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/2f/cf83499119bb2adccb8ea691b82d3f/1029_IWL-T1-TDNA-1_A23MHWWLT4_1.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/ae422e06771eeefe1dfbe4dc1a440f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/ae422e06771eeefe1dfbe4dc1a440f/.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/2f/cf83499119bb2adccb8ea691b82d3f/1029_IWL-T1-TDNA-1_A23MHWWLT4_1.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:154000001, elapsed 1.9s, est remaining 36.3s, peak mem 1972MB, user 44.2s, sys 1.8s, output queue size 146
progress 10% @chr2:90000001, elapsed 3.4s, est remaining 31.0s, peak mem 2516MB, user 92.7s, sys 3.7s, output queue size 117
progress 15% @chr3:8000001, elapsed 5.1s, est remaining 29.0s, peak mem 3160MB, user 142.8s, sys 5.1s, output queue size 122
progress 20% @chr3:149000001, elapsed 6.6s, est remaining 26.5s, peak mem 3267MB, user 188.6s, sys 5.7s, output queue size 141
progress 25% @chr4:109000001, elapsed 7.9s, est remaining 23.8s, peak mem 3382MB, user 228.8s, sys 6.3s, output queue size 302
progress 30% @chr5:104000001, elapsed 9.0s, est remaining 21.1s, peak mem 3447MB, user 261.1s, sys 6.7s, output queue size 464
progress 35% @chr5:150000001, elapsed 10.5s, est remaining 19.5s, peak mem 3600MB, user 301.7s, sys 7.1s, output queue size 625
progress 40% @chr7:56000001, elapsed 12.0s, est remaining 18.1s, peak mem 3868MB, user 345.8s, sys 7.7s, output queue size 786
progress 45% @chr8:70000001, elapsed 13.9s, est remaining 17.0s, peak mem 4093MB, user 404.9s, sys 8.4s, output queue size 204
progress 50% @chr9:89000001, elapsed 15.3s, est remaining 15.3s, peak mem 4290MB, user 442.3s, sys 8.8s, output queue size 366
progress 55% @chr10:104000001, elapsed 17.1s, est remaining 14.0s, peak mem 4290MB, user 496.8s, sys 9.5s, output queue size 527
progress 60% @chr11:134000001, elapsed 18.9s, est remaining 12.6s, peak mem 4290MB, user 554.8s, sys 10.0s, output queue size 510
progress 65% @chr12:106000001, elapsed 20.6s, est remaining 11.1s, peak mem 4290MB, user 608.0s, sys 10.5s, output queue size 672
progress 70% @chr14:72000001, elapsed 21.7s, est remaining 9.3s, peak mem 4290MB, user 639.2s, sys 10.8s, output queue size 833
progress 75% @chr16:41000001, elapsed 23.6s, est remaining 7.9s, peak mem 4290MB, user 691.4s, sys 11.3s, output queue size 995
progress 80% @chr18:9000001, elapsed 26.4s, est remaining 6.6s, peak mem 4392MB, user 774.0s, sys 12.2s, output queue size 623
progress 85% @chr20:9000001, elapsed 28.9s, est remaining 5.1s, peak mem 4392MB, user 854.8s, sys 13.2s, output queue size 785
progress 90% @chrX:34000001, elapsed 30.4s, est remaining 3.4s, peak mem 4416MB, user 915.8s, sys 13.8s, output queue size 78
progress 95% @chrY:52000001, elapsed 31.3s, est remaining 1.6s, peak mem 4486MB, user 945.3s, sys 14.3s, output queue size 240
progress 100% @chr22:23000001, elapsed 34.6s, est remaining 0.0s, peak mem 4486MB, user 971.7s, sys 14.7s, output queue size 3635
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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 33750600681
reads: 702845646
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.199 user 0.079 sys 0.306 real
VcfLineRecordHelper::sort: 32 calls 0.320 user 0.032 sys 0.351 real
advance: 3219322 calls 577.419 user 11.079 sys 589.350 real
calc: 3219322 calls 177.055 user 1.066 sys 178.071 real
done: 1 calls 0.199 user 0.079 sys 0.306 real
execute: 1 calls 0.006 user 0.004 sys 34.570 real
fetch: 3219322 calls 186.039 user 1.174 sys 187.603 real
idle: 162 calls 0.122 user 0.009 sys 123.717 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 4704727040 mem 973.735 user 14.976 sys 36.037 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:154000001, elapsed 12.8s, est remaining 242.4s, peak mem 2832MB, user 331.8s, sys 3.7s, output queue size 42
progress 10% @chr2:71000001, elapsed 22.2s, est remaining 200.2s, peak mem 3721MB, user 635.3s, sys 6.6s, output queue size 48
progress 15% @chr2:238000001, elapsed 33.4s, est remaining 189.2s, peak mem 4284MB, user 964.1s, sys 9.6s, output queue size 122
progress 20% @chr3:149000001, elapsed 43.7s, est remaining 174.7s, peak mem 4524MB, user 1273.5s, sys 12.0s, output queue size 141
progress 25% @chr4:109000001, elapsed 52.9s, est remaining 158.7s, peak mem 4679MB, user 1554.8s, sys 13.8s, output queue size 302
progress 30% @chr5:69000001, elapsed 60.2s, est remaining 140.6s, peak mem 4700MB, user 1798.3s, sys 15.6s, output queue size 464
progress 35% @chr6:72000001, elapsed 70.9s, est remaining 131.6s, peak mem 4731MB, user 2071.6s, sys 17.6s, output queue size 625
progress 40% @chr6:163000001, elapsed 81.6s, est remaining 122.4s, peak mem 4836MB, user 2429.6s, sys 19.9s, output queue size 194
progress 45% @chr8:77000001, elapsed 93.7s, est remaining 114.5s, peak mem 4951MB, user 2781.8s, sys 22.1s, output queue size 204
progress 50% @chr9:91000001, elapsed 103.6s, est remaining 103.6s, peak mem 5150MB, user 3065.1s, sys 23.9s, output queue size 366
progress 55% @chr10:109000001, elapsed 115.0s, est remaining 94.1s, peak mem 5164MB, user 3441.4s, sys 25.8s, output queue size 348
progress 60% @chr11:130000001, elapsed 127.2s, est remaining 84.8s, peak mem 5164MB, user 3803.7s, sys 27.7s, output queue size 510
progress 65% @chr13:33000001, elapsed 138.6s, est remaining 74.6s, peak mem 5176MB, user 4175.7s, sys 29.8s, output queue size 138
progress 70% @chr14:84000001, elapsed 146.0s, est remaining 62.6s, peak mem 5181MB, user 4421.9s, sys 31.3s, output queue size 299
progress 75% @chr16:42000001, elapsed 158.3s, est remaining 52.8s, peak mem 5188MB, user 4737.3s, sys 32.9s, output queue size 461
progress 80% @chr18:19000001, elapsed 175.9s, est remaining 44.0s, peak mem 5341MB, user 5279.5s, sys 35.5s, output queue size 189
progress 85% @chr20:18000001, elapsed 190.9s, est remaining 33.7s, peak mem 5348MB, user 5767.6s, sys 37.6s, output queue size 351
progress 90% @chrX:24000001, elapsed 201.1s, est remaining 22.3s, peak mem 5480MB, user 6113.8s, sys 39.5s, output queue size 78
progress 95% @chrY:54000001, elapsed 207.6s, est remaining 10.9s, peak mem 5506MB, user 6321.8s, sys 40.9s, output queue size 240
progress 100% @chr22:23000001, elapsed 220.5s, est remaining 0.0s, peak mem 5506MB, user 6468.4s, sys 42.0s, output queue size 3635
library 1029_IWL-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 7679652
duped 400355486
duped_chimeric_paired 852334
duped_paired 400352398
duped_unpaired 3088
optical_dup 17980589
paired 697627504
reads 702838860
secondary_supplementary 5204346
unmapped 10291
unpaired 3505
optical dup clusters 12527304, maxdup 52, total optical dup pairs 17980589
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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 33750600681
reads: 702845646
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2478038 calls 1.773 user 0.231 sys 2.565 real
MateInfoByVcf::load: 2478038 calls 1524.555 user 9.245 sys 1422.550 real
MateInfoByVcf::parse_events: 2478038 calls 1487.285 user 8.211 sys 1396.073 real
advance: 3219322 calls 519.785 user 10.859 sys 611.743 real
calc: 3219322 calls 4116.411 user 18.723 sys 4178.854 real
done: 1 calls 0.060 user 0.000 sys 0.063 real
exec_no_coor: 1 calls 0.016 user 0.014 sys 0.039 real
execute: 1 calls 0.004 user 0.003 sys 220.965 real
fetch: 3219323 calls 219.870 user 0.873 sys 223.062 real
find_pairEnds: 2478038 calls 250.650 user 0.542 sys 267.090 real
idle: 9961 calls 2.187 user 0.095 sys 342.101 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 2478038 calls 1045.014 user 3.884 sys 1129.960 real
vcfadvance: 2478038 calls 1.359 user 0.384 sys 1.792 real
write: 3219323 calls 3048.023 user 13.790 sys 3020.422 real
overall: 5774462976 mem 6474.637 user 52.627 sys 222.179 real