cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_11H-N1-BDNA-1_B23KGCJLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1029_11H-N1-BDNA-1_B23KGCJLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 1.1s, est remaining 21.1s, peak mem 1900MB, user 24.1s, sys 1.4s, output queue size 146
progress 10% @chr2:46000001, elapsed 2.0s, est remaining 17.8s, peak mem 2347MB, user 50.6s, sys 2.3s, output queue size 166
progress 15% @chr3:18000001, elapsed 3.0s, est remaining 17.0s, peak mem 3180MB, user 81.0s, sys 3.1s, output queue size 203
progress 20% @chr3:167000001, elapsed 3.9s, est remaining 15.4s, peak mem 3382MB, user 104.5s, sys 3.6s, output queue size 364
progress 25% @chr4:133000001, elapsed 4.7s, est remaining 14.0s, peak mem 3506MB, user 128.7s, sys 4.2s, output queue size 444
progress 30% @chr5:83000001, elapsed 5.3s, est remaining 12.3s, peak mem 3631MB, user 148.4s, sys 4.7s, output queue size 464
progress 35% @chr6:92000001, elapsed 6.1s, est remaining 11.3s, peak mem 3631MB, user 171.4s, sys 5.3s, output queue size 625
progress 40% @chr6:31000001, elapsed 7.0s, est remaining 10.5s, peak mem 3857MB, user 196.1s, sys 5.8s, output queue size 786
progress 45% @chr8:82000001, elapsed 8.2s, est remaining 10.0s, peak mem 3963MB, user 228.2s, sys 6.4s, output queue size 948
progress 50% @chr9:39000001, elapsed 9.1s, est remaining 9.1s, peak mem 4187MB, user 253.7s, sys 6.9s, output queue size 1110
progress 55% @chr10:100000001, elapsed 10.2s, est remaining 8.4s, peak mem 4246MB, user 290.6s, sys 7.4s, output queue size 527
progress 60% @chr11:121000001, elapsed 11.3s, est remaining 7.5s, peak mem 4246MB, user 322.1s, sys 7.7s, output queue size 689
progress 65% @chr13:39000001, elapsed 12.4s, est remaining 6.7s, peak mem 4319MB, user 357.5s, sys 8.2s, output queue size 672
progress 70% @chr14:71000001, elapsed 13.1s, est remaining 5.6s, peak mem 4352MB, user 378.2s, sys 8.4s, output queue size 833
progress 75% @chr16:24000001, elapsed 14.4s, est remaining 4.8s, peak mem 4459MB, user 410.3s, sys 8.8s, output queue size 995
progress 80% @chr17:78000001, elapsed 16.2s, est remaining 4.0s, peak mem 4584MB, user 459.6s, sys 9.2s, output queue size 1157
progress 85% @chr19:45000001, elapsed 17.8s, est remaining 3.1s, peak mem 4626MB, user 517.0s, sys 9.7s, output queue size 785
progress 90% @chrX:36000001, elapsed 18.9s, est remaining 2.1s, peak mem 4697MB, user 547.4s, sys 10.2s, output queue size 947
progress 95% @chrY:50000001, elapsed 19.8s, est remaining 1.0s, peak mem 4791MB, user 573.7s, sys 10.5s, output queue size 1109
progress 100% @chr15:88000001, elapsed 23.3s, est remaining 0.0s, peak mem 4882MB, user 623.8s, sys 11.1s, output queue size 4099
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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 20059887055
reads: 437628298
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.412 user 0.177 sys 0.686 real
VcfLineRecordHelper::sort: 33 calls 0.749 user 0.039 sys 0.778 real
advance: 3219322 calls 351.125 user 7.851 sys 358.752 real
calc: 3219322 calls 116.200 user 1.013 sys 117.797 real
done: 1 calls 0.412 user 0.177 sys 0.686 real
execute: 1 calls 0.001 user 0.006 sys 23.373 real
fetch: 3219322 calls 132.786 user 0.882 sys 134.368 real
idle: 160 calls 0.130 user 0.002 sys 133.920 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 5119700992 mem 627.481 user 11.628 sys 25.024 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_11H-N1-BDNA-1_B23KGCJLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1029_11H-N1-BDNA-1_B23KGCJLT4_1.md.score --metrics 1029_11H-N1-BDNA-1_B23KGCJLT4_1.md.metrics 1029_11H-N1-BDNA-1_B23KGCJLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:151000001, elapsed 7.7s, est remaining 146.1s, peak mem 2505MB, user 196.3s, sys 3.6s, output queue size 52
progress 10% @chr2:80000001, elapsed 13.4s, est remaining 120.6s, peak mem 3458MB, user 379.1s, sys 5.6s, output queue size 48
progress 15% @chr2:218000001, elapsed 20.7s, est remaining 117.0s, peak mem 3926MB, user 576.2s, sys 7.5s, output queue size 203
progress 20% @chr3:136000001, elapsed 26.5s, est remaining 106.0s, peak mem 4025MB, user 773.2s, sys 9.6s, output queue size 141
progress 25% @chr4:124000001, elapsed 31.6s, est remaining 94.8s, peak mem 4072MB, user 929.0s, sys 10.9s, output queue size 302
progress 30% @chr5:99000001, elapsed 35.6s, est remaining 83.1s, peak mem 4163MB, user 1058.7s, sys 12.1s, output queue size 464
progress 35% @chr6:41000001, elapsed 41.4s, est remaining 76.9s, peak mem 4164MB, user 1212.8s, sys 13.5s, output queue size 625
progress 40% @chr7:67000001, elapsed 48.4s, est remaining 72.6s, peak mem 4280MB, user 1397.0s, sys 15.1s, output queue size 786
progress 45% @chr8:58000001, elapsed 55.8s, est remaining 68.2s, peak mem 4359MB, user 1653.5s, sys 16.9s, output queue size 204
progress 50% @chr9:81000001, elapsed 62.3s, est remaining 62.3s, peak mem 4515MB, user 1806.6s, sys 18.1s, output queue size 366
progress 55% @chr10:109000001, elapsed 69.7s, est remaining 57.0s, peak mem 4613MB, user 2034.2s, sys 19.6s, output queue size 527
progress 60% @chr11:94000001, elapsed 79.0s, est remaining 52.7s, peak mem 4613MB, user 2320.1s, sys 21.6s, output queue size 510
progress 65% @chr13:31000001, elapsed 89.8s, est remaining 48.4s, peak mem 4622MB, user 2620.1s, sys 23.3s, output queue size 672
progress 70% @chr14:84000001, elapsed 95.9s, est remaining 41.1s, peak mem 4622MB, user 2826.9s, sys 24.7s, output queue size 833
progress 75% @chr16:42000001, elapsed 106.7s, est remaining 35.6s, peak mem 4648MB, user 3103.5s, sys 26.3s, output queue size 995
progress 80% @chr17:82000001, elapsed 122.1s, est remaining 30.5s, peak mem 4678MB, user 3567.0s, sys 28.9s, output queue size 623
progress 85% @chr20:9000001, elapsed 132.9s, est remaining 23.4s, peak mem 4716MB, user 3935.0s, sys 30.9s, output queue size 785
progress 90% @chrX:32000001, elapsed 140.7s, est remaining 15.6s, peak mem 4808MB, user 4214.1s, sys 32.4s, output queue size 513
progress 95% @chrY:20000001, elapsed 146.3s, est remaining 7.7s, peak mem 4925MB, user 4365.1s, sys 33.5s, output queue size 675
progress 100% @chrX:67000001, elapsed 158.3s, est remaining 0.0s, peak mem 4925MB, user 4578.1s, sys 35.0s, output queue size 3540
library 1029_11H-N1-BDNA-1_B23KGCJLT4_1:
chimeric_paired 4248290
duped 170799833
duped_chimeric_paired 530178
duped_paired 170798415
duped_unpaired 1418
optical_dup 49394451
paired 435644356
reads 437627048
secondary_supplementary 1979048
unmapped 3072
unpaired 1822
optical dup clusters 29283907, maxdup 26, total optical dup pairs 49394451
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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 20059887055
reads: 437628298
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2337702 calls 3.949 user 0.301 sys 4.666 real
MateInfoByVcf::load: 2337702 calls 1257.946 user 9.016 sys 1194.282 real
MateInfoByVcf::parse_events: 2337702 calls 1215.829 user 7.770 sys 1167.338 real
advance: 3219322 calls 360.205 user 8.775 sys 413.030 real
calc: 3219322 calls 2661.439 user 13.555 sys 2735.321 real
done: 1 calls 0.064 user 0.008 sys 0.076 real
exec_no_coor: 1 calls 0.000 user 0.004 sys 0.010 real
execute: 1 calls 0.001 user 0.001 sys 158.568 real
fetch: 3219323 calls 207.481 user 0.836 sys 199.132 real
find_pairEnds: 2337702 calls 212.544 user 0.587 sys 225.008 real
idle: 22527 calls 7.451 user 0.320 sys 288.403 real
init: 1 calls 0.000 user 0.010 sys 0.007 real
markDup: 2337702 calls 831.102 user 3.407 sys 889.023 real
vcfadvance: 2337702 calls 2.709 user 0.606 sys 3.146 real
write: 3219323 calls 1816.778 user 9.108 sys 1829.343 real
overall: 5164556288 mem 4589.955 user 41.778 sys 159.558 real