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/c3/2a6a14f618124df375c455b20fe1ff/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/77793f9244727208a997d2d587cf75/Filler-D0001322.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/2a6a14f618124df375c455b20fe1ff/.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/73/77793f9244727208a997d2d587cf75/Filler-D0001322.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0001322.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0001322.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 5.4s, est remaining 102.2s, peak mem 2770MB, user 121.6s, sys 8.8s, output queue size 160
progress 10% @chr2:68000001, elapsed 8.8s, est remaining 79.0s, peak mem 3289MB, user 241.2s, sys 11.5s, output queue size 166
progress 15% @chr3:18000001, elapsed 12.3s, est remaining 69.8s, peak mem 5505MB, user 342.5s, sys 13.7s, output queue size 203
progress 20% @chr3:178000001, elapsed 16.5s, est remaining 65.9s, peak mem 8310MB, user 439.3s, sys 15.3s, output queue size 364
progress 25% @chr4:76000001, elapsed 19.1s, est remaining 57.2s, peak mem 10417MB, user 547.7s, sys 17.6s, output queue size 525
progress 30% @chr5:73000001, elapsed 21.1s, est remaining 49.2s, peak mem 11740MB, user 603.4s, sys 18.2s, output queue size 687
progress 35% @chr6:92000001, elapsed 24.5s, est remaining 45.6s, peak mem 14382MB, user 692.8s, sys 19.1s, output queue size 848
progress 40% @chr7:79000001, elapsed 27.7s, est remaining 41.5s, peak mem 16595MB, user 777.0s, sys 20.0s, output queue size 1009
progress 45% @chr8:72000001, elapsed 31.9s, est remaining 39.0s, peak mem 20472MB, user 883.6s, sys 21.2s, output queue size 1171
progress 50% @chr9:33000001, elapsed 34.5s, est remaining 34.5s, peak mem 22675MB, user 972.9s, sys 23.0s, output queue size 1333
progress 55% @chr10:93000001, elapsed 38.8s, est remaining 31.7s, peak mem 25269MB, user 1100.9s, sys 25.3s, output queue size 1494
progress 60% @chr11:113000001, elapsed 43.8s, est remaining 29.2s, peak mem 26397MB, user 1241.8s, sys 26.6s, output queue size 1656
progress 65% @chr13:25000001, elapsed 48.1s, est remaining 25.9s, peak mem 26958MB, user 1365.8s, sys 27.9s, output queue size 1818
progress 70% @chr14:85000001, elapsed 52.0s, est remaining 22.3s, peak mem 26958MB, user 1492.9s, sys 29.2s, output queue size 1979
progress 75% @chr16:42000001, elapsed 57.0s, est remaining 19.0s, peak mem 26981MB, user 1616.1s, sys 30.4s, output queue size 2141
progress 80% @chr18:21000001, elapsed 67.8s, est remaining 16.9s, peak mem 28148MB, user 1886.7s, sys 32.6s, output queue size 2303
progress 85% @chr20:23000001, elapsed 76.4s, est remaining 13.5s, peak mem 28418MB, user 2184.1s, sys 35.2s, output queue size 2465
progress 90% @chrX:33000001, elapsed 86.4s, est remaining 9.6s, peak mem 32094MB, user 2509.3s, sys 50.8s, output queue size 529
progress 95% @chrY:51000001, elapsed 90.1s, est remaining 4.7s, peak mem 33756MB, user 2603.5s, sys 51.7s, output queue size 690
progress 100% @chr19:7000001, elapsed 153.1s, est remaining 0.0s, peak mem 39884MB, user 2966.0s, sys 62.3s, 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: 59121971257
reads: 2043529569
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 8.713 user 1.944 sys 14.329 real
VcfLineRecordHelper::sort: 252 calls 16.778 user 0.643 sys 17.412 real
advance: 3219322 calls 1364.354 user 46.597 sys 1414.612 real
calc: 3219322 calls 683.012 user 8.771 sys 690.538 real
done: 1 calls 8.713 user 1.944 sys 14.329 real
execute: 1 calls 0.001 user 0.001 sys 153.134 real
fetch: 3219322 calls 788.718 user 4.409 sys 794.612 real
idle: 2313 calls 0.797 user 0.016 sys 2178.768 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 41882443776 mem 3018.544 user 66.509 sys 168.902 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0001322.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0001322.md.score --metrics Filler-D0001322.md.metrics Filler-D0001322.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 27.7s, est remaining 526.3s, peak mem 3308MB, user 690.8s, sys 11.8s, output queue size 52
progress 10% @chr2:89000001, elapsed 46.7s, est remaining 420.1s, peak mem 4709MB, user 1331.7s, sys 18.7s, output queue size 94
progress 15% @chr3:3000001, elapsed 66.2s, est remaining 374.9s, peak mem 16436MB, user 1890.4s, sys 25.2s, output queue size 203
progress 20% @chr3:142000001, elapsed 90.2s, est remaining 360.7s, peak mem 27119MB, user 2448.5s, sys 32.5s, output queue size 364
progress 25% @chr4:134000001, elapsed 106.4s, est remaining 319.3s, peak mem 29401MB, user 3076.0s, sys 37.7s, output queue size 525
progress 30% @chr5:81000001, elapsed 119.7s, est remaining 279.3s, peak mem 30352MB, user 3477.1s, sys 40.7s, output queue size 687
progress 35% @chr6:91000001, elapsed 142.6s, est remaining 264.8s, peak mem 32741MB, user 4048.9s, sys 45.2s, output queue size 848
progress 40% @chr7:64000001, elapsed 162.8s, est remaining 244.2s, peak mem 34301MB, user 4619.0s, sys 50.0s, output queue size 1009
progress 45% @chr8:71000001, elapsed 188.4s, est remaining 230.2s, peak mem 35274MB, user 5386.7s, sys 55.7s, output queue size 1171
progress 50% @chr9:86000001, elapsed 204.7s, est remaining 204.7s, peak mem 35957MB, user 5904.6s, sys 59.8s, output queue size 1333
progress 55% @chr9:136000001, elapsed 232.0s, est remaining 189.8s, peak mem 36910MB, user 6700.9s, sys 63.8s, output queue size 1494
progress 60% @chr12:3000001, elapsed 263.3s, est remaining 175.5s, peak mem 37213MB, user 7559.7s, sys 67.9s, output queue size 1656
progress 65% @chr12:120000001, elapsed 289.2s, est remaining 155.7s, peak mem 38898MB, user 8307.9s, sys 71.5s, output queue size 1818
progress 70% @chr14:84000001, elapsed 314.9s, est remaining 135.0s, peak mem 39213MB, user 9107.0s, sys 75.8s, output queue size 1979
progress 75% @chr16:42000001, elapsed 345.7s, est remaining 115.2s, peak mem 39213MB, user 9875.5s, sys 80.7s, output queue size 2141
progress 80% @chr17:63000001, elapsed 406.7s, est remaining 101.7s, peak mem 39213MB, user 11692.4s, sys 92.4s, output queue size 2303
progress 85% @chr20:42000001, elapsed 456.6s, est remaining 80.6s, peak mem 39213MB, user 13144.4s, sys 100.0s, output queue size 2465
progress 90% @chrX:23000001, elapsed 514.7s, est remaining 57.2s, peak mem 48824MB, user 14680.2s, sys 106.5s, output queue size 2627
progress 95% @chrY:53000001, elapsed 538.3s, est remaining 28.3s, peak mem 48824MB, user 15284.0s, sys 109.3s, output queue size 2788
progress 100% @chr19:7000001, elapsed 764.6s, est remaining 0.0s, peak mem 50206MB, user 17394.5s, sys 155.5s, output queue size 3822
library Filler-D0001322:
chimeric_paired 62433900
duped 1706065443
duped_chimeric_paired 31094532
duped_paired 1706031305
duped_unpaired 34138
optical_dup 231241556
paired 2028525964
reads 2043500461
secondary_supplementary 14902643
unmapped 65035
unpaired 35927
optical dup clusters 69730787, maxdup 517, total optical dup pairs 231241556
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: 59121971257
reads: 2043529569
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2759989 calls 123.005 user 3.715 sys 130.111 real
MateInfoByVcf::load: 2759989 calls 2069.240 user 21.126 sys 1826.133 real
MateInfoByVcf::parse_events: 2759989 calls 1699.356 user 14.763 sys 1553.825 real
advance: 3219322 calls 1340.648 user 41.821 sys 1546.573 real
calc: 3219322 calls 12337.817 user 76.040 sys 12575.094 real
done: 1 calls 0.045 user 0.027 sys 0.081 real
exec_no_coor: 1 calls 0.244 user 0.068 sys 0.331 real
execute: 1 calls 0.003 user 0.002 sys 766.904 real
fetch: 3219323 calls 1208.051 user 6.782 sys 1212.842 real
find_pairEnds: 2759989 calls 1300.565 user 4.623 sys 1390.230 real
idle: 721520 calls 286.126 user 6.042 sys 5788.733 real
init: 1 calls 0.009 user 0.001 sys 0.007 real
markDup: 2759989 calls 5061.945 user 27.679 sys 5399.760 real
vcfadvance: 2759989 calls 22.918 user 4.928 sys 27.364 real
write: 3219323 calls 7144.515 user 47.117 sys 7016.106 real
overall: 52644868096 mem 17751.382 user 184.228 sys 769.315 real