cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0000789.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0000789.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 5.8s, est remaining 110.5s, peak mem 2871MB, user 127.4s, sys 14.3s, output queue size 160
progress 10% @chr2:68000001, elapsed 9.5s, est remaining 85.9s, peak mem 3467MB, user 257.9s, sys 16.8s, output queue size 121
progress 15% @chr2:27000001, elapsed 13.5s, est remaining 76.5s, peak mem 5682MB, user 371.3s, sys 18.8s, output queue size 208
progress 20% @chr3:174000001, elapsed 18.1s, est remaining 72.4s, peak mem 9206MB, user 476.9s, sys 20.1s, output queue size 364
progress 25% @chr4:112000001, elapsed 21.3s, est remaining 64.0s, peak mem 12135MB, user 599.5s, sys 21.6s, output queue size 525
progress 30% @chr5:73000001, elapsed 23.6s, est remaining 55.0s, peak mem 13383MB, user 673.0s, sys 23.2s, output queue size 687
progress 35% @chr6:79000001, elapsed 27.4s, est remaining 50.8s, peak mem 16331MB, user 765.6s, sys 24.2s, output queue size 848
progress 40% @chr7:70000001, elapsed 31.0s, est remaining 46.4s, peak mem 18732MB, user 852.9s, sys 25.0s, output queue size 1009
progress 45% @chr8:83000001, elapsed 35.9s, est remaining 43.8s, peak mem 21747MB, user 992.5s, sys 26.1s, output queue size 1171
progress 50% @chr9:88000001, elapsed 39.0s, est remaining 39.0s, peak mem 22959MB, user 1093.3s, sys 27.4s, output queue size 1333
progress 55% @chr10:118000001, elapsed 44.1s, est remaining 36.1s, peak mem 23307MB, user 1242.3s, sys 29.6s, output queue size 1494
progress 60% @chr11:67000001, elapsed 49.9s, est remaining 33.3s, peak mem 23307MB, user 1419.8s, sys 30.8s, output queue size 1656
progress 65% @chr13:25000001, elapsed 55.0s, est remaining 29.6s, peak mem 23307MB, user 1555.3s, sys 31.6s, output queue size 1818
progress 70% @chr14:79000001, elapsed 59.3s, est remaining 25.4s, peak mem 23307MB, user 1701.9s, sys 32.7s, output queue size 1979
progress 75% @chr16:40000001, elapsed 65.0s, est remaining 21.7s, peak mem 23307MB, user 1849.5s, sys 33.8s, output queue size 2141
progress 80% @chr18:21000001, elapsed 75.6s, est remaining 18.9s, peak mem 24132MB, user 2203.3s, sys 47.5s, output queue size 205
progress 85% @chr20:31000001, elapsed 85.5s, est remaining 15.1s, peak mem 24373MB, user 2502.0s, sys 49.4s, output queue size 367
progress 90% @chrX:35000001, elapsed 95.5s, est remaining 10.6s, peak mem 29327MB, user 2791.1s, sys 51.9s, output queue size 529
progress 95% @chrY:51000001, elapsed 99.5s, est remaining 5.2s, peak mem 31436MB, user 2888.0s, sys 52.9s, output queue size 690
progress 100% @chr19:7000001, elapsed 172.0s, est remaining 0.0s, peak mem 39531MB, user 3266.0s, sys 65.9s, 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: 64570198377
reads: 2171452659
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 7.199 user 1.663 sys 10.678 real
VcfLineRecordHelper::sort: 212 calls 14.129 user 0.859 sys 14.994 real
advance: 3219322 calls 1480.741 user 49.812 sys 1531.784 real
calc: 3219322 calls 738.202 user 9.376 sys 751.003 real
done: 1 calls 7.199 user 1.663 sys 10.678 real
execute: 1 calls 0.004 user 0.005 sys 172.056 real
fetch: 3219322 calls 901.500 user 4.405 sys 906.451 real
idle: 2483 calls 0.843 user 0.016 sys 2347.622 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 41451335680 mem 3310.143 user 69.356 sys 183.993 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0000789.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0000789.md.score --metrics Filler-D0000789.md.metrics Filler-D0000789.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 30.5s, est remaining 579.5s, peak mem 3409MB, user 769.7s, sys 11.9s, output queue size 52
progress 10% @chr2:55000001, elapsed 50.0s, est remaining 450.2s, peak mem 4842MB, user 1444.0s, sys 17.5s, output queue size 47
progress 15% @chr2:201000001, elapsed 70.8s, est remaining 401.0s, peak mem 17423MB, user 2020.8s, sys 24.6s, output queue size 203
progress 20% @chr3:176000001, elapsed 95.4s, est remaining 381.6s, peak mem 23992MB, user 2715.2s, sys 31.5s, output queue size 364
progress 25% @chr4:135000001, elapsed 111.7s, est remaining 335.2s, peak mem 26451MB, user 3263.7s, sys 36.1s, output queue size 525
progress 30% @chr5:105000001, elapsed 124.9s, est remaining 291.3s, peak mem 28767MB, user 3634.7s, sys 39.8s, output queue size 687
progress 35% @chr6:91000001, elapsed 147.7s, est remaining 274.3s, peak mem 29575MB, user 4202.5s, sys 44.3s, output queue size 848
progress 40% @chr7:56000001, elapsed 168.1s, est remaining 252.1s, peak mem 30226MB, user 4759.9s, sys 48.0s, output queue size 1009
progress 45% @chr8:71000001, elapsed 193.3s, est remaining 236.2s, peak mem 31417MB, user 5500.6s, sys 53.7s, output queue size 1171
progress 50% @chr9:66000001, elapsed 210.0s, est remaining 210.0s, peak mem 32857MB, user 6007.2s, sys 58.0s, output queue size 1333
progress 55% @chr10:95000001, elapsed 237.8s, est remaining 194.5s, peak mem 32857MB, user 6866.3s, sys 64.6s, output queue size 1494
progress 60% @chr11:125000001, elapsed 268.9s, est remaining 179.2s, peak mem 32857MB, user 7729.3s, sys 70.4s, output queue size 1656
progress 65% @chr13:25000001, elapsed 295.1s, est remaining 158.9s, peak mem 32857MB, user 8448.2s, sys 74.9s, output queue size 1818
progress 70% @chr14:82000001, elapsed 319.4s, est remaining 136.9s, peak mem 32857MB, user 9239.3s, sys 80.5s, output queue size 1979
progress 75% @chr16:42000001, elapsed 349.3s, est remaining 116.4s, peak mem 32857MB, user 10040.0s, sys 85.6s, output queue size 2141
progress 80% @chr18:3000001, elapsed 407.9s, est remaining 102.0s, peak mem 34642MB, user 11717.5s, sys 95.7s, output queue size 2303
progress 85% @chr20:23000001, elapsed 463.0s, est remaining 81.7s, peak mem 34642MB, user 13308.4s, sys 104.6s, output queue size 2465
progress 90% @chrX:15000001, elapsed 521.5s, est remaining 57.9s, peak mem 42724MB, user 15306.4s, sys 136.1s, output queue size 529
progress 95% @chrY:51000001, elapsed 543.7s, est remaining 28.6s, peak mem 42921MB, user 15880.2s, sys 139.8s, output queue size 690
progress 100% @chr19:7000001, elapsed 807.0s, est remaining 0.0s, peak mem 48216MB, user 17517.9s, sys 159.4s, output queue size 3822
library Filler-D0000789:
chimeric_paired 59796286
duped 1751097044
duped_chimeric_paired 27410964
duped_paired 1751063698
duped_unpaired 33346
optical_dup 185869733
paired 2154729602
reads 2171423199
secondary_supplementary 16622813
unmapped 64852
unpaired 35392
optical dup clusters 69874026, maxdup 524, total optical dup pairs 185869733
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: 64570198377
reads: 2171452659
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2820440 calls 91.527 user 2.746 sys 97.576 real
MateInfoByVcf::load: 2820440 calls 2094.701 user 20.536 sys 1856.268 real
MateInfoByVcf::parse_events: 2820440 calls 1767.752 user 14.833 sys 1622.439 real
advance: 3219322 calls 1358.651 user 46.966 sys 1594.655 real
calc: 3219322 calls 12627.465 user 77.647 sys 12831.438 real
done: 1 calls 0.064 user 0.010 sys 0.081 real
exec_no_coor: 1 calls 0.224 user 0.073 sys 0.310 real
execute: 1 calls 0.003 user 0.002 sys 809.612 real
fetch: 3219323 calls 1061.665 user 5.282 sys 1069.415 real
find_pairEnds: 2820440 calls 1188.040 user 3.627 sys 1280.253 real
idle: 674678 calls 217.890 user 6.337 sys 7096.907 real
init: 1 calls 0.009 user 0.001 sys 0.007 real
markDup: 2820440 calls 4791.660 user 27.639 sys 5142.863 real
vcfadvance: 2820440 calls 17.814 user 4.055 sys 21.231 real
write: 3219323 calls 7715.835 user 48.691 sys 7542.262 real
overall: 50558504960 mem 17777.550 user 191.221 sys 812.197 real