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/5c/d206d82037767ad9de025d971cf23f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/4ff38440da9c4dd1322728e477e781/1_25PercentHG514.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/d206d82037767ad9de025d971cf23f/.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/35/4ff38440da9c4dd1322728e477e781/1_25PercentHG514.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1_25PercentHG514.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1_25PercentHG514.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 14.3s, est remaining 272.2s, peak mem 6821MB, user 318.2s, sys 21.1s, output queue size 160
progress 10% @chr2:89000001, elapsed 24.8s, est remaining 223.1s, peak mem 7416MB, user 672.3s, sys 28.4s, output queue size 167
progress 15% @chr3:21000001, elapsed 35.6s, est remaining 201.9s, peak mem 14420MB, user 992.6s, sys 32.6s, output queue size 203
progress 20% @chr3:161000001, elapsed 47.5s, est remaining 190.0s, peak mem 22270MB, user 1272.4s, sys 36.7s, output queue size 364
progress 25% @chr4:70000001, elapsed 56.3s, est remaining 168.8s, peak mem 27331MB, user 1559.8s, sys 40.2s, output queue size 525
progress 30% @chr5:73000001, elapsed 63.0s, est remaining 146.9s, peak mem 28698MB, user 1778.7s, sys 43.0s, output queue size 687
progress 35% @chr6:94000001, elapsed 74.4s, est remaining 138.1s, peak mem 29829MB, user 2112.7s, sys 47.0s, output queue size 848
progress 40% @chr6:160000001, elapsed 84.2s, est remaining 126.3s, peak mem 30719MB, user 2384.0s, sys 49.7s, output queue size 1009
progress 45% @chr8:84000001, elapsed 96.0s, est remaining 117.3s, peak mem 30818MB, user 2728.7s, sys 52.8s, output queue size 1171
progress 50% @chr9:102000001, elapsed 103.7s, est remaining 103.7s, peak mem 31684MB, user 2984.5s, sys 55.4s, output queue size 1333
progress 55% @chr10:118000001, elapsed 116.6s, est remaining 95.4s, peak mem 31843MB, user 3406.7s, sys 74.3s, output queue size 423
progress 60% @chr11:113000001, elapsed 132.2s, est remaining 88.2s, peak mem 31843MB, user 3832.4s, sys 79.3s, output queue size 585
progress 65% @chr12:52000001, elapsed 146.0s, est remaining 78.6s, peak mem 31843MB, user 4272.2s, sys 82.1s, output queue size 747
progress 70% @chr14:86000001, elapsed 159.2s, est remaining 68.2s, peak mem 31843MB, user 4706.9s, sys 84.5s, output queue size 908
progress 75% @chr16:42000001, elapsed 174.5s, est remaining 58.2s, peak mem 31858MB, user 5119.2s, sys 86.9s, output queue size 1070
progress 80% @chr18:3000001, elapsed 206.6s, est remaining 51.7s, peak mem 34828MB, user 5999.6s, sys 92.9s, output queue size 1232
progress 85% @chr19:58000001, elapsed 236.4s, est remaining 41.7s, peak mem 35146MB, user 6800.1s, sys 97.4s, output queue size 1394
progress 90% @chrX:42000001, elapsed 266.3s, est remaining 29.6s, peak mem 45122MB, user 7803.1s, sys 102.9s, output queue size 529
progress 95% @chrY:54000001, elapsed 278.6s, est remaining 14.7s, peak mem 45122MB, user 8115.7s, sys 104.9s, output queue size 690
progress 100% @chr22:19000001, elapsed 418.7s, est remaining 0.0s, peak mem 51385MB, user 9097.8s, sys 121.8s, output queue size 3639
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: 152648854026
reads: 4813824514
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 15.261 user 2.952 sys 18.778 real
VcfLineRecordHelper::sort: 274 calls 18.464 user 0.419 sys 18.806 real
advance: 3219322 calls 3584.688 user 91.555 sys 3679.943 real
calc: 3219322 calls 2097.327 user 15.420 sys 2113.070 real
done: 1 calls 15.261 user 2.952 sys 18.778 real
execute: 1 calls 0.004 user 0.005 sys 418.840 real
fetch: 3219322 calls 2975.079 user 11.368 sys 2988.734 real
idle: 4568 calls 1.427 user 0.014 sys 4350.906 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 54093881344 mem 9171.220 user 128.529 sys 439.325 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1_25PercentHG514.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1_25PercentHG514.md.score --metrics 1_25PercentHG514.md.metrics 1_25PercentHG514.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 70.0s, est remaining 1329.3s, peak mem 7523MB, user 1704.5s, sys 26.6s, output queue size 160
progress 10% @chr2:68000001, elapsed 119.7s, est remaining 1077.7s, peak mem 9538MB, user 3429.6s, sys 37.0s, output queue size 74
progress 15% @chr3:3000001, elapsed 171.8s, est remaining 973.6s, peak mem 32457MB, user 4886.8s, sys 43.9s, output queue size 203
progress 20% @chr3:156000001, elapsed 228.8s, est remaining 915.4s, peak mem 37828MB, user 6311.2s, sys 50.3s, output queue size 364
progress 25% @chr3:184000001, elapsed 269.4s, est remaining 808.3s, peak mem 39487MB, user 7798.8s, sys 57.8s, output queue size 525
progress 30% @chr5:97000001, elapsed 302.8s, est remaining 706.5s, peak mem 42252MB, user 8675.3s, sys 63.1s, output queue size 687
progress 35% @chr6:92000001, elapsed 355.6s, est remaining 660.3s, peak mem 42252MB, user 10218.4s, sys 73.3s, output queue size 848
progress 40% @chr7:30000001, elapsed 403.8s, est remaining 605.7s, peak mem 42252MB, user 11702.5s, sys 84.2s, output queue size 1009
progress 45% @chr8:69000001, elapsed 460.5s, est remaining 562.8s, peak mem 42252MB, user 13156.0s, sys 92.4s, output queue size 1171
progress 50% @chr9:85000001, elapsed 499.6s, est remaining 499.6s, peak mem 45589MB, user 14577.6s, sys 101.8s, output queue size 1333
progress 55% @chr10:93000001, elapsed 564.0s, est remaining 461.5s, peak mem 45823MB, user 16248.2s, sys 109.4s, output queue size 1494
progress 60% @chr12:5000001, elapsed 638.5s, est remaining 425.6s, peak mem 45823MB, user 18243.8s, sys 118.1s, output queue size 1656
progress 65% @chr12:52000001, elapsed 702.1s, est remaining 378.1s, peak mem 45823MB, user 20690.6s, sys 155.7s, output queue size 747
progress 70% @chr14:86000001, elapsed 763.7s, est remaining 327.3s, peak mem 45823MB, user 22732.5s, sys 167.3s, output queue size 908
progress 75% @chr16:42000001, elapsed 831.7s, est remaining 277.2s, peak mem 45823MB, user 24574.0s, sys 178.7s, output queue size 1070
progress 80% @chr18:5000001, elapsed 968.9s, est remaining 242.2s, peak mem 45823MB, user 28216.0s, sys 203.3s, output queue size 1232
progress 85% @chr19:42000001, elapsed 1096.1s, est remaining 193.4s, peak mem 48874MB, user 31783.2s, sys 222.8s, output queue size 1394
progress 90% @chrX:36000001, elapsed 1233.9s, est remaining 137.1s, peak mem 56514MB, user 36318.5s, sys 251.1s, output queue size 529
progress 95% @chrY:54000001, elapsed 1287.2s, est remaining 67.7s, peak mem 56514MB, user 37721.5s, sys 259.7s, output queue size 690
progress 100% @chr19:7000001, elapsed 1742.9s, est remaining 0.0s, peak mem 65039MB, user 41689.4s, sys 306.3s, output queue size 3822
library 1_25PercentHG514:
chimeric_paired 89311806
duped 3607854727
duped_chimeric_paired 37196808
duped_paired 3607799650
duped_unpaired 55077
paired 4786484514
reads 4813723256
secondary_supplementary 27124528
unmapped 158365
unpaired 57107
optical dup clusters 0, maxdup 0, total optical dup pairs 0
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: 152648854026
reads: 4813824514
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2926042 calls 110.289 user 2.022 sys 117.584 real
MateInfoByVcf::load: 2926042 calls 2435.206 user 21.085 sys 2327.523 real
MateInfoByVcf::parse_events: 2926042 calls 2060.612 user 15.759 sys 2023.859 real
advance: 3219322 calls 3308.162 user 96.391 sys 3537.564 real
calc: 3219322 calls 31852.543 user 164.293 sys 32237.271 real
done: 1 calls 0.070 user 0.022 sys 0.099 real
exec_no_coor: 1 calls 0.855 user 0.505 sys 1.397 real
execute: 1 calls 0.000 user 0.005 sys 1752.365 real
fetch: 3219324 calls 3036.531 user 12.147 sys 3077.629 real
find_pairEnds: 2926042 calls 3691.563 user 6.172 sys 3789.630 real
idle: 1200337 calls 270.561 user 9.977 sys 11731.968 real
init: 1 calls 0.010 user 0.000 sys 0.008 real
markDup: 2926042 calls 12933.283 user 50.167 sys 13258.330 real
vcfadvance: 2926042 calls 41.652 user 5.737 sys 33.256 real
write: 3219324 calls 18607.009 user 112.453 sys 18629.736 real
overall: 68199161856 mem 42023.451 user 399.100 sys 1756.063 real