Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/b492b364d2134bc223ce3e5f2abca4/Filler-D0001089.bai
  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/ba/178d814716b662d65d51af0fd4797b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/178d814716b662d65d51af0fd4797b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/b492b364d2134bc223ce3e5f2abca4/Filler-D0001089.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-D0001089.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0001089.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 5.7s, est remaining 108.1s, peak mem 2870MB, user 135.7s, sys 8.1s, output queue size 145
progress 10% @chr2:72000001, elapsed 9.2s, est remaining 82.5s, peak mem 3404MB, user 255.8s, sys 10.0s, output queue size 94
progress 15% @chr2:215000001, elapsed 12.9s, est remaining 73.0s, peak mem 5902MB, user 359.7s, sys 11.3s, output queue size 203
progress 20% @chr3:168000001, elapsed 17.0s, est remaining 67.9s, peak mem 8884MB, user 468.6s, sys 13.3s, output queue size 364
progress 25% @chr4:138000001, elapsed 19.8s, est remaining 59.5s, peak mem 11329MB, user 554.7s, sys 14.9s, output queue size 525
progress 30% @chr5:107000001, elapsed 22.0s, est remaining 51.4s, peak mem 12862MB, user 630.2s, sys 15.9s, output queue size 686
progress 35% @chr6:91000001, elapsed 25.9s, est remaining 48.1s, peak mem 15758MB, user 734.5s, sys 16.8s, output queue size 848
progress 40% @chr7:65000001, elapsed 29.4s, est remaining 44.1s, peak mem 16567MB, user 824.6s, sys 17.6s, output queue size 1009
progress 45% @chr8:58000001, elapsed 33.8s, est remaining 41.3s, peak mem 17771MB, user 960.4s, sys 19.3s, output queue size 1171
progress 50% @chr9:102000001, elapsed 36.7s, est remaining 36.7s, peak mem 17954MB, user 1034.1s, sys 20.6s, output queue size 1333
progress 55% @chr10:93000001, elapsed 41.3s, est remaining 33.8s, peak mem 18392MB, user 1181.0s, sys 23.5s, output queue size 1494
progress 60% @chr11:126000001, elapsed 46.7s, est remaining 31.1s, peak mem 18661MB, user 1331.2s, sys 24.5s, output queue size 1656
progress 65% @chr12:56000001, elapsed 51.2s, est remaining 27.5s, peak mem 18661MB, user 1458.5s, sys 25.5s, output queue size 1818
progress 70% @chr14:58000001, elapsed 55.2s, est remaining 23.7s, peak mem 18661MB, user 1625.1s, sys 38.6s, output queue size 908
progress 75% @chr16:40000001, elapsed 60.1s, est remaining 20.0s, peak mem 18661MB, user 1752.1s, sys 39.6s, output queue size 1070
progress 80% @chr18:1, elapsed 69.8s, est remaining 17.5s, peak mem 19153MB, user 2050.0s, sys 41.6s, output queue size 205
progress 85% @chr20:23000001, elapsed 78.3s, est remaining 13.8s, peak mem 19802MB, user 2303.6s, sys 43.3s, output queue size 367
progress 90% @chr22:21000001, elapsed 87.3s, est remaining 9.7s, peak mem 25080MB, user 2560.1s, sys 44.6s, output queue size 529
progress 95% @chrY:49000001, elapsed 91.0s, est remaining 4.8s, peak mem 27051MB, user 2649.6s, sys 45.4s, output queue size 690
progress 100% @chr19:7000001, elapsed 159.9s, est remaining 0.0s, peak mem 42062MB, user 2987.0s, sys 66.5s, 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: 62888281544
reads: 2110716668
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 5.657 user 1.419 sys 8.184 real
VcfLineRecordHelper::sort: 163 calls 10.684 user 0.411 sys 11.160 real
advance: 3219322 calls 1406.850 user 46.335 sys 1456.242 real
calc: 3219322 calls 649.233 user 11.512 sys 664.284 real
done: 1 calls 5.657 user 1.419 sys 8.184 real
execute: 1 calls 0.002 user 0.003 sys 159.915 real
fetch: 3219322 calls 802.852 user 6.193 sys 806.917 real
idle: 2306 calls 0.861 user 0.009 sys 2169.033 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 44105924608 mem 3025.151 user 69.551 sys 169.327 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0001089.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0001089.md.score --metrics Filler-D0001089.md.metrics Filler-D0001089.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 27.5s, est remaining 522.2s, peak mem 3542MB, user 698.0s, sys 9.4s, output queue size 52
progress 10% @chr2:92000001, elapsed 45.3s, est remaining 408.1s, peak mem 4444MB, user 1307.2s, sys 14.7s, output queue size 94
progress 15% @chr3:3000001, elapsed 64.5s, est remaining 365.3s, peak mem 16493MB, user 1847.0s, sys 18.9s, output queue size 203
progress 20% @chr3:122000001, elapsed 87.2s, est remaining 348.7s, peak mem 19828MB, user 2459.5s, sys 23.0s, output queue size 364
progress 25% @chr4:87000001, elapsed 102.4s, est remaining 307.1s, peak mem 22436MB, user 2994.1s, sys 26.7s, output queue size 525
progress 30% @chr5:104000001, elapsed 114.9s, est remaining 268.1s, peak mem 23216MB, user 3366.7s, sys 29.1s, output queue size 687
progress 35% @chr6:39000001, elapsed 135.8s, est remaining 252.3s, peak mem 23988MB, user 3894.9s, sys 32.0s, output queue size 848
progress 40% @chr7:67000001, elapsed 155.1s, est remaining 232.7s, peak mem 25478MB, user 4417.5s, sys 35.6s, output queue size 1009
progress 45% @chr8:58000001, elapsed 179.0s, est remaining 218.8s, peak mem 25478MB, user 5151.1s, sys 41.0s, output queue size 1171
progress 50% @chr9:33000001, elapsed 195.3s, est remaining 195.3s, peak mem 25478MB, user 5692.9s, sys 46.8s, output queue size 1333
progress 55% @chr10:118000001, elapsed 223.2s, est remaining 182.6s, peak mem 25478MB, user 6411.6s, sys 51.2s, output queue size 1494
progress 60% @chr11:125000001, elapsed 254.7s, est remaining 169.8s, peak mem 25478MB, user 7293.0s, sys 55.8s, output queue size 1656
progress 65% @chr13:25000001, elapsed 282.3s, est remaining 152.0s, peak mem 26638MB, user 8073.4s, sys 59.3s, output queue size 1818
progress 70% @chr14:84000001, elapsed 307.9s, est remaining 131.9s, peak mem 26638MB, user 8927.4s, sys 63.7s, output queue size 1979
progress 75% @chr16:42000001, elapsed 336.7s, est remaining 112.2s, peak mem 26638MB, user 9659.5s, sys 67.0s, output queue size 2141
progress 80% @chr18:9000001, elapsed 388.6s, est remaining 97.2s, peak mem 26638MB, user 11533.9s, sys 88.6s, output queue size 205
progress 85% @chr20:18000001, elapsed 434.5s, est remaining 76.7s, peak mem 26638MB, user 12934.6s, sys 95.4s, output queue size 367
progress 90% @chrX:35000001, elapsed 488.1s, est remaining 54.2s, peak mem 39278MB, user 14390.9s, sys 101.7s, output queue size 529
progress 95% @chrY:52000001, elapsed 510.1s, est remaining 26.8s, peak mem 39281MB, user 14957.2s, sys 104.5s, output queue size 690
progress 100% @chr19:7000001, elapsed 837.2s, est remaining 0.0s, peak mem 49955MB, user 16668.7s, sys 131.2s, output queue size 3822
library Filler-D0001089:
chimeric_paired 55159208
duped 1711707356
duped_chimeric_paired 21832526
duped_paired 1711671567
duped_unpaired 35789
optical_dup 117767000
paired 2089707774
reads 2110680522
secondary_supplementary 20897076
unmapped 73982
unpaired 37836
optical dup clusters 52293137, maxdup 625, total optical dup pairs 117767000
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: 62888281544
reads: 2110716668
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2836635 calls 71.114 user 1.475 sys 74.928 real
MateInfoByVcf::load: 2836635 calls 1929.675 user 15.214 sys 1732.832 real
MateInfoByVcf::parse_events: 2836635 calls 1657.719 user 11.412 sys 1546.075 real
advance: 3219322 calls 1357.270 user 41.525 sys 1551.835 real
calc: 3219322 calls 11940.939 user 62.883 sys 12135.350 real
done: 1 calls 0.105 user 0.010 sys 0.123 real
exec_no_coor: 1 calls 0.241 user 0.065 sys 0.339 real
execute: 1 calls 0.003 user 0.001 sys 840.692 real
fetch: 3219323 calls 1086.453 user 4.538 sys 1085.217 real
find_pairEnds: 2836635 calls 1141.973 user 2.604 sys 1218.741 real
idle: 718086 calls 135.168 user 6.120 sys 9011.876 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 2836635 calls 4585.988 user 20.848 sys 4861.636 real
vcfadvance: 2836635 calls 15.451 user 3.321 sys 17.695 real
write: 3219323 calls 7229.994 user 40.807 sys 7127.583 real
overall: 52382060544 mem 16847.013 user 167.837 sys 843.751 real