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/39/442f4764e0a2309b4e240c45682a9f/Filler-D0002805.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/2105a6aa4a9e11aab75de646e7408d/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/2105a6aa4a9e11aab75de646e7408d/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/442f4764e0a2309b4e240c45682a9f/Filler-D0002805.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
==> STAGING COMPLETE (6 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0002805.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0002805.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:158000001, elapsed 4.5s, est remaining 85.8s, peak mem 2468MB, user 103.4s, sys 6.3s, output queue size 160
progress 10% @chr2:72000001, elapsed 7.4s, est remaining 66.3s, peak mem 2903MB, user 205.3s, sys 8.5s, output queue size 74
progress 15% @chr3:18000001, elapsed 10.5s, est remaining 59.2s, peak mem 4770MB, user 291.0s, sys 10.7s, output queue size 203
progress 20% @chr3:150000001, elapsed 13.8s, est remaining 55.0s, peak mem 6549MB, user 376.0s, sys 12.5s, output queue size 364
progress 25% @chr4:76000001, elapsed 16.0s, est remaining 47.9s, peak mem 8295MB, user 451.8s, sys 13.8s, output queue size 525
progress 30% @chr5:65000001, elapsed 17.8s, est remaining 41.6s, peak mem 9477MB, user 512.0s, sys 14.9s, output queue size 687
progress 35% @chr6:94000001, elapsed 20.9s, est remaining 38.8s, peak mem 11701MB, user 583.9s, sys 15.9s, output queue size 848
progress 40% @chr7:70000001, elapsed 23.6s, est remaining 35.4s, peak mem 13434MB, user 662.5s, sys 17.1s, output queue size 1009
progress 45% @chr8:78000001, elapsed 27.0s, est remaining 33.0s, peak mem 16052MB, user 755.5s, sys 18.5s, output queue size 1171
progress 50% @chr9:86000001, elapsed 29.1s, est remaining 29.1s, peak mem 17438MB, user 822.2s, sys 19.9s, output queue size 1333
progress 55% @chr9:136000001, elapsed 32.9s, est remaining 26.9s, peak mem 20246MB, user 942.9s, sys 22.0s, output queue size 1494
progress 60% @chr12:1000001, elapsed 37.1s, est remaining 24.7s, peak mem 22645MB, user 1052.5s, sys 23.3s, output queue size 1656
progress 65% @chr13:18000001, elapsed 40.5s, est remaining 21.8s, peak mem 23782MB, user 1157.2s, sys 24.5s, output queue size 1818
progress 70% @chr14:79000001, elapsed 43.9s, est remaining 18.8s, peak mem 24906MB, user 1261.0s, sys 25.6s, output queue size 1979
progress 75% @chr16:38000001, elapsed 47.9s, est remaining 16.0s, peak mem 25544MB, user 1366.1s, sys 27.1s, output queue size 2141
progress 80% @chr18:21000001, elapsed 55.8s, est remaining 14.0s, peak mem 26367MB, user 1566.5s, sys 29.1s, output queue size 2303
progress 85% @chr20:2000001, elapsed 62.8s, est remaining 11.1s, peak mem 27268MB, user 1793.9s, sys 31.4s, output queue size 2465
progress 90% @chrX:15000001, elapsed 70.3s, est remaining 7.8s, peak mem 29914MB, user 2000.3s, sys 33.9s, output queue size 2627
progress 95% @chrY:49000001, elapsed 73.5s, est remaining 3.9s, peak mem 31540MB, user 2070.4s, sys 35.0s, output queue size 2788
progress 100% @chr19:7000001, elapsed 132.6s, est remaining 0.0s, peak mem 43231MB, user 2432.0s, sys 79.0s, 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: 53136889415
reads: 1811422576
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 7.561 user 2.257 sys 15.822 real
VcfLineRecordHelper::sort: 281 calls 18.210 user 0.670 sys 18.823 real
advance: 3219322 calls 1182.876 user 56.329 sys 1243.324 real
calc: 3219322 calls 568.608 user 12.860 sys 582.168 real
done: 1 calls 7.561 user 2.257 sys 15.822 real
execute: 1 calls 0.002 user 0.002 sys 132.726 real
fetch: 3219322 calls 576.349 user 6.203 sys 583.299 real
idle: 2225 calls 0.739 user 0.018 sys 2107.979 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 45331296256 mem 2484.665 user 83.960 sys 149.861 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0002805.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0002805.md.score --metrics Filler-D0002805.md.metrics Filler-D0002805.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 23.3s, est remaining 443.5s, peak mem 2845MB, user 586.2s, sys 12.8s, output queue size 52
progress 10% @chr2:89000001, elapsed 39.3s, est remaining 353.3s, peak mem 3659MB, user 1127.7s, sys 18.2s, output queue size 47
progress 15% @chr3:3000001, elapsed 57.0s, est remaining 323.2s, peak mem 14791MB, user 1612.4s, sys 22.7s, output queue size 203
progress 20% @chr3:173000001, elapsed 76.3s, est remaining 305.3s, peak mem 26217MB, user 2134.6s, sys 27.6s, output queue size 364
progress 25% @chr4:120000001, elapsed 89.4s, est remaining 268.2s, peak mem 28782MB, user 2618.4s, sys 32.4s, output queue size 525
progress 30% @chr5:72000001, elapsed 100.5s, est remaining 234.4s, peak mem 29799MB, user 2930.5s, sys 34.7s, output queue size 687
progress 35% @chr6:42000001, elapsed 118.5s, est remaining 220.1s, peak mem 31286MB, user 3394.6s, sys 38.3s, output queue size 848
progress 40% @chr7:67000001, elapsed 135.2s, est remaining 202.9s, peak mem 33721MB, user 3850.3s, sys 42.1s, output queue size 1009
progress 45% @chr8:71000001, elapsed 155.4s, est remaining 189.9s, peak mem 35238MB, user 4464.3s, sys 46.8s, output queue size 1171
progress 50% @chr9:86000001, elapsed 168.5s, est remaining 168.5s, peak mem 35890MB, user 4901.0s, sys 51.1s, output queue size 1333
progress 55% @chr10:87000001, elapsed 189.9s, est remaining 155.4s, peak mem 36380MB, user 5502.5s, sys 55.1s, output queue size 1494
progress 60% @chr12:5000001, elapsed 215.7s, est remaining 143.8s, peak mem 36944MB, user 6185.4s, sys 59.7s, output queue size 1656
progress 65% @chr12:52000001, elapsed 236.7s, est remaining 127.4s, peak mem 39026MB, user 6808.1s, sys 63.3s, output queue size 1818
progress 70% @chr14:84000001, elapsed 258.2s, est remaining 110.7s, peak mem 39026MB, user 7472.1s, sys 67.4s, output queue size 1979
progress 75% @chr16:42000001, elapsed 282.7s, est remaining 94.2s, peak mem 39026MB, user 8107.4s, sys 71.5s, output queue size 2141
progress 80% @chr18:3000001, elapsed 330.9s, est remaining 82.7s, peak mem 39026MB, user 9341.2s, sys 79.4s, output queue size 2303
progress 85% @chr19:57000001, elapsed 373.7s, est remaining 65.9s, peak mem 39026MB, user 10774.4s, sys 87.3s, output queue size 2465
progress 90% @chrX:35000001, elapsed 422.0s, est remaining 46.9s, peak mem 49153MB, user 12065.0s, sys 94.1s, output queue size 2627
progress 95% @chrY:52000001, elapsed 442.0s, est remaining 23.3s, peak mem 49185MB, user 12537.2s, sys 97.0s, output queue size 2788
progress 100% @chr19:7000001, elapsed 712.1s, est remaining 0.0s, peak mem 60410MB, user 14573.7s, sys 140.8s, output queue size 3822
library Filler-D0002805:
chimeric_paired 62395293
duped 1566073951
duped_chimeric_paired 31138834
duped_paired 1566043056
duped_unpaired 30895
optical_dup 194471455
paired 1795154234
reads 1811398664
secondary_supplementary 16180090
unmapped 56082
unpaired 32170
optical dup clusters 50492429, maxdup 848, total optical dup pairs 194471455
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: 53136889415
reads: 1811422576
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2682695 calls 124.138 user 2.166 sys 130.540 real
MateInfoByVcf::load: 2682695 calls 1908.741 user 18.698 sys 1688.458 real
MateInfoByVcf::parse_events: 2682695 calls 1565.893 user 14.016 sys 1438.844 real
advance: 3219322 calls 1131.439 user 40.479 sys 1326.537 real
calc: 3219322 calls 10322.631 user 67.505 sys 10520.500 real
done: 1 calls 0.093 user 0.011 sys 0.107 real
exec_no_coor: 1 calls 0.114 user 0.088 sys 0.220 real
execute: 1 calls 0.002 user 0.001 sys 714.234 real
fetch: 3219323 calls 878.789 user 5.541 sys 872.228 real
find_pairEnds: 2682695 calls 1002.556 user 2.828 sys 1085.352 real
idle: 759199 calls 322.372 user 11.159 sys 6993.031 real
init: 1 calls 0.009 user 0.001 sys 0.006 real
markDup: 2682695 calls 4027.949 user 23.462 sys 4335.018 real
vcfadvance: 2682695 calls 22.864 user 4.337 sys 25.986 real
write: 3219323 calls 6190.657 user 42.585 sys 6058.820 real
overall: 63344742400 mem 14963.963 user 173.138 sys 716.507 real