Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/edf49844ce919a2d1daf38e08c2e3b/Filler-D0002881.bam
  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/be/d2de8b888157aff6226b4c945c5e29/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/d2de8b888157aff6226b4c945c5e29/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/edf49844ce919a2d1daf38e08c2e3b/Filler-D0002881.bai
  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-D0002881.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0002881.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 4.1s, est remaining 77.2s, peak mem 2087MB, user 93.1s, sys 4.9s, output queue size 160
progress 10% @chr2:38000001, elapsed 6.6s, est remaining 59.3s, peak mem 2478MB, user 184.0s, sys 7.5s, output queue size 94
progress 15% @chr3:18000001, elapsed 9.2s, est remaining 52.3s, peak mem 4155MB, user 258.5s, sys 8.8s, output queue size 203
progress 20% @chr3:176000001, elapsed 12.2s, est remaining 49.0s, peak mem 6334MB, user 336.2s, sys 10.0s, output queue size 364
progress 25% @chr4:76000001, elapsed 14.3s, est remaining 43.0s, peak mem 8155MB, user 412.8s, sys 11.3s, output queue size 525
progress 30% @chr5:107000001, elapsed 16.0s, est remaining 37.3s, peak mem 9257MB, user 459.0s, sys 12.2s, output queue size 687
progress 35% @chr6:79000001, elapsed 18.9s, est remaining 35.1s, peak mem 11357MB, user 529.8s, sys 13.1s, output queue size 848
progress 40% @chr6:33000001, elapsed 21.5s, est remaining 32.3s, peak mem 13146MB, user 604.6s, sys 14.3s, output queue size 1009
progress 45% @chr8:83000001, elapsed 24.6s, est remaining 30.1s, peak mem 15183MB, user 699.0s, sys 16.6s, output queue size 1171
progress 50% @chr9:91000001, elapsed 26.7s, est remaining 26.7s, peak mem 15581MB, user 763.3s, sys 18.3s, output queue size 1333
progress 55% @chr10:93000001, elapsed 30.0s, est remaining 24.5s, peak mem 16655MB, user 857.3s, sys 19.7s, output queue size 1494
progress 60% @chr11:126000001, elapsed 33.8s, est remaining 22.5s, peak mem 16655MB, user 957.6s, sys 20.8s, output queue size 1656
progress 65% @chr13:26000001, elapsed 37.1s, est remaining 20.0s, peak mem 16819MB, user 1051.6s, sys 21.7s, output queue size 1818
progress 70% @chr14:82000001, elapsed 40.4s, est remaining 17.3s, peak mem 16819MB, user 1159.4s, sys 22.8s, output queue size 1979
progress 75% @chr16:41000001, elapsed 44.5s, est remaining 14.8s, peak mem 17033MB, user 1259.4s, sys 24.4s, output queue size 2141
progress 80% @chr18:1, elapsed 51.9s, est remaining 13.0s, peak mem 17616MB, user 1518.1s, sys 35.4s, output queue size 205
progress 85% @chr19:48000001, elapsed 57.9s, est remaining 10.2s, peak mem 17648MB, user 1703.7s, sys 37.2s, output queue size 367
progress 90% @chr22:18000001, elapsed 65.1s, est remaining 7.2s, peak mem 21082MB, user 1898.9s, sys 39.0s, output queue size 529
progress 95% @chrY:50000001, elapsed 68.0s, est remaining 3.6s, peak mem 22422MB, user 1969.7s, sys 39.9s, output queue size 691
progress 100% @chr19:7000001, elapsed 110.0s, est remaining 0.0s, peak mem 26756MB, user 2210.3s, sys 50.1s, 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: 49482042186
reads: 1663922378
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 5.570 user 1.045 sys 7.537 real
VcfLineRecordHelper::sort: 139 calls 9.016 user 0.380 sys 9.352 real
advance: 3219322 calls 1102.019 user 37.006 sys 1139.427 real
calc: 3219322 calls 494.055 user 6.279 sys 501.309 real
done: 1 calls 5.570 user 1.045 sys 7.537 real
execute: 1 calls 0.005 user 0.004 sys 110.027 real
fetch: 3219322 calls 520.741 user 4.042 sys 526.258 real
idle: 1477 calls 0.487 user 0.005 sys 1403.097 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 28109262848 mem 2243.136 user 52.619 sys 118.873 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0002881.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0002881.md.score --metrics Filler-D0002881.md.metrics Filler-D0002881.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 22.2s, est remaining 422.3s, peak mem 2522MB, user 560.6s, sys 9.4s, output queue size 52
progress 10% @chr2:68000001, elapsed 36.6s, est remaining 329.3s, peak mem 3538MB, user 1062.2s, sys 14.0s, output queue size 47
progress 15% @chr2:169000001, elapsed 52.1s, est remaining 295.3s, peak mem 13072MB, user 1485.6s, sys 19.0s, output queue size 203
progress 20% @chr3:174000001, elapsed 70.3s, est remaining 281.1s, peak mem 17535MB, user 1999.6s, sys 23.6s, output queue size 364
progress 25% @chr4:120000001, elapsed 82.8s, est remaining 248.4s, peak mem 20009MB, user 2425.9s, sys 27.9s, output queue size 525
progress 30% @chr5:105000001, elapsed 93.1s, est remaining 217.1s, peak mem 20475MB, user 2708.6s, sys 30.0s, output queue size 687
progress 35% @chr6:77000001, elapsed 109.7s, est remaining 203.8s, peak mem 21228MB, user 3145.7s, sys 33.5s, output queue size 848
progress 40% @chr7:79000001, elapsed 124.6s, est remaining 187.0s, peak mem 22651MB, user 3600.7s, sys 36.8s, output queue size 1009
progress 45% @chr8:71000001, elapsed 143.1s, est remaining 174.9s, peak mem 22780MB, user 4144.1s, sys 40.4s, output queue size 1171
progress 50% @chr9:76000001, elapsed 155.7s, est remaining 155.7s, peak mem 22780MB, user 4502.8s, sys 43.2s, output queue size 1333
progress 55% @chr10:70000001, elapsed 176.1s, est remaining 144.1s, peak mem 22832MB, user 5083.0s, sys 46.5s, output queue size 1494
progress 60% @chr12:5000001, elapsed 199.5s, est remaining 133.0s, peak mem 23200MB, user 5722.3s, sys 50.1s, output queue size 1656
progress 65% @chr12:120000001, elapsed 218.3s, est remaining 117.5s, peak mem 24667MB, user 6276.4s, sys 53.6s, output queue size 1818
progress 70% @chr13:110000001, elapsed 238.7s, est remaining 102.3s, peak mem 24667MB, user 6929.5s, sys 57.7s, output queue size 1979
progress 75% @chr16:42000001, elapsed 262.7s, est remaining 87.6s, peak mem 24667MB, user 7540.8s, sys 60.8s, output queue size 2141
progress 80% @chr18:3000001, elapsed 307.8s, est remaining 77.0s, peak mem 24667MB, user 9141.7s, sys 80.2s, output queue size 205
progress 85% @chr19:48000001, elapsed 343.8s, est remaining 60.7s, peak mem 24667MB, user 10219.1s, sys 85.9s, output queue size 367
progress 90% @chrX:19000001, elapsed 383.5s, est remaining 42.6s, peak mem 29400MB, user 11334.7s, sys 93.1s, output queue size 529
progress 95% @chrY:54000001, elapsed 399.7s, est remaining 21.0s, peak mem 29655MB, user 11732.1s, sys 95.2s, output queue size 691
progress 100% @chr19:7000001, elapsed 567.3s, est remaining 0.0s, peak mem 32833MB, user 12879.1s, sys 105.7s, output queue size 3822
library Filler-D0002881:
chimeric_paired 41491523
duped 1338212906
duped_chimeric_paired 18255682
duped_paired 1338186700
duped_unpaired 26206
optical_dup 128066157
paired 1651746406
reads 1663872254
secondary_supplementary 12069772
unmapped 78162
unpaired 28038
optical dup clusters 49509710, maxdup 339, total optical dup pairs 128066157
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: 49482042186
reads: 1663922378
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2768422 calls 54.002 user 1.285 sys 56.872 real
MateInfoByVcf::load: 2768422 calls 1788.699 user 15.681 sys 1583.469 real
MateInfoByVcf::parse_events: 2768422 calls 1563.061 user 12.286 sys 1436.356 real
advance: 3219322 calls 1026.379 user 28.005 sys 1203.005 real
calc: 3219322 calls 9001.265 user 52.817 sys 9170.020 real
done: 1 calls 0.055 user 0.000 sys 0.064 real
exec_no_coor: 1 calls 0.325 user 0.067 sys 0.401 real
execute: 1 calls 0.004 user 0.004 sys 569.159 real
fetch: 3219323 calls 793.919 user 3.130 sys 789.481 real
find_pairEnds: 2768422 calls 841.931 user 2.606 sys 915.366 real
idle: 476620 calls 169.439 user 4.350 sys 4423.328 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 2768422 calls 3412.368 user 16.728 sys 3690.950 real
vcfadvance: 2768422 calls 13.094 user 2.694 sys 14.969 real
write: 3219323 calls 5500.099 user 34.928 sys 5371.304 real
overall: 34428080128 mem 13082.231 user 128.417 sys 571.050 real