cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1136_27F-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:173000001, elapsed 6.8s, est remaining 128.3s, peak mem 8105MB, user 143.8s, sys 7.7s, output queue size 146
progress 10% @chr2:38000001, elapsed 12.1s, est remaining 109.0s, peak mem 10446MB, user 314.6s, sys 12.9s, output queue size 166
progress 15% @chr2:237000001, elapsed 17.4s, est remaining 98.9s, peak mem 13330MB, user 479.8s, sys 16.9s, output queue size 203
progress 20% @chr3:176000001, elapsed 21.8s, est remaining 87.2s, peak mem 13559MB, user 611.4s, sys 19.9s, output queue size 283
progress 25% @chr4:135000001, elapsed 25.7s, est remaining 77.0s, peak mem 13714MB, user 722.0s, sys 20.9s, output queue size 444
progress 30% @chr5:107000001, elapsed 28.6s, est remaining 66.7s, peak mem 14149MB, user 804.9s, sys 21.7s, output queue size 606
progress 35% @chr6:86000001, elapsed 33.0s, est remaining 61.3s, peak mem 14726MB, user 941.3s, sys 22.9s, output queue size 625
progress 40% @chr6:156000001, elapsed 39.7s, est remaining 59.5s, peak mem 16592MB, user 1110.1s, sys 24.5s, output queue size 786
progress 45% @chr8:54000001, elapsed 46.0s, est remaining 56.3s, peak mem 17421MB, user 1326.3s, sys 26.6s, output queue size 212
progress 50% @chr9:37000001, elapsed 51.1s, est remaining 51.1s, peak mem 21064MB, user 1462.2s, sys 28.0s, output queue size 366
progress 55% @chr10:117000001, elapsed 57.5s, est remaining 47.0s, peak mem 24788MB, user 1638.1s, sys 29.2s, output queue size 485
progress 60% @chr12:16000001, elapsed 64.2s, est remaining 42.8s, peak mem 26308MB, user 1849.0s, sys 31.4s, output queue size 647
progress 65% @chr13:35000001, elapsed 70.1s, est remaining 37.7s, peak mem 26485MB, user 2016.2s, sys 32.3s, output queue size 809
progress 70% @chr14:85000001, elapsed 73.6s, est remaining 31.5s, peak mem 26505MB, user 2144.9s, sys 33.2s, output queue size 970
progress 75% @chr16:41000001, elapsed 80.4s, est remaining 26.8s, peak mem 26505MB, user 2334.3s, sys 34.5s, output queue size 1132
progress 80% @chr18:25000001, elapsed 89.5s, est remaining 22.4s, peak mem 26608MB, user 2567.6s, sys 36.3s, output queue size 1294
progress 85% @chr20:25000001, elapsed 98.9s, est remaining 17.4s, peak mem 28017MB, user 2829.8s, sys 38.5s, output queue size 1456
progress 90% @chrX:38000001, elapsed 105.6s, est remaining 11.7s, peak mem 28954MB, user 2986.5s, sys 40.2s, output queue size 1618
progress 95% @chrY:53000001, elapsed 108.9s, est remaining 5.7s, peak mem 29436MB, user 3129.3s, sys 41.8s, output queue size 1780
progress 100% @chr7:55000001, elapsed 454.2s, est remaining 0.0s, peak mem 34823MB, user 3747.5s, sys 66.6s, output queue size 5204
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: 97469575229
reads: 2068464941
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 1.317 user 0.400 sys 2.060 real
VcfLineRecordHelper::sort: 70 calls 3.000 user 0.040 sys 3.102 real
advance: 3219322 calls 1916.662 user 45.675 sys 1965.559 real
calc: 3219322 calls 752.535 user 9.719 sys 764.283 real
done: 1 calls 1.317 user 0.400 sys 2.060 real
execute: 1 calls 0.000 user 0.004 sys 454.268 real
fetch: 3219322 calls 931.576 user 8.649 sys 939.488 real
idle: 10574 calls 2.881 user 0.011 sys 10334.940 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 36515463168 mem 3778.469 user 68.132 sys 457.894 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1136_27F-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_27F-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_27F-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 40.4s, est remaining 766.7s, peak mem 9081MB, user 966.0s, sys 10.7s, output queue size 145
progress 10% @chr1:156000001, elapsed 74.3s, est remaining 668.7s, peak mem 13604MB, user 2063.2s, sys 17.2s, output queue size 166
progress 15% @chr2:238000001, elapsed 110.7s, est remaining 627.5s, peak mem 14904MB, user 3190.8s, sys 25.2s, output queue size 122
progress 20% @chr3:155000001, elapsed 141.4s, est remaining 565.8s, peak mem 14975MB, user 4099.8s, sys 28.9s, output queue size 283
progress 25% @chr4:136000001, elapsed 165.9s, est remaining 497.8s, peak mem 15066MB, user 4909.3s, sys 33.0s, output queue size 302
progress 30% @chr5:105000001, elapsed 184.4s, est remaining 430.2s, peak mem 15078MB, user 5488.0s, sys 35.9s, output queue size 464
progress 35% @chr6:81000001, elapsed 212.3s, est remaining 394.3s, peak mem 15979MB, user 6179.5s, sys 39.3s, output queue size 625
progress 40% @chr7:41000001, elapsed 253.1s, est remaining 379.7s, peak mem 18021MB, user 7250.6s, sys 43.9s, output queue size 786
progress 45% @chr8:74000001, elapsed 291.1s, est remaining 355.8s, peak mem 21987MB, user 8546.5s, sys 49.6s, output queue size 204
progress 50% @chr9:88000001, elapsed 320.9s, est remaining 320.9s, peak mem 25635MB, user 9423.9s, sys 52.5s, output queue size 324
progress 55% @chr10:104000001, elapsed 361.4s, est remaining 295.7s, peak mem 28369MB, user 10513.8s, sys 57.6s, output queue size 485
progress 60% @chr12:3000001, elapsed 399.0s, est remaining 266.0s, peak mem 28369MB, user 11770.4s, sys 62.7s, output queue size 647
progress 65% @chr12:106000001, elapsed 433.1s, est remaining 233.2s, peak mem 28369MB, user 12878.7s, sys 66.4s, output queue size 809
progress 70% @chr14:72000001, elapsed 455.7s, est remaining 195.3s, peak mem 28369MB, user 13522.4s, sys 68.8s, output queue size 970
progress 75% @chr16:42000001, elapsed 502.1s, est remaining 167.4s, peak mem 28517MB, user 14675.6s, sys 72.4s, output queue size 1132
progress 80% @chr17:68000001, elapsed 566.4s, est remaining 141.6s, peak mem 28825MB, user 16291.1s, sys 78.0s, output queue size 1294
progress 85% @chr19:35000001, elapsed 628.2s, est remaining 110.9s, peak mem 29641MB, user 18268.6s, sys 85.3s, output queue size 1456
progress 90% @chrX:39000001, elapsed 668.8s, est remaining 74.3s, peak mem 30621MB, user 19563.7s, sys 91.0s, output queue size 1618
progress 95% @chrY:53000001, elapsed 690.6s, est remaining 36.3s, peak mem 31030MB, user 20121.9s, sys 94.0s, output queue size 1780
progress 100% @chr7:55000001, elapsed 2194.9s, est remaining 0.0s, peak mem 36473MB, user 23101.2s, sys 149.1s, output queue size 5204
library 1136_27F-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 28960505
duped 1310281809
duped_chimeric_paired 5680278
duped_paired 1310273768
duped_unpaired 8041
optical_dup 166833585
paired 2051128350
reads 2068449701
secondary_supplementary 17303641
unmapped 24095
unpaired 8855
optical dup clusters 83706882, maxdup 63, total optical dup pairs 166833585
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: 97469575229
reads: 2068464941
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2806737 calls 20.212 user 0.415 sys 20.411 real
MateInfoByVcf::load: 2806737 calls 2538.646 user 12.310 sys 2506.276 real
MateInfoByVcf::parse_events: 2806737 calls 2398.449 user 10.600 sys 2418.307 real
advance: 3219322 calls 1803.382 user 44.593 sys 1915.644 real
calc: 3219322 calls 17282.562 user 77.439 sys 17466.692 real
done: 1 calls 0.186 user 0.098 sys 0.291 real
exec_no_coor: 1 calls 0.087 user 0.038 sys 0.135 real
execute: 1 calls 0.001 user 0.000 sys 2224.717 real
fetch: 3219323 calls 1082.108 user 8.451 sys 1076.452 real
find_pairEnds: 2806737 calls 1331.186 user 4.364 sys 1356.490 real
idle: 731342 calls 507.605 user 5.822 sys 45007.107 real
init: 1 calls 0.000 user 0.000 sys 0.007 real
markDup: 2806737 calls 5125.967 user 33.144 sys 5252.388 real
vcfadvance: 2806737 calls 9.048 user 1.092 sys 8.951 real
write: 3219323 calls 12040.325 user 43.104 sys 12090.163 real
overall: 38245072896 mem 23722.892 user 218.729 sys 2228.289 real