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/f1/355b3c2ee5224d911294129390dc16/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/8086daa1e92e40c86034d129c3cafc/Filler-D0002693.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/355b3c2ee5224d911294129390dc16/.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/c6/8086daa1e92e40c86034d129c3cafc/Filler-D0002693.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0002693.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0002693.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 6.6s, est remaining 125.6s, peak mem 3570MB, user 157.2s, sys 9.3s, output queue size 145
progress 10% @chr2:68000001, elapsed 10.9s, est remaining 98.5s, peak mem 4693MB, user 298.2s, sys 11.6s, output queue size 170
progress 15% @chr3:18000001, elapsed 15.5s, est remaining 87.6s, peak mem 7360MB, user 432.4s, sys 14.1s, output queue size 203
progress 20% @chr3:174000001, elapsed 20.3s, est remaining 81.3s, peak mem 10855MB, user 552.9s, sys 15.4s, output queue size 364
progress 25% @chr4:134000001, elapsed 24.0s, est remaining 71.9s, peak mem 13761MB, user 680.1s, sys 16.4s, output queue size 525
progress 30% @chr5:97000001, elapsed 26.7s, est remaining 62.3s, peak mem 15521MB, user 770.1s, sys 17.5s, output queue size 687
progress 35% @chr6:92000001, elapsed 31.0s, est remaining 57.6s, peak mem 18471MB, user 882.3s, sys 18.4s, output queue size 848
progress 40% @chr7:50000001, elapsed 35.0s, est remaining 52.5s, peak mem 21306MB, user 993.4s, sys 19.0s, output queue size 1009
progress 45% @chr8:83000001, elapsed 40.0s, est remaining 48.9s, peak mem 25395MB, user 1150.4s, sys 20.7s, output queue size 1171
progress 50% @chr9:61000001, elapsed 43.2s, est remaining 43.2s, peak mem 28279MB, user 1244.4s, sys 22.0s, output queue size 1333
progress 55% @chr10:95000001, elapsed 48.6s, est remaining 39.8s, peak mem 31896MB, user 1394.7s, sys 23.6s, output queue size 1494
progress 60% @chr12:3000001, elapsed 54.7s, est remaining 36.5s, peak mem 33658MB, user 1567.6s, sys 24.6s, output queue size 1656
progress 65% @chr13:34000001, elapsed 60.1s, est remaining 32.4s, peak mem 34945MB, user 1719.6s, sys 25.6s, output queue size 1818
progress 70% @chr14:85000001, elapsed 65.3s, est remaining 28.0s, peak mem 35366MB, user 1880.1s, sys 26.7s, output queue size 1979
progress 75% @chr16:38000001, elapsed 71.3s, est remaining 23.8s, peak mem 35509MB, user 2034.4s, sys 28.0s, output queue size 2141
progress 80% @chr18:7000001, elapsed 83.2s, est remaining 20.8s, peak mem 37792MB, user 2348.2s, sys 29.7s, output queue size 2303
progress 85% @chr20:37000001, elapsed 93.9s, est remaining 16.6s, peak mem 37792MB, user 2630.8s, sys 31.3s, output queue size 2465
progress 90% @chrX:35000001, elapsed 105.2s, est remaining 11.7s, peak mem 43016MB, user 3012.9s, sys 33.7s, output queue size 2627
progress 95% @chrY:50000001, elapsed 109.9s, est remaining 5.8s, peak mem 44710MB, user 3116.4s, sys 34.2s, output queue size 2788
progress 100% @chr19:7000001, elapsed 186.9s, est remaining 0.0s, peak mem 55370MB, user 3604.0s, sys 73.3s, output queue size 3822
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 71854728850
reads: 2501721484
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 11.372 user 3.073 sys 27.482 real
VcfLineRecordHelper::sort: 375 calls 25.292 user 0.442 sys 25.694 real
advance: 3219322 calls 1640.043 user 49.703 sys 1693.078 real
calc: 3219322 calls 835.344 user 12.664 sys 847.763 real
done: 1 calls 11.372 user 3.073 sys 27.482 real
execute: 1 calls 0.001 user 0.001 sys 186.992 real
fetch: 3219322 calls 972.942 user 7.789 sys 981.947 real
idle: 3176 calls 1.136 user 0.029 sys 2981.724 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 58060193792 mem 3687.163 user 79.592 sys 215.947 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0002693.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0002693.md.score --metrics Filler-D0002693.md.metrics Filler-D0002693.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 32.0s, est remaining 607.8s, peak mem 4303MB, user 811.4s, sys 13.4s, output queue size 52
progress 10% @chr2:65000001, elapsed 53.9s, est remaining 485.4s, peak mem 5192MB, user 1554.8s, sys 19.8s, output queue size 47
progress 15% @chr2:201000001, elapsed 76.8s, est remaining 435.1s, peak mem 19697MB, user 2198.6s, sys 24.4s, output queue size 203
progress 20% @chr3:161000001, elapsed 103.2s, est remaining 412.6s, peak mem 35212MB, user 2943.0s, sys 28.5s, output queue size 364
progress 25% @chr4:135000001, elapsed 122.3s, est remaining 366.9s, peak mem 40221MB, user 3513.0s, sys 34.8s, output queue size 525
progress 30% @chr5:81000001, elapsed 137.7s, est remaining 321.2s, peak mem 41294MB, user 4005.9s, sys 38.2s, output queue size 687
progress 35% @chr6:77000001, elapsed 163.2s, est remaining 303.1s, peak mem 43530MB, user 4682.9s, sys 42.4s, output queue size 848
progress 40% @chr7:64000001, elapsed 186.3s, est remaining 279.5s, peak mem 45521MB, user 5310.2s, sys 47.0s, output queue size 1009
progress 45% @chr8:71000001, elapsed 213.1s, est remaining 260.4s, peak mem 49144MB, user 6237.3s, sys 55.1s, output queue size 1171
progress 50% @chr9:86000001, elapsed 231.5s, est remaining 231.5s, peak mem 50177MB, user 6705.0s, sys 58.8s, output queue size 1333
progress 55% @chr10:118000001, elapsed 262.6s, est remaining 214.9s, peak mem 50630MB, user 7575.8s, sys 64.1s, output queue size 1494
progress 60% @chr11:113000001, elapsed 297.6s, est remaining 198.4s, peak mem 51288MB, user 8558.1s, sys 68.3s, output queue size 1656
progress 65% @chr12:52000001, elapsed 326.6s, est remaining 175.9s, peak mem 51849MB, user 9400.0s, sys 72.0s, output queue size 1818
progress 70% @chr14:21000001, elapsed 355.9s, est remaining 152.5s, peak mem 54834MB, user 10327.4s, sys 76.5s, output queue size 1979
progress 75% @chr16:42000001, elapsed 388.3s, est remaining 129.4s, peak mem 54834MB, user 11161.6s, sys 80.8s, output queue size 2141
progress 80% @chr18:7000001, elapsed 452.9s, est remaining 113.2s, peak mem 54834MB, user 12839.4s, sys 94.3s, output queue size 2303
progress 85% @chr19:35000001, elapsed 509.8s, est remaining 90.0s, peak mem 54834MB, user 14712.6s, sys 109.0s, output queue size 2465
progress 90% @chrX:15000001, elapsed 573.8s, est remaining 63.8s, peak mem 64462MB, user 16418.5s, sys 123.4s, output queue size 2627
progress 95% @chrY:52000001, elapsed 600.1s, est remaining 31.6s, peak mem 64495MB, user 17072.1s, sys 129.4s, output queue size 2788
progress 100% @chr2:32000001, elapsed 1013.3s, est remaining 0.0s, peak mem 77960MB, user 19948.3s, sys 237.2s, output queue size 6213
library Filler-D0002693:
chimeric_paired 86309172
duped 2205925237
duped_chimeric_paired 46643316
duped_paired 2205884694
duped_unpaired 40543
optical_dup 295452251
paired 2480896628
reads 2501688934
secondary_supplementary 20707676
unmapped 74865
unpaired 42315
optical dup clusters 68472882, maxdup 698, total optical dup pairs 295452251
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 71854728850
reads: 2501721484
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2717852 calls 187.798 user 5.408 sys 199.429 real
MateInfoByVcf::load: 2717852 calls 2140.060 user 25.744 sys 1928.048 real
MateInfoByVcf::parse_events: 2717852 calls 1673.528 user 15.854 sys 1556.735 real
advance: 3219322 calls 1544.257 user 56.987 sys 1770.837 real
calc: 3219322 calls 14598.977 user 130.687 sys 14885.956 real
done: 1 calls 0.031 user 0.039 sys 0.072 real
exec_no_coor: 1 calls 0.144 user 0.126 sys 0.302 real
execute: 1 calls 0.004 user 0.000 sys 1035.547 real
fetch: 3219323 calls 1208.733 user 11.535 sys 1207.883 real
find_pairEnds: 2717852 calls 1409.355 user 7.228 sys 1504.447 real
idle: 1062623 calls 281.540 user 11.558 sys 11465.055 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 2717852 calls 5684.570 user 60.275 sys 6040.107 real
vcfadvance: 2717852 calls 27.299 user 5.835 sys 31.438 real
write: 3219323 calls 8763.719 user 68.878 sys 8667.951 real
overall: 81747685376 mem 20307.834 user 294.422 sys 1040.162 real