cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_T05-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1029_T05-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:46000001, elapsed 4.4s, est remaining 84.2s, peak mem 5986MB, user 101.7s, sys 4.4s, output queue size 146
progress 10% @chr1:226000001, elapsed 8.4s, est remaining 75.9s, peak mem 8814MB, user 212.2s, sys 7.8s, output queue size 166
progress 15% @chr2:25000001, elapsed 12.4s, est remaining 70.3s, peak mem 11700MB, user 340.4s, sys 12.7s, output queue size 210
progress 20% @chr3:174000001, elapsed 16.1s, est remaining 64.4s, peak mem 12844MB, user 438.2s, sys 14.5s, output queue size 364
progress 25% @chr4:109000001, elapsed 19.0s, est remaining 57.1s, peak mem 12906MB, user 534.1s, sys 17.8s, output queue size 444
progress 30% @chr5:101000001, elapsed 21.3s, est remaining 49.6s, peak mem 13103MB, user 611.2s, sys 19.0s, output queue size 464
progress 35% @chr6:81000001, elapsed 24.6s, est remaining 45.8s, peak mem 13766MB, user 701.7s, sys 20.3s, output queue size 625
progress 40% @chr6:33000001, elapsed 28.5s, est remaining 42.8s, peak mem 14020MB, user 802.2s, sys 21.4s, output queue size 786
progress 45% @chr8:79000001, elapsed 33.1s, est remaining 40.4s, peak mem 14162MB, user 940.9s, sys 23.1s, output queue size 948
progress 50% @chr9:102000001, elapsed 36.7s, est remaining 36.7s, peak mem 14611MB, user 1046.7s, sys 24.3s, output queue size 366
progress 55% @chr10:103000001, elapsed 41.0s, est remaining 33.5s, peak mem 15001MB, user 1168.6s, sys 25.5s, output queue size 527
progress 60% @chr11:134000001, elapsed 44.9s, est remaining 30.0s, peak mem 15001MB, user 1311.2s, sys 26.9s, output queue size 510
progress 65% @chr13:35000001, elapsed 48.8s, est remaining 26.3s, peak mem 15509MB, user 1412.7s, sys 28.0s, output queue size 672
progress 70% @chr14:86000001, elapsed 51.4s, est remaining 22.0s, peak mem 15533MB, user 1483.3s, sys 28.8s, output queue size 833
progress 75% @chr16:41000001, elapsed 55.9s, est remaining 18.6s, peak mem 15803MB, user 1620.8s, sys 29.9s, output queue size 797
progress 80% @chr18:10000001, elapsed 62.3s, est remaining 15.6s, peak mem 16066MB, user 1821.4s, sys 31.5s, output queue size 623
progress 85% @chr19:57000001, elapsed 68.7s, est remaining 12.1s, peak mem 16066MB, user 2005.8s, sys 32.9s, output queue size 785
progress 90% @chrX:42000001, elapsed 73.2s, est remaining 8.1s, peak mem 16468MB, user 2122.4s, sys 34.0s, output queue size 947
progress 95% @chrY:52000001, elapsed 76.6s, est remaining 4.0s, peak mem 16545MB, user 2222.7s, sys 34.9s, output queue size 1109
progress 100% @chr15:88000001, elapsed 91.5s, est remaining 0.0s, peak mem 16545MB, user 2430.9s, sys 36.8s, output queue size 4099
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 78223957301
reads: 1549027000
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 2.016 user 0.628 sys 3.465 real
VcfLineRecordHelper::sort: 96 calls 3.891 user 0.140 sys 3.983 real
advance: 3219322 calls 1356.637 user 29.766 sys 1385.418 real
calc: 3219322 calls 462.800 user 2.962 sys 469.269 real
done: 1 calls 2.016 user 0.628 sys 3.465 real
execute: 1 calls 0.002 user 0.003 sys 91.492 real
fetch: 3219322 calls 528.844 user 2.109 sys 531.211 real
idle: 526 calls 0.139 user 0.002 sys 502.929 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 17349128192 mem 2443.212 user 38.444 sys 96.340 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_T05-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1029_T05-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1029_T05-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1029_T05-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 30.8s, est remaining 585.2s, peak mem 6932MB, user 752.0s, sys 7.6s, output queue size 42
progress 10% @chr2:80000001, elapsed 58.7s, est remaining 528.5s, peak mem 11751MB, user 1641.9s, sys 12.8s, output queue size 117
progress 15% @chr2:201000001, elapsed 87.3s, est remaining 494.9s, peak mem 13992MB, user 2500.9s, sys 18.2s, output queue size 203
progress 20% @chr3:158000001, elapsed 114.7s, est remaining 459.0s, peak mem 14180MB, user 3366.1s, sys 24.1s, output queue size 141
progress 25% @chr4:124000001, elapsed 135.9s, est remaining 407.7s, peak mem 14302MB, user 4014.5s, sys 27.0s, output queue size 302
progress 30% @chr5:104000001, elapsed 153.2s, est remaining 357.5s, peak mem 14465MB, user 4576.0s, sys 29.3s, output queue size 464
progress 35% @chr6:79000001, elapsed 178.8s, est remaining 332.0s, peak mem 15189MB, user 5217.5s, sys 31.9s, output queue size 625
progress 40% @chr7:41000001, elapsed 208.9s, est remaining 313.3s, peak mem 15189MB, user 6055.4s, sys 35.9s, output queue size 786
progress 45% @chr8:8000001, elapsed 241.3s, est remaining 294.9s, peak mem 16035MB, user 7168.1s, sys 40.3s, output queue size 204
progress 50% @chr8:144000001, elapsed 267.6s, est remaining 267.6s, peak mem 16323MB, user 7838.6s, sys 42.7s, output queue size 366
progress 55% @chr10:115000001, elapsed 302.0s, est remaining 247.1s, peak mem 16767MB, user 8932.9s, sys 47.0s, output queue size 348
progress 60% @chr11:134000001, elapsed 332.4s, est remaining 221.6s, peak mem 16767MB, user 9897.6s, sys 50.6s, output queue size 510
progress 65% @chr13:23000001, elapsed 361.7s, est remaining 194.8s, peak mem 16870MB, user 10775.6s, sys 53.8s, output queue size 474
progress 70% @chr13:102000001, elapsed 381.0s, est remaining 163.3s, peak mem 16870MB, user 11404.8s, sys 56.1s, output queue size 635
progress 75% @chr16:42000001, elapsed 411.0s, est remaining 137.0s, peak mem 16870MB, user 12331.0s, sys 59.4s, output queue size 461
progress 80% @chr18:20000001, elapsed 458.4s, est remaining 114.6s, peak mem 16948MB, user 13611.1s, sys 63.7s, output queue size 623
progress 85% @chr20:39000001, elapsed 505.0s, est remaining 89.1s, peak mem 17036MB, user 15075.6s, sys 68.5s, output queue size 785
progress 90% @chrX:30000001, elapsed 539.1s, est remaining 59.9s, peak mem 17363MB, user 15956.2s, sys 71.6s, output queue size 947
progress 95% @chrY:55000001, elapsed 564.9s, est remaining 29.7s, peak mem 17632MB, user 16668.9s, sys 74.4s, output queue size 1109
progress 100% @chrX:67000001, elapsed 618.6s, est remaining 0.0s, peak mem 17632MB, user 17811.7s, sys 78.1s, output queue size 3540
library 1029_T05-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 26878738
duped 1000930442
duped_chimeric_paired 6763194
duped_paired 1000923805
duped_unpaired 6637
optical_dup 169741184
paired 1538193740
reads 1549020226
secondary_supplementary 10811230
unmapped 14402
unpaired 7628
optical dup clusters 77377753, maxdup 97, total optical dup pairs 169741184
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 78223957301
reads: 1549027000
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2656808 calls 18.422 user 0.325 sys 18.775 real
MateInfoByVcf::load: 2656808 calls 2449.687 user 9.672 sys 2396.641 real
MateInfoByVcf::parse_events: 2656808 calls 2315.572 user 8.091 sys 2320.438 real
advance: 3219322 calls 1355.787 user 26.635 sys 1450.000 real
calc: 3219322 calls 13071.575 user 36.377 sys 13188.006 real
done: 1 calls 0.067 user 0.008 sys 0.080 real
exec_no_coor: 1 calls 0.010 user 0.021 sys 0.043 real
execute: 1 calls 0.000 user 0.001 sys 619.584 real
fetch: 3219323 calls 690.297 user 1.656 sys 669.665 real
find_pairEnds: 2656808 calls 817.364 user 0.997 sys 837.940 real
idle: 85552 calls 30.451 user 0.567 sys 1238.420 real
init: 1 calls 0.000 user 0.010 sys 0.006 real
markDup: 2656808 calls 3111.644 user 7.898 sys 3201.776 real
vcfadvance: 2656808 calls 9.009 user 1.197 sys 9.688 real
write: 3219323 calls 9886.742 user 27.142 sys 9907.965 real
overall: 18488897536 mem 17853.239 user 103.209 sys 621.215 real