cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_N5D-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1029_N5D-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 6.7s, est remaining 128.0s, peak mem 9253MB, user 139.7s, sys 8.0s, output queue size 150
progress 10% @chr1:119000001, elapsed 12.5s, est remaining 112.1s, peak mem 12150MB, user 324.6s, sys 14.2s, output queue size 203
progress 15% @chr2:98000001, elapsed 18.3s, est remaining 103.7s, peak mem 17194MB, user 491.3s, sys 21.0s, output queue size 210
progress 20% @chr3:160000001, elapsed 23.8s, est remaining 95.1s, peak mem 19680MB, user 645.6s, sys 24.9s, output queue size 364
progress 25% @chr4:129000001, elapsed 28.2s, est remaining 84.6s, peak mem 19863MB, user 792.8s, sys 27.7s, output queue size 525
progress 30% @chr5:107000001, elapsed 31.6s, est remaining 73.6s, peak mem 20344MB, user 885.5s, sys 32.9s, output queue size 464
progress 35% @chr6:27000001, elapsed 36.7s, est remaining 68.2s, peak mem 21199MB, user 1027.8s, sys 35.9s, output queue size 625
progress 40% @chr7:48000001, elapsed 42.5s, est remaining 63.8s, peak mem 22581MB, user 1181.7s, sys 38.2s, output queue size 786
progress 45% @chr8:67000001, elapsed 49.1s, est remaining 60.0s, peak mem 23953MB, user 1376.4s, sys 40.2s, output queue size 948
progress 50% @chr9:81000001, elapsed 54.1s, est remaining 54.1s, peak mem 24163MB, user 1550.2s, sys 42.1s, output queue size 366
progress 55% @chr10:100000001, elapsed 60.5s, est remaining 49.5s, peak mem 24163MB, user 1706.5s, sys 43.7s, output queue size 527
progress 60% @chr12:5000001, elapsed 67.0s, est remaining 44.6s, peak mem 24163MB, user 1917.2s, sys 45.5s, output queue size 562
progress 65% @chr12:111000001, elapsed 73.6s, est remaining 39.6s, peak mem 24163MB, user 2088.0s, sys 46.8s, output queue size 724
progress 70% @chr13:28000001, elapsed 77.4s, est remaining 33.2s, peak mem 24163MB, user 2214.8s, sys 48.1s, output queue size 885
progress 75% @chr16:42000001, elapsed 85.1s, est remaining 28.4s, peak mem 24163MB, user 2428.7s, sys 49.9s, output queue size 1047
progress 80% @chr18:10000001, elapsed 95.1s, est remaining 23.8s, peak mem 24784MB, user 2762.8s, sys 53.1s, output queue size 623
progress 85% @chr19:57000001, elapsed 104.5s, est remaining 18.4s, peak mem 25341MB, user 3049.8s, sys 55.3s, output queue size 785
progress 90% @chrX:42000001, elapsed 110.2s, est remaining 12.2s, peak mem 25341MB, user 3194.8s, sys 56.4s, output queue size 947
progress 95% @chrY:53000001, elapsed 113.7s, est remaining 6.0s, peak mem 25532MB, user 3316.9s, sys 57.5s, output queue size 1109
progress 100% @chr15:88000001, elapsed 144.6s, est remaining 0.0s, peak mem 25532MB, user 3575.9s, sys 59.4s, output queue size 4099
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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 106363725463
reads: 2060211395
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 5.203 user 1.085 sys 9.961 real
VcfLineRecordHelper::sort: 166 calls 7.915 user 0.210 sys 8.206 real
advance: 3219322 calls 1805.741 user 47.751 sys 1856.592 real
calc: 3219322 calls 737.592 user 6.506 sys 743.243 real
done: 1 calls 5.203 user 1.085 sys 9.961 real
execute: 1 calls 0.006 user 0.003 sys 144.621 real
fetch: 3219322 calls 882.162 user 2.767 sys 886.169 real
idle: 1244 calls 0.284 user 0.003 sys 1181.255 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 26773127168 mem 3603.203 user 61.968 sys 155.898 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_N5D-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1029_N5D-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1029_N5D-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1029_N5D-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 46.5s, est remaining 883.8s, peak mem 9458MB, user 1178.2s, sys 13.1s, output queue size 44
progress 10% @chr2:79000001, elapsed 82.8s, est remaining 745.4s, peak mem 16855MB, user 2325.2s, sys 19.9s, output queue size 117
progress 15% @chr2:201000001, elapsed 124.2s, est remaining 703.7s, peak mem 20580MB, user 3534.6s, sys 26.6s, output queue size 203
progress 20% @chr3:158000001, elapsed 163.5s, est remaining 653.9s, peak mem 21444MB, user 4622.6s, sys 32.7s, output queue size 364
progress 25% @chr4:135000001, elapsed 195.3s, est remaining 586.0s, peak mem 22018MB, user 5742.5s, sys 41.6s, output queue size 302
progress 30% @chr5:99000001, elapsed 220.6s, est remaining 514.7s, peak mem 22307MB, user 6477.6s, sys 45.6s, output queue size 464
progress 35% @chr6:56000001, elapsed 258.1s, est remaining 479.3s, peak mem 23571MB, user 7513.7s, sys 51.3s, output queue size 625
progress 40% @chr7:41000001, elapsed 301.5s, est remaining 452.3s, peak mem 24741MB, user 8614.8s, sys 56.1s, output queue size 786
progress 45% @chr8:70000001, elapsed 348.6s, est remaining 426.0s, peak mem 26710MB, user 10211.8s, sys 63.5s, output queue size 356
progress 50% @chr9:37000001, elapsed 385.5s, est remaining 385.5s, peak mem 27206MB, user 11234.7s, sys 67.7s, output queue size 366
progress 55% @chr10:104000001, elapsed 433.0s, est remaining 354.2s, peak mem 27830MB, user 12674.0s, sys 73.5s, output queue size 400
progress 60% @chr11:130000001, elapsed 481.0s, est remaining 320.6s, peak mem 27935MB, user 13979.8s, sys 79.5s, output queue size 562
progress 65% @chr13:26000001, elapsed 528.4s, est remaining 284.5s, peak mem 28015MB, user 15314.5s, sys 86.9s, output queue size 724
progress 70% @chr12:57000001, elapsed 556.6s, est remaining 238.5s, peak mem 28054MB, user 16397.4s, sys 92.7s, output queue size 885
progress 75% @chr16:41000001, elapsed 608.1s, est remaining 202.7s, peak mem 28127MB, user 18115.5s, sys 102.2s, output queue size 461
progress 80% @chr18:1, elapsed 680.4s, est remaining 170.1s, peak mem 28477MB, user 20049.7s, sys 113.1s, output queue size 623
progress 85% @chr20:20000001, elapsed 744.9s, est remaining 131.5s, peak mem 28690MB, user 22073.5s, sys 123.9s, output queue size 785
progress 90% @chrX:39000001, elapsed 788.8s, est remaining 87.6s, peak mem 29324MB, user 23449.6s, sys 131.3s, output queue size 947
progress 95% @chrY:55000001, elapsed 813.2s, est remaining 42.8s, peak mem 29360MB, user 24408.7s, sys 136.4s, output queue size 675
progress 100% @chr15:88000001, elapsed 963.8s, est remaining 0.0s, peak mem 29360MB, user 25527.1s, sys 142.2s, output queue size 4099
library 1029_N5D-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 35306532
duped 1294791064
duped_chimeric_paired 8589256
duped_paired 1294781950
duped_unpaired 9114
optical_dup 257441977
paired 2048116304
reads 2060201657
secondary_supplementary 12064625
unmapped 20102
unpaired 10364
optical dup clusters 116658448, maxdup 102, total optical dup pairs 257441977
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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 106363725463
reads: 2060211395
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2771518 calls 33.169 user 0.545 sys 35.716 real
MateInfoByVcf::load: 2771518 calls 2809.139 user 15.049 sys 2777.444 real
MateInfoByVcf::parse_events: 2771518 calls 2648.814 user 13.015 sys 2665.081 real
advance: 3219322 calls 1760.012 user 44.338 sys 1851.936 real
calc: 3219322 calls 19480.478 user 73.079 sys 19676.432 real
done: 1 calls 0.074 user 0.008 sys 0.091 real
exec_no_coor: 1 calls 0.054 user 0.033 sys 0.101 real
execute: 1 calls 0.003 user 0.003 sys 973.072 real
fetch: 3219323 calls 1067.153 user 3.784 sys 1059.472 real
find_pairEnds: 2771518 calls 1345.656 user 2.009 sys 1375.890 real
idle: 141635 calls 78.508 user 1.425 sys 4305.047 real
init: 1 calls 0.009 user 0.001 sys 0.007 real
markDup: 2771518 calls 4930.458 user 14.999 sys 5061.661 real
vcfadvance: 2771518 calls 24.836 user 2.358 sys 21.541 real
write: 3219323 calls 14443.018 user 56.615 sys 14499.083 real
overall: 30787203072 mem 25624.738 user 187.473 sys 974.504 real