cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 659_cfy-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 4.1s, est remaining 78.3s, peak mem 6152MB, user 93.5s, sys 4.6s, output queue size 146
progress 10% @chr2:42000001, elapsed 7.5s, est remaining 67.9s, peak mem 7890MB, user 195.7s, sys 7.7s, output queue size 117
progress 15% @chr2:232000001, elapsed 11.5s, est remaining 65.2s, peak mem 10192MB, user 308.4s, sys 10.9s, output queue size 203
progress 20% @chr3:175000001, elapsed 14.8s, est remaining 59.2s, peak mem 10757MB, user 410.2s, sys 13.8s, output queue size 283
progress 25% @chr4:109000001, elapsed 17.8s, est remaining 53.3s, peak mem 10969MB, user 500.8s, sys 15.9s, output queue size 335
progress 30% @chr5:83000001, elapsed 20.0s, est remaining 46.6s, peak mem 11250MB, user 573.2s, sys 16.9s, output queue size 464
progress 35% @chr6:91000001, elapsed 23.2s, est remaining 43.0s, peak mem 11442MB, user 662.4s, sys 18.4s, output queue size 625
progress 40% @chr7:79000001, elapsed 26.3s, est remaining 39.5s, peak mem 11580MB, user 744.5s, sys 19.2s, output queue size 786
progress 45% @chr8:82000001, elapsed 30.6s, est remaining 37.3s, peak mem 12126MB, user 863.9s, sys 20.3s, output queue size 948
progress 50% @chr8:143000001, elapsed 33.5s, est remaining 33.5s, peak mem 12474MB, user 944.6s, sys 21.2s, output queue size 1110
progress 55% @chr10:100000001, elapsed 37.1s, est remaining 30.3s, peak mem 12474MB, user 1050.9s, sys 22.2s, output queue size 1271
progress 60% @chr12:2000001, elapsed 40.9s, est remaining 27.3s, peak mem 12678MB, user 1147.1s, sys 23.1s, output queue size 1433
progress 65% @chr13:24000001, elapsed 45.6s, est remaining 24.5s, peak mem 12982MB, user 1303.0s, sys 24.5s, output queue size 851
progress 70% @chr14:70000001, elapsed 48.1s, est remaining 20.6s, peak mem 12982MB, user 1367.6s, sys 25.3s, output queue size 1012
progress 75% @chr16:42000001, elapsed 52.9s, est remaining 17.6s, peak mem 13485MB, user 1505.6s, sys 26.2s, output queue size 1174
progress 80% @chr18:13000001, elapsed 59.4s, est remaining 14.9s, peak mem 13602MB, user 1705.0s, sys 27.8s, output queue size 1157
progress 85% @chr20:25000001, elapsed 65.4s, est remaining 11.5s, peak mem 13684MB, user 1868.2s, sys 28.8s, output queue size 1319
progress 90% @chrX:42000001, elapsed 69.6s, est remaining 7.7s, peak mem 14148MB, user 2002.2s, sys 30.0s, output queue size 1481
progress 95% @chrY:53000001, elapsed 72.7s, est remaining 3.8s, peak mem 14433MB, user 2113.2s, sys 30.7s, output queue size 1643
progress 100% @chrX:67000001, elapsed 81.9s, est remaining 0.0s, peak mem 14463MB, user 2296.4s, sys 31.9s, output queue size 3540
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: 68177098965
reads: 1410512872
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.687 user 0.214 sys 1.076 real
VcfLineRecordHelper::sort: 38 calls 1.493 user 0.050 sys 1.551 real
advance: 3219322 calls 1175.537 user 26.318 sys 1204.064 real
calc: 3219322 calls 461.161 user 2.249 sys 463.712 real
done: 1 calls 0.687 user 0.214 sys 1.076 real
execute: 1 calls 0.003 user 0.003 sys 81.912 real
fetch: 3219322 calls 561.808 user 1.535 sys 562.829 real
idle: 296 calls 0.151 user 0.002 sys 269.330 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 15165681664 mem 2302.348 user 32.744 sys 84.210 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 659_cfy-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.metrics 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:181000001, elapsed 28.7s, est remaining 544.4s, peak mem 7323MB, user 732.0s, sys 8.6s, output queue size 44
progress 10% @chr2:5000001, elapsed 50.8s, est remaining 457.2s, peak mem 10704MB, user 1441.9s, sys 13.4s, output queue size 68
progress 15% @chr3:8000001, elapsed 79.6s, est remaining 451.2s, peak mem 12240MB, user 2260.1s, sys 18.4s, output queue size 122
progress 20% @chr3:155000001, elapsed 103.1s, est remaining 412.3s, peak mem 12937MB, user 2974.6s, sys 21.7s, output queue size 174
progress 25% @chr4:124000001, elapsed 123.0s, est remaining 369.0s, peak mem 12937MB, user 3619.1s, sys 25.3s, output queue size 302
progress 30% @chr5:105000001, elapsed 139.5s, est remaining 325.5s, peak mem 13003MB, user 4114.5s, sys 28.1s, output queue size 464
progress 35% @chr6:41000001, elapsed 161.9s, est remaining 300.8s, peak mem 13156MB, user 4766.1s, sys 30.7s, output queue size 625
progress 40% @chr7:67000001, elapsed 185.2s, est remaining 277.8s, peak mem 13268MB, user 5379.6s, sys 33.7s, output queue size 786
progress 45% @chr8:79000001, elapsed 214.6s, est remaining 262.3s, peak mem 13592MB, user 6211.3s, sys 36.9s, output queue size 948
progress 50% @chr9:88000001, elapsed 235.8s, est remaining 235.8s, peak mem 13834MB, user 6761.7s, sys 39.2s, output queue size 1110
progress 55% @chr10:96000001, elapsed 261.0s, est remaining 213.5s, peak mem 13867MB, user 7669.0s, sys 42.6s, output queue size 527
progress 60% @chr11:134000001, elapsed 287.4s, est remaining 191.6s, peak mem 13994MB, user 8356.9s, sys 45.4s, output queue size 689
progress 65% @chr12:106000001, elapsed 316.5s, est remaining 170.4s, peak mem 14232MB, user 9424.5s, sys 49.1s, output queue size 672
progress 70% @chr14:84000001, elapsed 334.1s, est remaining 143.2s, peak mem 14232MB, user 9997.0s, sys 51.3s, output queue size 833
progress 75% @chr16:42000001, elapsed 365.8s, est remaining 121.9s, peak mem 14440MB, user 10744.0s, sys 53.9s, output queue size 995
progress 80% @chr18:9000001, elapsed 409.4s, est remaining 102.3s, peak mem 14680MB, user 11878.6s, sys 58.2s, output queue size 1157
progress 85% @chr20:18000001, elapsed 448.2s, est remaining 79.1s, peak mem 14778MB, user 13112.5s, sys 62.5s, output queue size 1319
progress 90% @chrX:34000001, elapsed 476.6s, est remaining 53.0s, peak mem 14789MB, user 14080.4s, sys 65.9s, output queue size 1481
progress 95% @chrY:53000001, elapsed 496.8s, est remaining 26.1s, peak mem 14875MB, user 14860.3s, sys 68.4s, output queue size 675
progress 100% @chrX:67000001, elapsed 546.6s, est remaining 0.0s, peak mem 15007MB, user 15654.4s, sys 71.0s, output queue size 3540
library 659_cfy-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 12084960
duped 785551525
duped_chimeric_paired 1354976
duped_paired 785546498
duped_unpaired 5027
optical_dup 144252760
paired 1403521362
reads 1410506610
secondary_supplementary 6973682
unmapped 12045
unpaired 5783
optical dup clusters 74601470, maxdup 65, total optical dup pairs 144252760
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: 68177098965
reads: 1410512872
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2730789 calls 10.925 user 0.382 sys 11.622 real
MateInfoByVcf::load: 2730789 calls 2185.126 user 10.012 sys 2124.744 real
MateInfoByVcf::parse_events: 2730789 calls 2107.959 user 8.561 sys 2065.243 real
advance: 3219322 calls 1119.204 user 22.203 sys 1208.254 real
calc: 3219322 calls 11484.113 user 34.259 sys 11598.623 real
done: 1 calls 0.058 user 0.000 sys 0.065 real
exec_no_coor: 1 calls 0.000 user 0.020 sys 0.031 real
execute: 1 calls 0.002 user 0.001 sys 547.190 real
fetch: 3219323 calls 623.272 user 1.522 sys 625.257 real
find_pairEnds: 2730789 calls 770.905 user 0.874 sys 792.902 real
idle: 73029 calls 30.245 user 0.712 sys 1127.246 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 2730789 calls 2927.791 user 5.883 sys 3033.701 real
vcfadvance: 2730789 calls 4.999 user 0.682 sys 5.490 real
write: 3219323 calls 8496.956 user 27.156 sys 8499.400 real
overall: 15736254464 mem 15693.872 user 92.245 sys 548.013 real