cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_3U6-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1136_3U6-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 5.9s, est remaining 111.2s, peak mem 8508MB, user 121.9s, sys 7.9s, output queue size 150
progress 10% @chr2:46000001, elapsed 10.7s, est remaining 96.4s, peak mem 11786MB, user 266.2s, sys 13.5s, output queue size 166
progress 15% @chr3:18000001, elapsed 16.1s, est remaining 91.4s, peak mem 15341MB, user 424.3s, sys 18.6s, output queue size 203
progress 20% @chr3:178000001, elapsed 20.6s, est remaining 82.4s, peak mem 17093MB, user 557.4s, sys 21.6s, output queue size 364
progress 25% @chr4:124000001, elapsed 24.8s, est remaining 74.3s, peak mem 17480MB, user 682.2s, sys 23.5s, output queue size 525
progress 30% @chr5:106000001, elapsed 27.8s, est remaining 64.9s, peak mem 17677MB, user 770.9s, sys 24.5s, output queue size 687
progress 35% @chr6:56000001, elapsed 32.2s, est remaining 59.8s, peak mem 18081MB, user 913.2s, sys 28.7s, output queue size 625
progress 40% @chr7:66000001, elapsed 37.4s, est remaining 56.1s, peak mem 19427MB, user 1041.6s, sys 30.4s, output queue size 786
progress 45% @chr8:78000001, elapsed 43.4s, est remaining 53.0s, peak mem 19544MB, user 1221.9s, sys 32.7s, output queue size 948
progress 50% @chr9:94000001, elapsed 48.1s, est remaining 48.1s, peak mem 19544MB, user 1342.7s, sys 33.9s, output queue size 1110
progress 55% @chr10:104000001, elapsed 53.9s, est remaining 44.1s, peak mem 20221MB, user 1526.7s, sys 35.4s, output queue size 527
progress 60% @chr11:94000001, elapsed 59.6s, est remaining 39.7s, peak mem 20221MB, user 1704.1s, sys 36.7s, output queue size 647
progress 65% @chr13:35000001, elapsed 65.3s, est remaining 35.1s, peak mem 20344MB, user 1882.7s, sys 38.1s, output queue size 672
progress 70% @chr14:71000001, elapsed 68.6s, est remaining 29.4s, peak mem 20569MB, user 1994.1s, sys 39.0s, output queue size 833
progress 75% @chr16:42000001, elapsed 75.3s, est remaining 25.1s, peak mem 21352MB, user 2159.8s, sys 40.6s, output queue size 995
progress 80% @chr18:29000001, elapsed 84.9s, est remaining 21.2s, peak mem 21473MB, user 2446.2s, sys 42.6s, output queue size 623
progress 85% @chr20:48000001, elapsed 93.6s, est remaining 16.5s, peak mem 21578MB, user 2711.4s, sys 44.8s, output queue size 785
progress 90% @chrX:36000001, elapsed 99.0s, est remaining 11.0s, peak mem 21768MB, user 2900.5s, sys 46.1s, output queue size 947
progress 95% @chrY:51000001, elapsed 103.3s, est remaining 5.4s, peak mem 21958MB, user 3011.5s, sys 47.0s, output queue size 1108
progress 100% @chr15:88000001, elapsed 120.5s, est remaining 0.0s, peak mem 21992MB, user 3263.8s, sys 48.4s, 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: 96892903634
reads: 1941527573
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 2.621 user 0.833 sys 5.876 real
VcfLineRecordHelper::sort: 109 calls 4.890 user 0.130 sys 5.002 real
advance: 3219322 calls 1745.957 user 39.548 sys 1785.813 real
calc: 3219322 calls 641.699 user 4.188 sys 647.418 real
done: 1 calls 2.621 user 0.833 sys 5.876 real
execute: 1 calls 0.006 user 0.003 sys 120.490 real
fetch: 3219322 calls 759.953 user 2.643 sys 762.653 real
idle: 671 calls 0.187 user 0.003 sys 631.218 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 23060910080 mem 3281.105 user 50.513 sys 127.812 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_3U6-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1136_3U6-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_3U6-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_3U6-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 41.7s, est remaining 792.8s, peak mem 9868MB, user 1015.6s, sys 9.1s, output queue size 145
progress 10% @chr2:80000001, elapsed 73.6s, est remaining 662.3s, peak mem 14599MB, user 2061.9s, sys 15.2s, output queue size 117
progress 15% @chr3:8000001, elapsed 111.0s, est remaining 629.0s, peak mem 18880MB, user 3132.4s, sys 21.4s, output queue size 203
progress 20% @chr3:176000001, elapsed 145.0s, est remaining 580.1s, peak mem 19256MB, user 4166.5s, sys 26.2s, output queue size 364
progress 25% @chr4:124000001, elapsed 173.4s, est remaining 520.2s, peak mem 19393MB, user 5120.9s, sys 33.5s, output queue size 302
progress 30% @chr5:104000001, elapsed 195.6s, est remaining 456.3s, peak mem 19448MB, user 5838.5s, sys 36.3s, output queue size 464
progress 35% @chr6:79000001, elapsed 227.5s, est remaining 422.5s, peak mem 20317MB, user 6625.0s, sys 39.6s, output queue size 625
progress 40% @chr7:66000001, elapsed 266.6s, est remaining 399.8s, peak mem 21186MB, user 7556.4s, sys 42.9s, output queue size 786
progress 45% @chr8:74000001, elapsed 313.5s, est remaining 383.1s, peak mem 21362MB, user 9235.6s, sys 49.3s, output queue size 204
progress 50% @chr9:81000001, elapsed 355.9s, est remaining 355.9s, peak mem 21370MB, user 10247.7s, sys 52.8s, output queue size 366
progress 55% @chr10:99000001, elapsed 403.6s, est remaining 330.2s, peak mem 21705MB, user 11925.7s, sys 57.6s, output queue size 348
progress 60% @chr11:117000001, elapsed 454.3s, est remaining 302.9s, peak mem 21705MB, user 13467.2s, sys 62.4s, output queue size 510
progress 65% @chr13:23000001, elapsed 503.4s, est remaining 271.1s, peak mem 21971MB, user 14818.1s, sys 66.7s, output queue size 672
progress 70% @chr14:79000001, elapsed 534.4s, est remaining 229.0s, peak mem 21971MB, user 15830.4s, sys 70.0s, output queue size 833
progress 75% @chr16:42000001, elapsed 590.9s, est remaining 197.0s, peak mem 22452MB, user 17331.2s, sys 74.9s, output queue size 995
progress 80% @chr18:10000001, elapsed 672.3s, est remaining 168.1s, peak mem 22786MB, user 19821.6s, sys 83.2s, output queue size 623
progress 85% @chr20:9000001, elapsed 738.7s, est remaining 130.4s, peak mem 23036MB, user 21942.5s, sys 93.0s, output queue size 785
progress 90% @chrX:35000001, elapsed 778.8s, est remaining 86.5s, peak mem 23329MB, user 23492.1s, sys 100.3s, output queue size 513
progress 95% @chrY:54000001, elapsed 810.1s, est remaining 42.6s, peak mem 23501MB, user 24246.6s, sys 104.5s, output queue size 675
progress 100% @chr22:23000001, elapsed 881.6s, est remaining 0.0s, peak mem 23523MB, user 25488.8s, sys 110.7s, output queue size 3635
library 1136_3U6-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 24834550
duped 1211943557
duped_chimeric_paired 4585324
duped_paired 1211935278
duped_unpaired 8279
optical_dup 235981125
paired 1931183962
reads 1941516891
secondary_supplementary 10314273
unmapped 20010
unpaired 9328
optical dup clusters 109805166, maxdup 66, total optical dup pairs 235981125
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: 96892903634
reads: 1941527573
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2743787 calls 26.768 user 0.527 sys 28.051 real
MateInfoByVcf::load: 2743787 calls 2884.394 user 11.298 sys 2851.450 real
MateInfoByVcf::parse_events: 2743787 calls 2736.678 user 9.365 sys 2753.005 real
advance: 3219322 calls 1893.007 user 40.310 sys 1990.183 real
calc: 3219322 calls 19349.811 user 51.611 sys 19492.683 real
done: 1 calls 0.068 user 0.018 sys 0.089 real
exec_no_coor: 1 calls 0.050 user 0.019 sys 0.094 real
execute: 1 calls 0.000 user 0.001 sys 882.884 real
fetch: 3219323 calls 1000.734 user 3.123 sys 991.366 real
find_pairEnds: 2743787 calls 1194.199 user 1.267 sys 1214.792 real
idle: 118279 calls 51.026 user 0.914 sys 1640.486 real
init: 1 calls 0.000 user 0.010 sys 0.008 real
markDup: 2743787 calls 4575.777 user 11.725 sys 4671.658 real
vcfadvance: 2743787 calls 16.247 user 1.501 sys 16.034 real
write: 3219323 calls 14672.266 user 38.460 sys 14713.060 real
overall: 24666230784 mem 25554.416 user 143.861 sys 884.833 real