cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0000890.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0000890.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 3.8s, est remaining 71.4s, peak mem 2064MB, user 88.3s, sys 8.8s, output queue size 52
progress 10% @chr2:55000001, elapsed 6.2s, est remaining 55.9s, peak mem 2763MB, user 163.8s, sys 11.6s, output queue size 170
progress 15% @chr3:18000001, elapsed 8.7s, est remaining 49.5s, peak mem 4336MB, user 237.4s, sys 14.0s, output queue size 203
progress 20% @chr3:133000001, elapsed 11.6s, est remaining 46.4s, peak mem 6408MB, user 312.1s, sys 15.0s, output queue size 364
progress 25% @chr4:76000001, elapsed 13.7s, est remaining 41.0s, peak mem 8251MB, user 380.5s, sys 16.2s, output queue size 525
progress 30% @chr5:77000001, elapsed 15.3s, est remaining 35.7s, peak mem 9320MB, user 431.8s, sys 17.0s, output queue size 686
progress 35% @chr6:39000001, elapsed 17.9s, est remaining 33.2s, peak mem 10823MB, user 499.6s, sys 18.5s, output queue size 848
progress 40% @chr6:160000001, elapsed 20.2s, est remaining 30.2s, peak mem 12302MB, user 558.6s, sys 19.3s, output queue size 1009
progress 45% @chr8:82000001, elapsed 23.1s, est remaining 28.2s, peak mem 14846MB, user 650.0s, sys 20.8s, output queue size 1171
progress 50% @chr9:102000001, elapsed 24.8s, est remaining 24.8s, peak mem 16124MB, user 707.7s, sys 21.9s, output queue size 1333
progress 55% @chr10:95000001, elapsed 28.1s, est remaining 23.0s, peak mem 18780MB, user 795.4s, sys 23.4s, output queue size 1494
progress 60% @chr11:134000001, elapsed 31.8s, est remaining 21.2s, peak mem 20235MB, user 900.2s, sys 24.4s, output queue size 1656
progress 65% @chr13:25000001, elapsed 34.9s, est remaining 18.8s, peak mem 20838MB, user 986.3s, sys 25.3s, output queue size 1818
progress 70% @chr14:79000001, elapsed 37.6s, est remaining 16.1s, peak mem 21200MB, user 1074.1s, sys 26.4s, output queue size 1979
progress 75% @chr16:41000001, elapsed 41.0s, est remaining 13.7s, peak mem 21200MB, user 1163.2s, sys 27.2s, output queue size 2141
progress 80% @chr18:9000001, elapsed 48.1s, est remaining 12.0s, peak mem 22306MB, user 1365.4s, sys 29.3s, output queue size 2303
progress 85% @chr19:38000001, elapsed 54.0s, est remaining 9.5s, peak mem 22306MB, user 1535.6s, sys 30.9s, output queue size 2465
progress 90% @chrX:19000001, elapsed 60.4s, est remaining 6.7s, peak mem 25472MB, user 1707.1s, sys 32.6s, output queue size 2627
progress 95% @chrY:51000001, elapsed 63.1s, est remaining 3.3s, peak mem 26925MB, user 1774.4s, sys 33.5s, output queue size 2788
progress 100% @chr19:7000001, elapsed 125.2s, est remaining 0.0s, peak mem 39088MB, user 2073.5s, sys 67.8s, output queue size 3822
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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 46507347765
reads: 1602999702
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 5.410 user 1.294 sys 8.539 real
VcfLineRecordHelper::sort: 192 calls 12.441 user 0.370 sys 12.801 real
advance: 3219322 calls 1031.581 user 54.133 sys 1090.243 real
calc: 3219322 calls 474.575 user 7.597 sys 481.262 real
done: 1 calls 5.410 user 1.294 sys 8.539 real
execute: 1 calls 0.002 user 0.002 sys 125.210 real
fetch: 3219322 calls 479.433 user 3.541 sys 483.919 real
idle: 2100 calls 0.709 user 0.005 sys 2018.552 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 40987439104 mem 2112.313 user 70.898 sys 135.195 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0000890.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0000890.md.score --metrics Filler-D0000890.md.metrics Filler-D0000890.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 20.1s, est remaining 381.5s, peak mem 2965MB, user 508.6s, sys 11.7s, output queue size 52
progress 10% @chr2:92000001, elapsed 33.6s, est remaining 302.1s, peak mem 3831MB, user 966.3s, sys 16.8s, output queue size 47
progress 15% @chr3:3000001, elapsed 47.8s, est remaining 271.0s, peak mem 12817MB, user 1357.3s, sys 20.5s, output queue size 203
progress 20% @chr3:122000001, elapsed 64.1s, est remaining 256.5s, peak mem 21231MB, user 1822.0s, sys 25.9s, output queue size 364
progress 25% @chr4:135000001, elapsed 75.3s, est remaining 225.9s, peak mem 23975MB, user 2194.5s, sys 31.7s, output queue size 525
progress 30% @chr5:97000001, elapsed 84.8s, est remaining 197.9s, peak mem 24966MB, user 2457.2s, sys 35.7s, output queue size 687
progress 35% @chr6:77000001, elapsed 100.8s, est remaining 187.2s, peak mem 27345MB, user 2863.8s, sys 40.5s, output queue size 848
progress 40% @chr7:64000001, elapsed 114.9s, est remaining 172.3s, peak mem 28494MB, user 3262.2s, sys 44.0s, output queue size 1009
progress 45% @chr8:58000001, elapsed 131.5s, est remaining 160.7s, peak mem 28925MB, user 3823.4s, sys 49.1s, output queue size 1171
progress 50% @chr9:37000001, elapsed 142.9s, est remaining 142.9s, peak mem 29678MB, user 4119.9s, sys 52.7s, output queue size 1333
progress 55% @chr10:118000001, elapsed 162.5s, est remaining 133.0s, peak mem 29854MB, user 4671.4s, sys 57.0s, output queue size 1494
progress 60% @chr11:113000001, elapsed 184.8s, est remaining 123.2s, peak mem 30238MB, user 5292.4s, sys 60.5s, output queue size 1656
progress 65% @chr12:52000001, elapsed 202.9s, est remaining 109.3s, peak mem 30559MB, user 5808.1s, sys 63.4s, output queue size 1818
progress 70% @chr14:82000001, elapsed 221.0s, est remaining 94.7s, peak mem 32008MB, user 6392.5s, sys 67.3s, output queue size 1979
progress 75% @chr16:42000001, elapsed 242.1s, est remaining 80.7s, peak mem 32008MB, user 6938.5s, sys 70.7s, output queue size 2141
progress 80% @chr18:7000001, elapsed 283.4s, est remaining 70.9s, peak mem 32008MB, user 8178.4s, sys 82.5s, output queue size 2303
progress 85% @chr19:48000001, elapsed 322.3s, est remaining 56.9s, peak mem 32591MB, user 9242.6s, sys 90.5s, output queue size 2465
progress 90% @chrX:35000001, elapsed 362.7s, est remaining 40.3s, peak mem 41959MB, user 10328.0s, sys 98.7s, output queue size 2627
progress 95% @chrY:52000001, elapsed 379.8s, est remaining 20.0s, peak mem 41959MB, user 10774.8s, sys 102.0s, output queue size 2788
progress 100% @chr19:7000001, elapsed 632.6s, est remaining 0.0s, peak mem 51857MB, user 12415.8s, sys 159.2s, output queue size 3822
library Filler-D0000890:
chimeric_paired 54679673
duped 1371175961
duped_chimeric_paired 25385538
duped_paired 1371145038
duped_unpaired 30923
optical_dup 147711236
paired 1586250600
reads 1602971536
secondary_supplementary 16655910
unmapped 60679
unpaired 32513
optical dup clusters 42205265, maxdup 683, total optical dup pairs 147711236
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 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 46507347765
reads: 1602999702
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2673985 calls 90.394 user 2.191 sys 95.389 real
MateInfoByVcf::load: 2673985 calls 1793.478 user 21.113 sys 1569.504 real
MateInfoByVcf::parse_events: 2673985 calls 1498.650 user 15.963 sys 1356.937 real
advance: 3219322 calls 965.060 user 43.491 sys 1171.133 real
calc: 3219322 calls 8688.759 user 79.918 sys 8894.299 real
done: 1 calls 0.078 user 0.018 sys 0.099 real
exec_no_coor: 1 calls 0.159 user 0.061 sys 0.236 real
execute: 1 calls 0.001 user 0.001 sys 635.634 real
fetch: 3219323 calls 708.369 user 6.222 sys 708.604 real
find_pairEnds: 2673985 calls 809.661 user 6.442 sys 899.021 real
idle: 657079 calls 278.639 user 5.887 sys 6754.023 real
init: 1 calls 0.000 user 0.010 sys 0.006 real
markDup: 2673985 calls 3364.808 user 33.764 sys 3695.637 real
vcfadvance: 2673985 calls 14.521 user 3.561 sys 16.749 real
write: 3219323 calls 5236.915 user 44.716 sys 5090.660 real
overall: 54376017920 mem 12754.890 user 186.866 sys 638.763 real