cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 9.7s, est remaining 184.9s, peak mem 12410MB, user 211.6s, sys 18.0s, output queue size 146
progress 10% @chr2:84000001, elapsed 17.5s, est remaining 157.2s, peak mem 15149MB, user 450.4s, sys 26.0s, output queue size 117
progress 15% @chr3:8000001, elapsed 26.7s, est remaining 151.2s, peak mem 21248MB, user 729.8s, sys 38.4s, output queue size 122
progress 20% @chr3:178000001, elapsed 34.3s, est remaining 137.1s, peak mem 22148MB, user 941.6s, sys 41.6s, output queue size 283
progress 25% @chr4:129000001, elapsed 41.3s, est remaining 123.8s, peak mem 22720MB, user 1167.4s, sys 44.2s, output queue size 302
progress 30% @chr5:106000001, elapsed 46.5s, est remaining 108.6s, peak mem 22720MB, user 1331.7s, sys 46.1s, output queue size 464
progress 35% @chr6:81000001, elapsed 53.8s, est remaining 99.9s, peak mem 22720MB, user 1540.3s, sys 47.8s, output queue size 625
progress 40% @chr7:64000001, elapsed 62.1s, est remaining 93.2s, peak mem 24072MB, user 1760.2s, sys 49.8s, output queue size 786
progress 45% @chr8:66000001, elapsed 72.4s, est remaining 88.5s, peak mem 24680MB, user 2019.9s, sys 52.1s, output queue size 948
progress 50% @chr9:93000001, elapsed 81.0s, est remaining 81.0s, peak mem 25897MB, user 2256.0s, sys 54.6s, output queue size 1110
progress 55% @chr10:101000001, elapsed 89.7s, est remaining 73.4s, peak mem 25984MB, user 2595.1s, sys 57.0s, output queue size 527
progress 60% @chr12:2000001, elapsed 98.8s, est remaining 65.8s, peak mem 26153MB, user 2832.1s, sys 58.8s, output queue size 689
progress 65% @chr12:111000001, elapsed 108.8s, est remaining 58.6s, peak mem 26681MB, user 3101.6s, sys 60.7s, output queue size 851
progress 70% @chr14:83000001, elapsed 114.7s, est remaining 49.2s, peak mem 26718MB, user 3271.5s, sys 61.8s, output queue size 1012
progress 75% @chr16:42000001, elapsed 124.8s, est remaining 41.6s, peak mem 26718MB, user 3629.7s, sys 63.8s, output queue size 995
progress 80% @chr18:25000001, elapsed 138.9s, est remaining 34.7s, peak mem 26721MB, user 3995.1s, sys 65.9s, output queue size 1157
progress 85% @chr20:9000001, elapsed 151.7s, est remaining 26.8s, peak mem 27066MB, user 4346.6s, sys 67.8s, output queue size 1319
progress 90% @chrX:34000001, elapsed 160.3s, est remaining 17.8s, peak mem 27861MB, user 4724.7s, sys 70.1s, output queue size 947
progress 95% @chrY:52000001, elapsed 166.7s, est remaining 8.8s, peak mem 28040MB, user 4887.7s, sys 71.3s, output queue size 1109
progress 100% @chr15:88000001, elapsed 197.9s, est remaining 0.0s, peak mem 28124MB, user 5264.1s, sys 73.3s, 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: 137200559904
reads: 3098808471
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 1.197 user 0.331 sys 1.654 real
VcfLineRecordHelper::sort: 50 calls 2.360 user 0.030 sys 2.361 real
advance: 3219322 calls 2503.444 user 60.352 sys 2566.391 real
calc: 3219322 calls 1127.416 user 5.416 sys 1138.061 real
done: 1 calls 1.197 user 0.331 sys 1.654 real
execute: 1 calls 0.004 user 0.002 sys 197.931 real
fetch: 3219322 calls 1393.406 user 5.177 sys 1397.481 real
idle: 961 calls 0.371 user 0.008 sys 869.850 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 29490982912 mem 5276.007 user 74.309 sys 201.020 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 56.9s, est remaining 1081.4s, peak mem 14223MB, user 1424.8s, sys 17.1s, output queue size 58
progress 10% @chr2:71000001, elapsed 102.7s, est remaining 924.5s, peak mem 19515MB, user 2908.6s, sys 24.8s, output queue size 56
progress 15% @chr2:218000001, elapsed 159.8s, est remaining 905.5s, peak mem 22873MB, user 4554.1s, sys 34.6s, output queue size 122
progress 20% @chr3:174000001, elapsed 207.9s, est remaining 831.6s, peak mem 23848MB, user 5988.9s, sys 40.9s, output queue size 174
progress 25% @chr4:129000001, elapsed 251.3s, est remaining 753.9s, peak mem 24218MB, user 7393.5s, sys 46.4s, output queue size 302
progress 30% @chr5:107000001, elapsed 285.3s, est remaining 665.7s, peak mem 24487MB, user 8444.7s, sys 51.4s, output queue size 464
progress 35% @chr6:81000001, elapsed 332.5s, est remaining 617.5s, peak mem 24869MB, user 9756.1s, sys 57.4s, output queue size 625
progress 40% @chr7:65000001, elapsed 388.1s, est remaining 582.1s, peak mem 25812MB, user 11223.2s, sys 64.4s, output queue size 786
progress 45% @chr8:79000001, elapsed 453.6s, est remaining 554.4s, peak mem 26620MB, user 13018.4s, sys 72.4s, output queue size 948
progress 50% @chr9:62000001, elapsed 507.2s, est remaining 507.2s, peak mem 27527MB, user 14383.9s, sys 79.4s, output queue size 1110
progress 55% @chr10:103000001, elapsed 565.7s, est remaining 462.8s, peak mem 27532MB, user 16526.5s, sys 90.1s, output queue size 527
progress 60% @chr12:1000001, elapsed 624.5s, est remaining 416.3s, peak mem 27548MB, user 18253.9s, sys 99.8s, output queue size 689
progress 65% @chr13:18000001, elapsed 688.2s, est remaining 370.6s, peak mem 28326MB, user 20241.5s, sys 110.4s, output queue size 672
progress 70% @chr14:84000001, elapsed 726.7s, est remaining 311.4s, peak mem 28326MB, user 21380.9s, sys 117.2s, output queue size 833
progress 75% @chr16:42000001, elapsed 790.9s, est remaining 263.6s, peak mem 28326MB, user 23154.3s, sys 126.1s, output queue size 995
progress 80% @chr17:78000001, elapsed 879.2s, est remaining 219.8s, peak mem 28882MB, user 25899.7s, sys 139.3s, output queue size 623
progress 85% @chr20:20000001, elapsed 953.5s, est remaining 168.3s, peak mem 28882MB, user 28231.8s, sys 151.4s, output queue size 785
progress 90% @chrX:34000001, elapsed 1007.3s, est remaining 111.9s, peak mem 29373MB, user 29875.9s, sys 161.8s, output queue size 947
progress 95% @chrY:53000001, elapsed 1048.9s, est remaining 55.2s, peak mem 29420MB, user 31286.8s, sys 170.3s, output queue size 675
progress 100% @chr15:88000001, elapsed 1157.0s, est remaining 0.0s, peak mem 29541MB, user 32904.2s, sys 182.6s, output queue size 4099
library 1047_JG-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 25876639
duped 2107786541
duped_chimeric_paired 3629656
duped_paired 2107774886
duped_unpaired 11655
optical_dup 224638416
paired 3083040314
reads 3098782751
secondary_supplementary 15717151
unmapped 38363
unpaired 12643
optical dup clusters 105489519, maxdup 78, total optical dup pairs 224638416
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: 137200559904
reads: 3098808471
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2883130 calls 21.251 user 0.411 sys 23.633 real
MateInfoByVcf::load: 2883130 calls 2617.952 user 14.856 sys 2606.584 real
MateInfoByVcf::parse_events: 2883130 calls 2482.295 user 13.088 sys 2491.340 real
advance: 3219322 calls 2409.702 user 65.561 sys 2541.323 real
calc: 3219322 calls 25670.160 user 93.827 sys 25955.016 real
done: 1 calls 0.114 user 0.047 sys 0.168 real
exec_no_coor: 1 calls 0.253 user 0.068 sys 0.335 real
execute: 1 calls 0.001 user 0.001 sys 1170.878 real
fetch: 3219323 calls 1619.270 user 3.858 sys 1648.591 real
find_pairEnds: 2883130 calls 2008.530 user 1.934 sys 2058.867 real
idle: 176182 calls 140.043 user 1.935 sys 2802.414 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 2883130 calls 7631.610 user 15.909 sys 7844.073 real
vcfadvance: 2883130 calls 11.987 user 0.992 sys 9.282 real
write: 3219323 calls 17855.045 user 76.812 sys 17913.171 real
overall: 30976077824 mem 33075.940 user 254.475 sys 1173.056 real