cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 3.3s, est remaining 62.6s, peak mem 4045MB, user 75.1s, sys 3.2s, output queue size 146
progress 10% @chr2:46000001, elapsed 6.1s, est remaining 54.6s, peak mem 5031MB, user 158.5s, sys 6.9s, output queue size 166
progress 15% @chr2:237000001, elapsed 9.2s, est remaining 52.2s, peak mem 6606MB, user 249.6s, sys 11.4s, output queue size 203
progress 20% @chr3:174000001, elapsed 11.8s, est remaining 47.1s, peak mem 6902MB, user 325.3s, sys 14.7s, output queue size 283
progress 25% @chr4:133000001, elapsed 13.8s, est remaining 41.5s, peak mem 7222MB, user 387.4s, sys 15.3s, output queue size 444
progress 30% @chr5:104000001, elapsed 15.4s, est remaining 36.0s, peak mem 7351MB, user 445.1s, sys 16.4s, output queue size 464
progress 35% @chr6:70000001, elapsed 17.9s, est remaining 33.3s, peak mem 7587MB, user 508.4s, sys 17.2s, output queue size 625
progress 40% @chr7:66000001, elapsed 21.0s, est remaining 31.5s, peak mem 8261MB, user 582.9s, sys 18.1s, output queue size 786
progress 45% @chr8:66000001, elapsed 24.1s, est remaining 29.5s, peak mem 8441MB, user 691.8s, sys 19.4s, output queue size 356
progress 50% @chr9:87000001, elapsed 27.4s, est remaining 27.4s, peak mem 9054MB, user 777.7s, sys 20.5s, output queue size 366
progress 55% @chr10:104000001, elapsed 30.7s, est remaining 25.1s, peak mem 9627MB, user 881.9s, sys 21.7s, output queue size 485
progress 60% @chr12:5000001, elapsed 34.1s, est remaining 22.7s, peak mem 9653MB, user 991.0s, sys 22.7s, output queue size 510
progress 65% @chr12:123000001, elapsed 37.4s, est remaining 20.2s, peak mem 9663MB, user 1095.0s, sys 23.5s, output queue size 474
progress 70% @chr14:72000001, elapsed 39.7s, est remaining 17.0s, peak mem 9776MB, user 1170.0s, sys 24.2s, output queue size 459
progress 75% @chr16:42000001, elapsed 43.1s, est remaining 14.4s, peak mem 9802MB, user 1267.3s, sys 25.1s, output queue size 461
progress 80% @chr18:11000001, elapsed 48.7s, est remaining 12.2s, peak mem 10369MB, user 1415.4s, sys 26.4s, output queue size 623
progress 85% @chr19:55000001, elapsed 53.7s, est remaining 9.5s, peak mem 10380MB, user 1579.5s, sys 27.3s, output queue size 785
progress 90% @chrX:30000001, elapsed 57.2s, est remaining 6.4s, peak mem 10626MB, user 1670.0s, sys 28.2s, output queue size 947
progress 95% @chrY:18000001, elapsed 59.2s, est remaining 3.1s, peak mem 10801MB, user 1760.2s, sys 28.9s, output queue size 675
progress 100% @chr22:23000001, elapsed 66.1s, est remaining 0.0s, peak mem 10804MB, user 1850.8s, sys 29.7s, output queue size 3635
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 53670188330
reads: 1048916945
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.807 user 0.236 sys 1.191 real
VcfLineRecordHelper::sort: 36 calls 1.797 user 0.100 sys 1.901 real
advance: 3219322 calls 1129.864 user 23.804 sys 1153.006 real
calc: 3219322 calls 334.483 user 2.073 sys 336.908 real
done: 1 calls 0.807 user 0.236 sys 1.191 real
execute: 1 calls 0.002 user 0.001 sys 66.202 real
fetch: 3219322 calls 331.431 user 1.921 sys 335.417 real
idle: 278 calls 0.125 user 0.012 sys 236.042 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 11329347584 mem 1858.296 user 30.677 sys 68.679 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:154000001, elapsed 24.5s, est remaining 466.3s, peak mem 4667MB, user 605.1s, sys 6.1s, output queue size 145
progress 10% @chr2:93000001, elapsed 43.9s, est remaining 394.9s, peak mem 6881MB, user 1258.0s, sys 9.7s, output queue size 48
progress 15% @chr2:224000001, elapsed 66.3s, est remaining 375.8s, peak mem 7948MB, user 1927.6s, sys 14.0s, output queue size 122
progress 20% @chr3:155000001, elapsed 86.3s, est remaining 345.1s, peak mem 7948MB, user 2528.9s, sys 17.5s, output queue size 141
progress 25% @chr4:124000001, elapsed 101.9s, est remaining 305.6s, peak mem 7948MB, user 3009.7s, sys 19.9s, output queue size 302
progress 30% @chr5:35000001, elapsed 113.8s, est remaining 265.6s, peak mem 7957MB, user 3419.3s, sys 21.7s, output queue size 464
progress 35% @chr6:78000001, elapsed 133.6s, est remaining 248.2s, peak mem 8121MB, user 3968.1s, sys 24.0s, output queue size 97
progress 40% @chr7:56000001, elapsed 156.4s, est remaining 234.6s, peak mem 8599MB, user 4615.8s, sys 26.6s, output queue size 197
progress 45% @chr8:72000001, elapsed 179.8s, est remaining 219.7s, peak mem 8967MB, user 5325.0s, sys 29.6s, output queue size 204
progress 50% @chr9:32000001, elapsed 203.0s, est remaining 203.0s, peak mem 9681MB, user 5904.5s, sys 32.0s, output queue size 366
progress 55% @chr10:109000001, elapsed 227.3s, est remaining 185.9s, peak mem 9871MB, user 6783.3s, sys 36.0s, output queue size 348
progress 60% @chr11:130000001, elapsed 252.3s, est remaining 168.2s, peak mem 9958MB, user 7560.7s, sys 39.0s, output queue size 312
progress 65% @chr12:106000001, elapsed 276.8s, est remaining 149.1s, peak mem 10201MB, user 8336.9s, sys 41.5s, output queue size 138
progress 70% @chr14:78000001, elapsed 292.8s, est remaining 125.5s, peak mem 10369MB, user 8819.2s, sys 43.6s, output queue size 299
progress 75% @chr16:42000001, elapsed 318.3s, est remaining 106.1s, peak mem 10482MB, user 9533.2s, sys 46.4s, output queue size 461
progress 80% @chr18:20000001, elapsed 358.0s, est remaining 89.5s, peak mem 10681MB, user 10599.2s, sys 50.0s, output queue size 623
progress 85% @chr20:29000001, elapsed 392.4s, est remaining 69.2s, peak mem 10810MB, user 11870.0s, sys 54.1s, output queue size 351
progress 90% @chrX:31000001, elapsed 418.3s, est remaining 46.5s, peak mem 11107MB, user 12612.9s, sys 56.7s, output queue size 513
progress 95% @chrY:53000001, elapsed 432.9s, est remaining 22.8s, peak mem 11107MB, user 13047.1s, sys 58.2s, output queue size 675
progress 100% @chr22:23000001, elapsed 453.6s, est remaining 0.0s, peak mem 11107MB, user 13556.1s, sys 60.1s, output queue size 3635
library 1136_4GR-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 17208056
duped 560823517
duped_chimeric_paired 3323798
duped_paired 560819442
duped_unpaired 4075
optical_dup 81447611
paired 1040205284
reads 1048911417
secondary_supplementary 8696705
unmapped 10242
unpaired 4714
optical dup clusters 45168282, maxdup 80, total optical dup pairs 81447611
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 53670188330
reads: 1048916945
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2688541 calls 8.501 user 0.369 sys 8.360 real
MateInfoByVcf::load: 2688541 calls 2508.772 user 10.575 sys 2437.120 real
MateInfoByVcf::parse_events: 2688541 calls 2419.043 user 8.730 sys 2386.645 real
advance: 3219322 calls 1101.199 user 18.948 sys 1183.124 real
calc: 3219322 calls 9376.309 user 25.423 sys 9471.273 real
done: 1 calls 0.064 user 0.000 sys 0.073 real
exec_no_coor: 1 calls 0.010 user 0.008 sys 0.017 real
execute: 1 calls 0.007 user 0.002 sys 454.319 real
fetch: 3219323 calls 410.841 user 1.303 sys 395.832 real
find_pairEnds: 2688541 calls 491.248 user 0.780 sys 503.458 real
idle: 26095 calls 28.371 user 0.149 sys 401.468 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 2688541 calls 2028.546 user 5.723 sys 2098.928 real
vcfadvance: 2688541 calls 4.317 user 0.985 sys 4.760 real
write: 3219323 calls 7306.875 user 18.405 sys 7326.819 real
overall: 11647168512 mem 13593.407 user 80.131 sys 455.064 real