67000001, elapsed 20.3s, est remaining 30.5s, peak mem 11673MB, user 578.1s, sys 14.9s, output queue size 1009
progress 45% @chr8:60000001, elapsed 23.0s, est remaining 28.2s, peak mem 13800MB, user 660.9s, sys 16.1s, output queue size 1171
progress 50% @chr9:102000001, elapsed 24.9s, est remaining 24.9s, peak mem 15138MB, user 713.5s, sys 17.4s, output queue size 1333
progress 55% @chr10:96000001, elapsed 28.1s, est remaining 23.0s, peak mem 16841MB, user 791.7s, sys 18.3s, output queue size 1494
progress 60% @chr11:130000001, elapsed 31.9s, est remaining 21.3s, peak mem 17541MB, user 906.1s, sys 19.7s, output queue size 1656
progress 65% @chr12:56000001, elapsed 35.1s, est remaining 18.9s, peak mem 17541MB, user 998.5s, sys 20.8s, output queue size 1818
progress 70% @chr14:79000001, elapsed 38.0s, est remaining 16.3s, peak mem 17541MB, user 1090.6s, sys 22.2s, output queue size 1979
progress 75% @chr16:37000001, elapsed 41.3s, est remaining 13.8s, peak mem 17587MB, user 1176.3s, sys 23.2s, output queue size 2141
progress 80% @chr18:6000001, elapsed 48.4s, est remaining 12.1s, peak mem 18722MB, user 1350.9s, sys 26.4s, output queue size 2303
progress 85% @chr20:42000001, elapsed 54.6s, est remaining 9.6s, peak mem 19006MB, user 1558.3s, sys 29.4s, output queue size 2465
progress 90% @chr21:46000001, elapsed 61.1s, est remaining 6.8s, peak mem 21215MB, user 1772.8s, sys 47.9s, output queue size 529
progress 95% @chrY:48000001, elapsed 63.7s, est remaining 3.4s, peak mem 22527MB, user 1833.5s, sys 48.7s, output queue size 690
progress 100% @chr19:7000001, elapsed 132.0s, est remaining 0.0s, peak mem 35873MB, user 2091.2s, sys 70.3s, output queue size 3822
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: 47622860037
reads: 1619139196
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 5.900 user 1.326 sys 8.734 real
VcfLineRecordHelper::sort: 168 calls 10.568 user 0.751 sys 11.285 real
advance: 3219322 calls 1051.643 user 45.426 sys 1101.341 real
calc: 3219322 calls 470.067 user 14.747 sys 485.436 real
done: 1 calls 5.900 user 1.326 sys 8.734 real
execute: 1 calls 0.001 user 0.002 sys 132.147 real
fetch: 3219322 calls 482.608 user 7.381 sys 488.820 real
idle: 2308 calls 0.737 user 0.017 sys 2216.280 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 37615620096 mem 2131.829 user 73.396 sys 141.966 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0001104.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0001104.md.score --metrics Filler-D0001104.md.metrics Filler-D0001104.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 21.2s, est remaining 403.1s, peak mem 2686MB, user 536.6s, sys 8.1s, output queue size 52
progress 10% @chr2:89000001, elapsed 35.3s, est remaining 318.0s, peak mem 3419MB, user 1017.6s, sys 13.0s, output queue size 47
progress 15% @chr3:3000001, elapsed 50.2s, est remaining 284.4s, peak mem 12253MB, user 1432.9s, sys 17.3s, output queue size 203
progress 20% @chr3:168000001, elapsed 67.0s, est remaining 268.1s, peak mem 18417MB, user 1905.8s, sys 22.6s, output queue size 364
progress 25% @chr4:134000001, elapsed 79.0s, est remaining 236.9s, peak mem 19930MB, user 2296.9s, sys 26.2s, output queue size 525
progress 30% @chr5:97000001, elapsed 89.2s, est remaining 208.0s, peak mem 21212MB, user 2597.8s, sys 29.9s, output queue size 687
progress 35% @chr6:39000001, elapsed 105.0s, est remaining 195.1s, peak mem 22292MB, user 3038.1s, sys 34.4s, output queue size 848
progress 40% @chr7:56000001, elapsed 119.1s, est remaining 178.6s, peak mem 22668MB, user 3446.5s, sys 38.5s, output queue size 1009
progress 45% @chr8:71000001, elapsed 136.4s, est remaining 166.7s, peak mem 23319MB, user 3970.8s, sys 43.2s, output queue size 1171
progress 50% @chr9:37000001, elapsed 148.2s, est remaining 148.2s, peak mem 24149MB, user 4307.5s, sys 46.8s, output queue size 1333
progress 55% @chr10:95000001, elapsed 167.9s, est remaining 137.4s, peak mem 25502MB, user 4840.9s, sys 51.2s, output queue size 1494
progress 60% @chr11:113000001, elapsed 191.0s, est remaining 127.3s, peak mem 25502MB, user 5474.0s, sys 55.9s, output queue size 1656
progress 65% @chr13:18000001, elapsed 209.8s, est remaining 113.0s, peak mem 25502MB, user 6013.1s, sys 59.6s, output queue size 1818
progress 70% @chr14:82000001, elapsed 228.4s, est remaining 97.9s, peak mem 25502MB, user 6617.0s, sys 64.0s, output queue size 1979
progress 75% @chr16:42000001, elapsed 249.9s, est remaining 83.3s, peak mem 25502MB, user 7167.0s, sys 67.7s, output queue size 2141
progress 80% @chr18:7000001, elapsed 296.4s, est remaining 74.1s, peak mem 25502MB, user 8291.9s, sys 73.6s, output queue size 2303
progress 85% @chr20:18000001, elapsed 337.8s, est remaining 59.6s, peak mem 28262MB, user 9703.0s, sys 80.7s, output queue size 2465
progress 90% @chrX:19000001, elapsed 382.3s, est remaining 42.5s, peak mem 36755MB, user 10911.1s, sys 86.6s, output queue size 2627
progress 95% @chrY:51000001, elapsed 401.9s, est remaining 21.2s, peak mem 36755MB, user 11362.7s, sys 89.1s, output queue size 2788
progress 100% @chr19:7000001, elapsed 687.7s, est remaining 0.0s, peak mem 46260MB, user 13091.2s, sys 137.2s, output queue size 3822
library Filler-D0001104:
chimeric_paired 47847369
duped 1341953930
duped_chimeric_paired 19342254
duped_paired 1341922399
duped_unpaired 31531
optical_dup 156636561
paired 1602337504
reads 1619106814
secondary_supplementary 16703342
unmapped 65366
unpaired 32984
optical dup clusters 49942193, maxdup 523, total optical dup pairs 156636561
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: 47622860037
reads: 1619139196
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2704715 calls 80.624 user 1.726 sys 85.429 real
MateInfoByVcf::load: 2704715 calls 1870.573 user 18.874 sys 1620.492 real
MateInfoByVcf::parse_events: 2704715 calls 1593.638 user 14.351 sys 1422.781 real
advance: 3219322 calls 992.430 user 39.839 sys 1215.546 real
calc: 3219322 calls 9160.463 user 66.572 sys 9342.983 real
done: 1 calls 0.065 user 0.000 sys 0.071 real
exec_no_coor: 1 calls 0.187 user 0.041 sys 0.245 real
execute: 1 calls 0.001 user 0.001 sys 689.754 real
fetch: 3219323 calls 785.053 user 4.566 sys 801.763 real
find_pairEnds: 2704715 calls 870.208 user 4.365 sys 963.890 real
idle: 582352 calls 222.949 user 4.931 sys 7826.876 real
init: 1 calls 0.000 user 0.010 sys 0.007 real
markDup: 2704715 calls 3522.838 user 27.063 sys 3877.124 real
vcfadvance: 2704715 calls 15.249 user 3.327 sys 18.104 real
write: 3219323 calls 5545.704 user 38.068 sys 5352.164 real
overall: 48507838464 mem 13368.656 user 161.335 sys 692.263 real