cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_81F-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:154000001, elapsed 3.9s, est remaining 74.0s, peak mem 3825MB, user 91.2s, sys 4.0s, output queue size 146
progress 10% @chr2:58000001, elapsed 6.7s, est remaining 60.3s, peak mem 5159MB, user 178.3s, sys 5.4s, output queue size 166
progress 15% @chr2:224000001, elapsed 9.7s, est remaining 54.7s, peak mem 5890MB, user 276.4s, sys 7.7s, output queue size 122
progress 20% @chr3:149000001, elapsed 12.4s, est remaining 49.8s, peak mem 5979MB, user 357.2s, sys 9.0s, output queue size 283
progress 25% @chr4:136000001, elapsed 14.9s, est remaining 44.6s, peak mem 6099MB, user 429.0s, sys 10.5s, output queue size 302
progress 30% @chr5:75000001, elapsed 16.6s, est remaining 38.8s, peak mem 6155MB, user 489.9s, sys 11.5s, output queue size 268
progress 35% @chr6:81000001, elapsed 19.4s, est remaining 36.0s, peak mem 6610MB, user 564.1s, sys 12.3s, output queue size 106
progress 40% @chr7:45000001, elapsed 22.2s, est remaining 33.3s, peak mem 6982MB, user 648.6s, sys 13.4s, output queue size 195
progress 45% @chr8:78000001, elapsed 25.4s, est remaining 31.0s, peak mem 7064MB, user 742.4s, sys 14.4s, output queue size 204
progress 50% @chr9:89000001, elapsed 27.9s, est remaining 27.9s, peak mem 7461MB, user 817.9s, sys 14.9s, output queue size 324
progress 55% @chr10:100000001, elapsed 31.2s, est remaining 25.5s, peak mem 8052MB, user 918.2s, sys 15.9s, output queue size 348
progress 60% @chr12:2000001, elapsed 35.1s, est remaining 23.4s, peak mem 8633MB, user 1023.9s, sys 17.0s, output queue size 312
progress 65% @chr13:26000001, elapsed 38.4s, est remaining 20.7s, peak mem 8881MB, user 1133.8s, sys 17.9s, output queue size 216
progress 70% @chr14:79000001, elapsed 40.3s, est remaining 17.3s, peak mem 8932MB, user 1190.5s, sys 18.7s, output queue size 370
progress 75% @chr16:42000001, elapsed 44.0s, est remaining 14.7s, peak mem 9344MB, user 1291.3s, sys 19.6s, output queue size 531
progress 80% @chr18:1, elapsed 49.4s, est remaining 12.3s, peak mem 9437MB, user 1456.1s, sys 20.9s, output queue size 280
progress 85% @chr19:40000001, elapsed 54.8s, est remaining 9.7s, peak mem 9796MB, user 1627.5s, sys 22.2s, output queue size 351
progress 90% @chrX:39000001, elapsed 57.6s, est remaining 6.4s, peak mem 9796MB, user 1740.0s, sys 23.3s, output queue size 121
progress 95% @chrY:51000001, elapsed 60.1s, est remaining 3.2s, peak mem 9796MB, user 1808.4s, sys 24.1s, output queue size 240
progress 100% @chrX:67000001, elapsed 63.8s, est remaining 0.0s, peak mem 9802MB, user 1872.4s, sys 24.8s, output queue size 3540
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 62050622695
reads: 1187143287
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.551 user 0.137 sys 0.727 real
VcfLineRecordHelper::sort: 33 calls 1.132 user 0.030 sys 1.185 real
advance: 3219322 calls 1050.849 user 20.362 sys 1069.218 real
calc: 3219322 calls 357.852 user 1.494 sys 362.217 real
done: 1 calls 0.551 user 0.137 sys 0.727 real
execute: 1 calls 0.002 user 0.002 sys 63.870 real
fetch: 3219322 calls 398.303 user 1.239 sys 400.850 real
idle: 158 calls 0.139 user 0.001 sys 125.449 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 10279170048 mem 1877.227 user 25.515 sys 65.607 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_81F-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 23.6s, est remaining 448.4s, peak mem 4987MB, user 612.2s, sys 6.7s, output queue size 52
progress 10% @chr2:79000001, elapsed 39.7s, est remaining 357.2s, peak mem 6433MB, user 1143.0s, sys 10.9s, output queue size 48
progress 15% @chr3:5000001, elapsed 57.6s, est remaining 326.2s, peak mem 7440MB, user 1678.9s, sys 14.7s, output queue size 122
progress 20% @chr3:157000001, elapsed 75.8s, est remaining 303.3s, peak mem 7452MB, user 2234.8s, sys 17.9s, output queue size 141
progress 25% @chr4:125000001, elapsed 92.5s, est remaining 277.4s, peak mem 7530MB, user 2718.2s, sys 20.8s, output queue size 302
progress 30% @chr5:81000001, elapsed 104.1s, est remaining 242.9s, peak mem 7773MB, user 3136.0s, sys 23.3s, output queue size 201
progress 35% @chr6:41000001, elapsed 122.6s, est remaining 227.7s, peak mem 8006MB, user 3648.1s, sys 25.8s, output queue size 70
progress 40% @chr7:71000001, elapsed 140.2s, est remaining 210.3s, peak mem 8453MB, user 4197.3s, sys 28.8s, output queue size 195
progress 45% @chr8:66000001, elapsed 161.7s, est remaining 197.6s, peak mem 8493MB, user 4799.7s, sys 32.0s, output queue size 204
progress 50% @chr9:88000001, elapsed 177.6s, est remaining 177.6s, peak mem 8840MB, user 5295.2s, sys 34.6s, output queue size 187
progress 55% @chr10:93000001, elapsed 198.2s, est remaining 162.2s, peak mem 9264MB, user 5942.7s, sys 37.6s, output queue size 342
progress 60% @chr11:108000001, elapsed 222.2s, est remaining 148.2s, peak mem 9851MB, user 6640.0s, sys 40.8s, output queue size 136
progress 65% @chr12:112000001, elapsed 242.2s, est remaining 130.4s, peak mem 10117MB, user 7269.2s, sys 44.0s, output queue size 209
progress 70% @chr14:78000001, elapsed 254.9s, est remaining 109.2s, peak mem 10435MB, user 7635.0s, sys 46.1s, output queue size 369
progress 75% @chr16:42000001, elapsed 277.0s, est remaining 92.3s, peak mem 10665MB, user 8299.8s, sys 49.0s, output queue size 461
progress 80% @chr18:1, elapsed 308.8s, est remaining 77.2s, peak mem 10832MB, user 9277.5s, sys 53.4s, output queue size 189
progress 85% @chr19:8000001, elapsed 339.1s, est remaining 59.8s, peak mem 10871MB, user 10240.7s, sys 57.2s, output queue size 73
progress 90% @chr22:20000001, elapsed 357.0s, est remaining 39.7s, peak mem 10873MB, user 10865.5s, sys 59.9s, output queue size 78
progress 95% @chrY:54000001, elapsed 373.6s, est remaining 19.7s, peak mem 11129MB, user 11316.1s, sys 62.0s, output queue size 240
progress 100% @chrX:67000001, elapsed 388.9s, est remaining 0.0s, peak mem 11129MB, user 11657.3s, sys 63.9s, output queue size 3540
library 1136_81F-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 21233089
duped 658945008
duped_chimeric_paired 2972238
duped_paired 658940249
duped_unpaired 4759
optical_dup 24708138
paired 1170841282
reads 1187134133
secondary_supplementary 16282189
unmapped 14485
unpaired 5331
optical dup clusters 18565999, maxdup 42, total optical dup pairs 24708138
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 62050622695
reads: 1187143287
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2695136 calls 5.568 user 0.283 sys 6.031 real
MateInfoByVcf::load: 2695136 calls 2006.782 user 11.663 sys 1899.689 real
MateInfoByVcf::parse_events: 2695136 calls 1933.825 user 10.189 sys 1856.507 real
advance: 3219322 calls 962.572 user 18.400 sys 1085.195 real
calc: 3219322 calls 8078.519 user 29.475 sys 8170.680 real
done: 1 calls 0.073 user 0.001 sys 0.078 real
exec_no_coor: 1 calls 0.053 user 0.010 sys 0.069 real
execute: 1 calls 0.003 user 0.004 sys 389.449 real
fetch: 3219323 calls 455.746 user 1.333 sys 444.286 real
find_pairEnds: 2695136 calls 480.963 user 0.668 sys 495.411 real
idle: 23159 calls 6.270 user 0.240 sys 312.915 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 2695136 calls 1936.171 user 5.390 sys 2028.025 real
vcfadvance: 2695136 calls 3.165 user 0.519 sys 3.474 real
write: 3219323 calls 6100.015 user 22.846 sys 6094.115 real
overall: 11670614016 mem 11668.507 user 83.901 sys 390.257 real