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/1d/1fcf1d5d4cdf7b51d80120094af5c4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/1fcf1d5d4cdf7b51d80120094af5c4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/30ccabe058204350e166f26bd45711/1136_00H-T1-TDNA-1_A23MHWWLT4_1.bam
  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/fc/30ccabe058204350e166f26bd45711/1136_00H-T1-TDNA-1_A23MHWWLT4_1.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_00H-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 4.2s, est remaining 79.3s, peak mem 6349MB, user 90.7s, sys 5.6s, output queue size 146
progress 10% @chr2:84000001, elapsed 7.5s, est remaining 67.3s, peak mem 8651MB, user 189.8s, sys 9.1s, output queue size 166
progress 15% @chr3:17000001, elapsed 11.1s, est remaining 63.0s, peak mem 12282MB, user 295.3s, sys 11.9s, output queue size 203
progress 20% @chr3:158000001, elapsed 14.1s, est remaining 56.5s, peak mem 14121MB, user 384.3s, sys 13.8s, output queue size 364
progress 25% @chr4:133000001, elapsed 17.1s, est remaining 51.2s, peak mem 14938MB, user 469.5s, sys 15.4s, output queue size 525
progress 30% @chr5:100000001, elapsed 19.2s, est remaining 44.9s, peak mem 15080MB, user 533.1s, sys 16.4s, output queue size 687
progress 35% @chr6:91000001, elapsed 22.2s, est remaining 41.3s, peak mem 15133MB, user 617.1s, sys 18.1s, output queue size 848
progress 40% @chr7:66000001, elapsed 25.7s, est remaining 38.5s, peak mem 15555MB, user 715.9s, sys 21.9s, output queue size 786
progress 45% @chr8:82000001, elapsed 29.6s, est remaining 36.2s, peak mem 15801MB, user 829.6s, sys 23.2s, output queue size 948
progress 50% @chr9:102000001, elapsed 32.9s, est remaining 32.9s, peak mem 16311MB, user 919.1s, sys 24.0s, output queue size 1110
progress 55% @chr10:101000001, elapsed 36.8s, est remaining 30.1s, peak mem 16802MB, user 1048.0s, sys 25.0s, output queue size 527
progress 60% @chr12:2000001, elapsed 40.8s, est remaining 27.2s, peak mem 16802MB, user 1149.4s, sys 26.3s, output queue size 689
progress 65% @chr13:35000001, elapsed 44.5s, est remaining 24.0s, peak mem 16802MB, user 1282.6s, sys 27.7s, output queue size 672
progress 70% @chr13:102000001, elapsed 46.8s, est remaining 20.1s, peak mem 16802MB, user 1347.6s, sys 28.4s, output queue size 833
progress 75% @chr16:42000001, elapsed 51.7s, est remaining 17.2s, peak mem 17002MB, user 1465.1s, sys 29.3s, output queue size 995
progress 80% @chr17:65000001, elapsed 58.2s, est remaining 14.6s, peak mem 17230MB, user 1696.5s, sys 31.6s, output queue size 623
progress 85% @chr19:57000001, elapsed 63.7s, est remaining 11.2s, peak mem 17230MB, user 1856.4s, sys 32.9s, output queue size 785
progress 90% @chrX:38000001, elapsed 67.3s, est remaining 7.5s, peak mem 17230MB, user 1966.7s, sys 34.2s, output queue size 947
progress 95% @chrY:52000001, elapsed 69.2s, est remaining 3.6s, peak mem 17230MB, user 2027.3s, sys 34.7s, output queue size 1109
progress 100% @chr15:88000001, elapsed 83.8s, est remaining 0.0s, peak mem 17230MB, user 2180.1s, sys 36.0s, output queue size 4099
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 72750459686
reads: 1364658919
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 3.746 user 1.045 sys 8.815 real
VcfLineRecordHelper::sort: 138 calls 5.796 user 0.189 sys 6.067 real
advance: 3219322 calls 1220.427 user 28.898 sys 1250.303 real
calc: 3219322 calls 416.796 user 3.186 sys 423.486 real
done: 1 calls 3.746 user 1.045 sys 8.815 real
execute: 1 calls 0.001 user 0.001 sys 83.902 real
fetch: 3219322 calls 471.232 user 1.955 sys 470.478 real
idle: 719 calls 0.180 user 0.002 sys 680.896 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 18067476480 mem 2201.424 user 38.334 sys 93.964 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_00H-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 31.5s, est remaining 597.7s, peak mem 7249MB, user 796.3s, sys 7.0s, output queue size 52
progress 10% @chr2:90000001, elapsed 55.7s, est remaining 501.4s, peak mem 11734MB, user 1555.0s, sys 11.7s, output queue size 117
progress 15% @chr3:8000001, elapsed 83.8s, est remaining 474.6s, peak mem 16124MB, user 2367.0s, sys 16.1s, output queue size 203
progress 20% @chr3:167000001, elapsed 109.3s, est remaining 437.2s, peak mem 16819MB, user 3125.8s, sys 19.3s, output queue size 364
progress 25% @chr4:124000001, elapsed 131.4s, est remaining 394.3s, peak mem 16819MB, user 3788.5s, sys 21.8s, output queue size 525
progress 30% @chr5:99000001, elapsed 149.1s, est remaining 347.9s, peak mem 16819MB, user 4406.6s, sys 27.9s, output queue size 464
progress 35% @chr6:56000001, elapsed 172.6s, est remaining 320.6s, peak mem 16819MB, user 5049.4s, sys 30.6s, output queue size 625
progress 40% @chr7:67000001, elapsed 202.0s, est remaining 303.0s, peak mem 16997MB, user 5777.9s, sys 33.8s, output queue size 786
progress 45% @chr8:72000001, elapsed 231.4s, est remaining 282.8s, peak mem 17020MB, user 6873.4s, sys 38.3s, output queue size 204
progress 50% @chr9:89000001, elapsed 255.8s, est remaining 255.8s, peak mem 17467MB, user 7528.0s, sys 40.7s, output queue size 366
progress 55% @chr10:99000001, elapsed 288.0s, est remaining 235.6s, peak mem 17777MB, user 8537.3s, sys 45.1s, output queue size 348
progress 60% @chr11:134000001, elapsed 318.7s, est remaining 212.5s, peak mem 17777MB, user 9478.2s, sys 48.6s, output queue size 510
progress 65% @chr13:33000001, elapsed 349.2s, est remaining 188.1s, peak mem 18141MB, user 10313.9s, sys 51.6s, output queue size 672
progress 70% @chr14:79000001, elapsed 368.8s, est remaining 158.0s, peak mem 18141MB, user 10843.8s, sys 53.6s, output queue size 833
progress 75% @chr16:40000001, elapsed 403.9s, est remaining 134.6s, peak mem 18141MB, user 12075.9s, sys 58.3s, output queue size 461
progress 80% @chr18:10000001, elapsed 461.2s, est remaining 115.3s, peak mem 18361MB, user 13561.9s, sys 63.0s, output queue size 623
progress 85% @chr20:20000001, elapsed 506.7s, est remaining 89.4s, peak mem 18384MB, user 15142.4s, sys 67.7s, output queue size 785
progress 90% @chr22:39000001, elapsed 535.0s, est remaining 59.4s, peak mem 18618MB, user 16135.3s, sys 71.1s, output queue size 513
progress 95% @chrY:53000001, elapsed 551.0s, est remaining 29.0s, peak mem 18693MB, user 16578.9s, sys 73.0s, output queue size 675
progress 100% @chr22:23000001, elapsed 610.0s, est remaining 0.0s, peak mem 18697MB, user 17336.9s, sys 75.8s, output queue size 3635
library 1136_00H-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 21169005
duped 792748672
duped_chimeric_paired 3373194
duped_paired 792742872
duped_unpaired 5800
optical_dup 192222813
paired 1357065106
reads 1364653255
secondary_supplementary 7574543
unmapped 12467
unpaired 6803
optical dup clusters 91137436, maxdup 81, total optical dup pairs 192222813
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 72750459686
reads: 1364658919
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2698187 calls 24.012 user 0.524 sys 24.963 real
MateInfoByVcf::load: 2698187 calls 2560.001 user 10.523 sys 2519.098 real
MateInfoByVcf::parse_events: 2698187 calls 2425.992 user 8.714 sys 2437.780 real
advance: 3219322 calls 1248.343 user 25.610 sys 1319.136 real
calc: 3219322 calls 12675.574 user 33.055 sys 12781.600 real
done: 1 calls 0.073 user 0.000 sys 0.083 real
exec_no_coor: 1 calls 0.000 user 0.013 sys 0.023 real
execute: 1 calls 0.004 user 0.004 sys 611.249 real
fetch: 3219323 calls 619.253 user 1.933 sys 599.896 real
find_pairEnds: 2698187 calls 734.341 user 1.143 sys 752.133 real
idle: 74845 calls 30.462 user 0.493 sys 1471.820 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 2698187 calls 2781.965 user 7.616 sys 2853.046 real
vcfadvance: 2698187 calls 13.919 user 1.788 sys 15.509 real
write: 3219323 calls 9834.851 user 24.273 sys 9866.192 real
overall: 19605762048 mem 17378.373 user 105.738 sys 612.864 real