Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/639e7f9a2a9942aa092a62d55b30a9/1029_BKVL-N1-BDNA-1_B23KFG5LT4_1.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/863dd6561f4a96cc0374e1aa724447/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/863dd6561f4a96cc0374e1aa724447/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/639e7f9a2a9942aa092a62d55b30a9/1029_BKVL-N1-BDNA-1_B23KFG5LT4_1.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 0.7s, est remaining 14.2s, peak mem 1484MB, user 16.6s, sys 1.1s, output queue size 146
progress 10% @chr2:70000001, elapsed 1.4s, est remaining 12.2s, peak mem 1929MB, user 35.5s, sys 1.8s, output queue size 79
progress 15% @chr2:218000001, elapsed 2.1s, est remaining 11.7s, peak mem 2500MB, user 55.9s, sys 2.2s, output queue size 203
progress 20% @chr3:175000001, elapsed 2.7s, est remaining 10.8s, peak mem 2949MB, user 72.4s, sys 2.8s, output queue size 364
progress 25% @chr4:133000001, elapsed 3.3s, est remaining 9.9s, peak mem 3129MB, user 91.3s, sys 3.7s, output queue size 525
progress 30% @chr5:106000001, elapsed 3.7s, est remaining 8.7s, peak mem 3303MB, user 103.0s, sys 4.0s, output queue size 687
progress 35% @chr5:132000001, elapsed 4.3s, est remaining 8.0s, peak mem 3364MB, user 121.4s, sys 5.0s, output queue size 625
progress 40% @chr7:66000001, elapsed 5.0s, est remaining 7.5s, peak mem 3517MB, user 138.9s, sys 5.3s, output queue size 786
progress 45% @chr8:82000001, elapsed 5.8s, est remaining 7.1s, peak mem 3647MB, user 160.4s, sys 5.8s, output queue size 948
progress 50% @chr9:87000001, elapsed 6.5s, est remaining 6.5s, peak mem 3824MB, user 177.7s, sys 6.4s, output queue size 1110
progress 55% @chr10:104000001, elapsed 7.2s, est remaining 5.9s, peak mem 3889MB, user 204.4s, sys 7.0s, output queue size 527
progress 60% @chr12:2000001, elapsed 7.9s, est remaining 5.3s, peak mem 3940MB, user 223.9s, sys 7.5s, output queue size 689
progress 65% @chr12:106000001, elapsed 8.7s, est remaining 4.7s, peak mem 4033MB, user 245.2s, sys 7.8s, output queue size 851
progress 70% @chr14:76000001, elapsed 9.2s, est remaining 3.9s, peak mem 4061MB, user 258.7s, sys 8.1s, output queue size 1012
progress 75% @chr16:42000001, elapsed 10.1s, est remaining 3.4s, peak mem 4111MB, user 289.8s, sys 8.5s, output queue size 995
progress 80% @chr18:25000001, elapsed 11.4s, est remaining 2.8s, peak mem 4202MB, user 319.8s, sys 9.1s, output queue size 1157
progress 85% @chr20:43000001, elapsed 12.5s, est remaining 2.2s, peak mem 4245MB, user 352.7s, sys 9.5s, output queue size 1319
progress 90% @chrX:43000001, elapsed 13.3s, est remaining 1.5s, peak mem 4400MB, user 378.0s, sys 10.0s, output queue size 1481
progress 95% @chrY:49000001, elapsed 14.0s, est remaining 0.7s, peak mem 4496MB, user 392.6s, sys 10.3s, output queue size 1643
progress 100% @chr15:88000001, elapsed 18.3s, est remaining 0.0s, peak mem 4537MB, user 440.7s, sys 11.1s, output queue size 4099
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 14138046561
reads: 310582275
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.799 user 0.277 sys 1.570 real
VcfLineRecordHelper::sort: 40 calls 1.524 user 0.238 sys 1.764 real
advance: 3219322 calls 250.554 user 7.062 sys 258.930 real
calc: 3219322 calls 82.712 user 1.245 sys 85.047 real
done: 1 calls 0.799 user 0.277 sys 1.570 real
execute: 1 calls 0.008 user 0.002 sys 18.291 real
fetch: 3219322 calls 90.060 user 1.040 sys 90.959 real
idle: 221 calls 0.140 user 0.003 sys 189.596 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 4837883904 mem 447.487 user 11.969 sys 20.956 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1.md.score --metrics 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1.md.metrics 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 5.8s, est remaining 110.1s, peak mem 2032MB, user 151.5s, sys 2.6s, output queue size 44
progress 10% @chr2:92000001, elapsed 9.9s, est remaining 88.9s, peak mem 2658MB, user 281.4s, sys 4.1s, output queue size 48
progress 15% @chr3:8000001, elapsed 15.1s, est remaining 85.5s, peak mem 3599MB, user 421.0s, sys 6.0s, output queue size 203
progress 20% @chr3:173000001, elapsed 19.7s, est remaining 78.6s, peak mem 3780MB, user 559.8s, sys 7.4s, output queue size 364
progress 25% @chr3:186000001, elapsed 23.6s, est remaining 70.9s, peak mem 3780MB, user 692.6s, sys 9.2s, output queue size 302
progress 30% @chr5:101000001, elapsed 26.6s, est remaining 62.0s, peak mem 3784MB, user 787.2s, sys 10.1s, output queue size 464
progress 35% @chr6:41000001, elapsed 30.8s, est remaining 57.1s, peak mem 3784MB, user 898.5s, sys 11.2s, output queue size 625
progress 40% @chr7:70000001, elapsed 35.7s, est remaining 53.6s, peak mem 3844MB, user 1032.6s, sys 12.6s, output queue size 786
progress 45% @chr8:70000001, elapsed 41.2s, est remaining 50.3s, peak mem 3958MB, user 1214.5s, sys 14.0s, output queue size 204
progress 50% @chr9:42000001, elapsed 45.6s, est remaining 45.6s, peak mem 4009MB, user 1342.7s, sys 14.9s, output queue size 366
progress 55% @chr10:104000001, elapsed 51.0s, est remaining 41.8s, peak mem 4021MB, user 1488.6s, sys 16.2s, output queue size 527
progress 60% @chr11:130000001, elapsed 57.5s, est remaining 38.4s, peak mem 4021MB, user 1673.7s, sys 17.3s, output queue size 689
progress 65% @chr13:30000001, elapsed 64.0s, est remaining 34.4s, peak mem 4058MB, user 1867.4s, sys 18.8s, output queue size 672
progress 70% @chr14:82000001, elapsed 67.5s, est remaining 28.9s, peak mem 4065MB, user 2011.1s, sys 19.7s, output queue size 833
progress 75% @chr16:42000001, elapsed 73.6s, est remaining 24.5s, peak mem 4153MB, user 2158.3s, sys 21.0s, output queue size 995
progress 80% @chr18:13000001, elapsed 83.7s, est remaining 20.9s, peak mem 4153MB, user 2445.7s, sys 23.0s, output queue size 623
progress 85% @chr20:23000001, elapsed 91.9s, est remaining 16.2s, peak mem 4153MB, user 2753.0s, sys 25.1s, output queue size 351
progress 90% @chrX:1000001, elapsed 97.6s, est remaining 10.8s, peak mem 4232MB, user 2920.8s, sys 26.5s, output queue size 513
progress 95% @chrY:24000001, elapsed 102.8s, est remaining 5.4s, peak mem 4312MB, user 3044.3s, sys 27.4s, output queue size 675
progress 100% @chr15:88000001, elapsed 113.1s, est remaining 0.0s, peak mem 4312MB, user 3228.8s, sys 28.9s, output queue size 4099
library 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1:
chimeric_paired 3734644
duped 128813075
duped_chimeric_paired 463358
duped_paired 128812030
duped_unpaired 1045
optical_dup 45592681
paired 309088688
reads 310581223
secondary_supplementary 1489691
unmapped 2474
unpaired 1422
optical dup clusters 23839941, maxdup 29, total optical dup pairs 45592681
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 14138046561
reads: 310582275
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2090686 calls 6.023 user 0.195 sys 6.303 real
MateInfoByVcf::load: 2090686 calls 1034.923 user 8.445 sys 979.840 real
MateInfoByVcf::parse_events: 2090686 calls 983.075 user 7.403 sys 953.455 real
advance: 3219322 calls 256.200 user 6.902 sys 296.410 real
calc: 3219322 calls 1719.091 user 9.740 sys 1784.412 real
done: 1 calls 0.048 user 0.009 sys 0.063 real
exec_no_coor: 1 calls 0.000 user 0.007 sys 0.007 real
execute: 1 calls 0.003 user 0.002 sys 113.819 real
fetch: 3219323 calls 149.595 user 0.888 sys 136.266 real
find_pairEnds: 2090686 calls 147.014 user 0.586 sys 155.940 real
idle: 18391 calls 13.005 user 0.167 sys 269.798 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 2090686 calls 573.575 user 2.785 sys 612.763 real
vcfadvance: 2090686 calls 3.534 user 0.681 sys 4.004 real
write: 3219323 calls 1135.371 user 6.112 sys 1159.079 real
overall: 4522319872 mem 3246.572 user 34.264 sys 115.064 real