cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_85O-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1136_85O-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 2.6s, est remaining 49.4s, peak mem 3319MB, user 55.9s, sys 3.0s, output queue size 146
progress 10% @chr2:94000001, elapsed 4.9s, est remaining 43.9s, peak mem 4852MB, user 128.4s, sys 4.9s, output queue size 117
progress 15% @chr2:224000001, elapsed 7.0s, est remaining 39.9s, peak mem 6017MB, user 194.4s, sys 7.0s, output queue size 203
progress 20% @chr3:178000001, elapsed 8.9s, est remaining 35.5s, peak mem 6310MB, user 246.8s, sys 8.3s, output queue size 283
progress 25% @chr4:124000001, elapsed 10.6s, est remaining 31.7s, peak mem 6363MB, user 302.7s, sys 9.5s, output queue size 302
progress 30% @chr5:101000001, elapsed 11.8s, est remaining 27.6s, peak mem 6558MB, user 341.0s, sys 10.1s, output queue size 464
progress 35% @chr6:82000001, elapsed 14.1s, est remaining 26.2s, peak mem 7197MB, user 399.4s, sys 11.4s, output queue size 625
progress 40% @chr7:48000001, elapsed 16.3s, est remaining 24.5s, peak mem 8224MB, user 453.3s, sys 12.3s, output queue size 786
progress 45% @chr8:78000001, elapsed 19.0s, est remaining 23.3s, peak mem 8304MB, user 527.6s, sys 13.8s, output queue size 948
progress 50% @chr9:76000001, elapsed 21.2s, est remaining 21.2s, peak mem 8514MB, user 602.5s, sys 15.2s, output queue size 518
progress 55% @chr9:136000001, elapsed 23.3s, est remaining 19.1s, peak mem 8621MB, user 676.0s, sys 15.9s, output queue size 527
progress 60% @chr11:134000001, elapsed 25.4s, est remaining 16.9s, peak mem 8621MB, user 739.9s, sys 16.6s, output queue size 510
progress 65% @chr13:24000001, elapsed 27.6s, est remaining 14.8s, peak mem 8729MB, user 800.0s, sys 17.2s, output queue size 672
progress 70% @chr12:57000001, elapsed 28.9s, est remaining 12.4s, peak mem 8785MB, user 845.8s, sys 17.7s, output queue size 833
progress 75% @chr15:43000001, elapsed 31.4s, est remaining 10.5s, peak mem 8935MB, user 906.5s, sys 18.2s, output queue size 995
progress 80% @chr18:10000001, elapsed 34.5s, est remaining 8.6s, peak mem 9009MB, user 999.5s, sys 19.0s, output queue size 1157
progress 85% @chr18:63000001, elapsed 37.2s, est remaining 6.6s, peak mem 9009MB, user 1090.1s, sys 19.8s, output queue size 785
progress 90% @chrX:30000001, elapsed 39.0s, est remaining 4.3s, peak mem 9039MB, user 1143.4s, sys 20.4s, output queue size 947
progress 95% @chrY:49000001, elapsed 40.2s, est remaining 2.1s, peak mem 9041MB, user 1174.2s, sys 20.8s, output queue size 1109
progress 100% @chr15:88000001, elapsed 48.8s, est remaining 0.0s, peak mem 9041MB, user 1264.1s, sys 21.6s, 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: 44057164419
reads: 870183887
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.624 user 0.259 sys 0.977 real
VcfLineRecordHelper::sort: 35 calls 1.367 user 0.060 sys 1.440 real
advance: 3219322 calls 757.220 user 17.376 sys 776.990 real
calc: 3219322 calls 226.625 user 1.518 sys 227.411 real
done: 1 calls 0.624 user 0.259 sys 0.977 real
execute: 1 calls 0.001 user 0.003 sys 48.845 real
fetch: 3219322 calls 242.472 user 1.071 sys 243.446 real
idle: 312 calls 0.166 user 0.002 sys 286.100 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 9480441856 mem 1269.923 user 22.502 sys 51.108 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_85O-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1136_85O-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_85O-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_85O-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:154000001, elapsed 17.9s, est remaining 340.5s, peak mem 4213MB, user 440.7s, sys 4.8s, output queue size 42
progress 10% @chr2:90000001, elapsed 34.2s, est remaining 307.7s, peak mem 6266MB, user 964.3s, sys 8.2s, output queue size 79
progress 15% @chr3:3000001, elapsed 49.7s, est remaining 281.6s, peak mem 6818MB, user 1439.7s, sys 11.5s, output queue size 122
progress 20% @chr3:136000001, elapsed 63.6s, est remaining 254.4s, peak mem 7099MB, user 1881.6s, sys 14.4s, output queue size 141
progress 25% @chr4:136000001, elapsed 76.0s, est remaining 228.1s, peak mem 7151MB, user 2236.4s, sys 16.1s, output queue size 302
progress 30% @chr5:70000001, elapsed 85.9s, est remaining 200.5s, peak mem 7295MB, user 2574.9s, sys 18.2s, output queue size 464
progress 35% @chr6:56000001, elapsed 103.0s, est remaining 191.3s, peak mem 7962MB, user 2995.5s, sys 20.7s, output queue size 625
progress 40% @chr7:41000001, elapsed 120.1s, est remaining 180.2s, peak mem 8832MB, user 3478.7s, sys 23.3s, output queue size 197
progress 45% @chr8:75000001, elapsed 138.7s, est remaining 169.5s, peak mem 9001MB, user 4042.7s, sys 26.5s, output queue size 358
progress 50% @chr9:42000001, elapsed 152.6s, est remaining 152.6s, peak mem 9099MB, user 4551.3s, sys 29.0s, output queue size 366
progress 55% @chr10:96000001, elapsed 168.5s, est remaining 137.9s, peak mem 9170MB, user 5031.6s, sys 31.5s, output queue size 348
progress 60% @chr11:94000001, elapsed 184.1s, est remaining 122.7s, peak mem 9170MB, user 5495.1s, sys 33.6s, output queue size 510
progress 65% @chr13:33000001, elapsed 200.3s, est remaining 107.9s, peak mem 9238MB, user 5938.1s, sys 35.6s, output queue size 672
progress 70% @chr14:83000001, elapsed 210.7s, est remaining 90.3s, peak mem 9253MB, user 6394.4s, sys 37.4s, output queue size 299
progress 75% @chr16:42000001, elapsed 227.7s, est remaining 75.9s, peak mem 9275MB, user 6833.2s, sys 39.4s, output queue size 461
progress 80% @chr18:10000001, elapsed 249.9s, est remaining 62.5s, peak mem 9358MB, user 7435.2s, sys 41.7s, output queue size 623
progress 85% @chr20:18000001, elapsed 269.5s, est remaining 47.6s, peak mem 9412MB, user 8062.3s, sys 44.3s, output queue size 785
progress 90% @chrX:31000001, elapsed 282.5s, est remaining 31.4s, peak mem 9431MB, user 8552.2s, sys 46.2s, output queue size 513
progress 95% @chrY:51000001, elapsed 291.4s, est remaining 15.3s, peak mem 9431MB, user 8770.4s, sys 47.4s, output queue size 675
progress 100% @chr15:88000001, elapsed 309.8s, est remaining 0.0s, peak mem 9431MB, user 9135.5s, sys 49.0s, output queue size 4099
library 1136_85O-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 15767210
duped 475635921
duped_chimeric_paired 2753132
duped_paired 475632081
duped_unpaired 3840
optical_dup 65156620
paired 860963276
reads 870178335
secondary_supplementary 9206079
unmapped 10042
unpaired 4490
optical dup clusters 35552210, maxdup 65, total optical dup pairs 65156620
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: 44057164419
reads: 870183887
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2631732 calls 6.072 user 0.302 sys 6.138 real
MateInfoByVcf::load: 2631732 calls 1913.489 user 9.476 sys 1850.732 real
MateInfoByVcf::parse_events: 2631732 calls 1831.242 user 8.119 sys 1808.981 real
advance: 3219322 calls 740.460 user 15.354 sys 816.274 real
calc: 3219322 calls 6050.031 user 20.295 sys 6124.989 real
done: 1 calls 0.066 user 0.018 sys 0.086 real
exec_no_coor: 1 calls 0.000 user 0.021 sys 0.037 real
execute: 1 calls 0.010 user 0.001 sys 311.516 real
fetch: 3219323 calls 314.278 user 1.045 sys 297.335 real
find_pairEnds: 2631732 calls 366.269 user 0.686 sys 377.445 real
idle: 23252 calls 6.583 user 0.127 sys 463.301 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 2631732 calls 1440.739 user 4.705 sys 1498.040 real
vcfadvance: 2631732 calls 3.394 user 0.552 sys 3.723 real
write: 3219323 calls 4579.065 user 14.500 sys 4592.898 real
overall: 9889722368 mem 9147.511 user 63.194 sys 313.059 real