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/63/456515477734624a14499cd2dd6116/1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/e9c80fed45cad6c15f82ff1df9ecf8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/e9c80fed45cad6c15f82ff1df9ecf8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/456515477734624a14499cd2dd6116/1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.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 1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 2.3s, est remaining 43.0s, peak mem 2778MB, user 49.6s, sys 3.5s, output queue size 146
progress 10% @chr2:84000001, elapsed 4.1s, est remaining 37.0s, peak mem 3747MB, user 103.0s, sys 5.3s, output queue size 166
progress 15% @chr3:3000001, elapsed 6.0s, est remaining 33.9s, peak mem 4755MB, user 162.5s, sys 9.3s, output queue size 203
progress 20% @chr3:149000001, elapsed 7.7s, est remaining 30.6s, peak mem 4858MB, user 209.5s, sys 10.6s, output queue size 283
progress 25% @chr4:135000001, elapsed 9.1s, est remaining 27.2s, peak mem 4858MB, user 257.4s, sys 11.4s, output queue size 302
progress 30% @chr5:75000001, elapsed 10.2s, est remaining 23.9s, peak mem 4858MB, user 291.1s, sys 11.8s, output queue size 464
progress 35% @chr6:79000001, elapsed 11.9s, est remaining 22.2s, peak mem 5041MB, user 336.8s, sys 12.8s, output queue size 625
progress 40% @chr7:64000001, elapsed 13.8s, est remaining 20.7s, peak mem 5393MB, user 386.6s, sys 13.9s, output queue size 786
progress 45% @chr8:78000001, elapsed 15.7s, est remaining 19.2s, peak mem 5478MB, user 453.4s, sys 14.7s, output queue size 204
progress 50% @chr9:88000001, elapsed 17.3s, est remaining 17.3s, peak mem 5921MB, user 497.6s, sys 15.5s, output queue size 366
progress 55% @chr10:103000001, elapsed 19.4s, est remaining 15.9s, peak mem 6241MB, user 556.0s, sys 16.2s, output queue size 485
progress 60% @chr11:117000001, elapsed 21.4s, est remaining 14.3s, peak mem 6241MB, user 619.4s, sys 16.9s, output queue size 510
progress 65% @chr13:23000001, elapsed 23.4s, est remaining 12.6s, peak mem 6316MB, user 681.9s, sys 17.6s, output queue size 474
progress 70% @chr14:72000001, elapsed 24.6s, est remaining 10.5s, peak mem 6379MB, user 720.8s, sys 18.1s, output queue size 635
progress 75% @chr16:42000001, elapsed 26.8s, est remaining 8.9s, peak mem 6475MB, user 787.9s, sys 18.9s, output queue size 461
progress 80% @chr17:74000001, elapsed 29.9s, est remaining 7.5s, peak mem 6684MB, user 871.7s, sys 19.7s, output queue size 623
progress 85% @chr20:9000001, elapsed 32.8s, est remaining 5.8s, peak mem 6743MB, user 959.9s, sys 20.5s, output queue size 785
progress 90% @chr22:42000001, elapsed 34.6s, est remaining 3.8s, peak mem 6794MB, user 1017.2s, sys 21.1s, output queue size 947
progress 95% @chrY:52000001, elapsed 35.8s, est remaining 1.9s, peak mem 6961MB, user 1060.7s, sys 21.6s, output queue size 675
progress 100% @chr15:88000001, elapsed 41.2s, est remaining 0.0s, peak mem 6997MB, user 1113.7s, sys 22.1s, output queue size 4099
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: 39230677996
reads: 753549713
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.663 user 0.148 sys 0.842 real
VcfLineRecordHelper::sort: 33 calls 1.141 user 0.030 sys 1.201 real
advance: 3219322 calls 652.720 user 17.173 sys 670.355 real
calc: 3219322 calls 202.220 user 1.570 sys 204.689 real
done: 1 calls 0.663 user 0.148 sys 0.842 real
execute: 1 calls 0.002 user 0.000 sys 41.204 real
fetch: 3219322 calls 221.686 user 1.953 sys 223.886 real
idle: 221 calls 0.143 user 0.002 sys 192.658 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 7337082880 mem 1118.839 user 22.631 sys 43.175 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 15.6s, est remaining 296.9s, peak mem 3409MB, user 399.7s, sys 5.4s, output queue size 42
progress 10% @chr2:79000001, elapsed 27.1s, est remaining 244.0s, peak mem 4990MB, user 777.6s, sys 8.2s, output queue size 48
progress 15% @chr3:5000001, elapsed 40.2s, est remaining 227.9s, peak mem 5391MB, user 1169.6s, sys 11.1s, output queue size 122
progress 20% @chr3:155000001, elapsed 52.5s, est remaining 209.8s, peak mem 5428MB, user 1539.2s, sys 13.6s, output queue size 141
progress 25% @chr4:109000001, elapsed 63.2s, est remaining 189.5s, peak mem 5621MB, user 1863.4s, sys 15.9s, output queue size 302
progress 30% @chr5:88000001, elapsed 71.4s, est remaining 166.6s, peak mem 5652MB, user 2137.3s, sys 17.8s, output queue size 464
progress 35% @chr6:72000001, elapsed 83.8s, est remaining 155.7s, peak mem 5865MB, user 2496.9s, sys 19.6s, output queue size 70
progress 40% @chr7:47000001, elapsed 96.5s, est remaining 144.8s, peak mem 6138MB, user 2878.5s, sys 21.6s, output queue size 194
progress 45% @chr8:77000001, elapsed 110.7s, est remaining 135.3s, peak mem 6284MB, user 3290.4s, sys 23.7s, output queue size 204
progress 50% @chr9:91000001, elapsed 122.7s, est remaining 122.7s, peak mem 6541MB, user 3596.5s, sys 25.2s, output queue size 366
progress 55% @chr10:73000001, elapsed 136.9s, est remaining 112.0s, peak mem 6777MB, user 4063.3s, sys 27.1s, output queue size 348
progress 60% @chr11:121000001, elapsed 151.5s, est remaining 101.0s, peak mem 6785MB, user 4504.0s, sys 29.5s, output queue size 510
progress 65% @chr12:106000001, elapsed 164.6s, est remaining 88.6s, peak mem 6808MB, user 4970.0s, sys 31.7s, output queue size 138
progress 70% @chr13:101000001, elapsed 173.3s, est remaining 74.3s, peak mem 6808MB, user 5245.0s, sys 33.0s, output queue size 299
progress 75% @chr16:42000001, elapsed 188.5s, est remaining 62.8s, peak mem 6907MB, user 5653.8s, sys 35.1s, output queue size 461
progress 80% @chr18:20000001, elapsed 211.0s, est remaining 52.8s, peak mem 7039MB, user 6243.3s, sys 37.9s, output queue size 623
progress 85% @chr19:15000001, elapsed 229.6s, est remaining 40.5s, peak mem 7049MB, user 6945.7s, sys 40.8s, output queue size 351
progress 90% @chrX:34000001, elapsed 242.6s, est remaining 27.0s, peak mem 7377MB, user 7313.2s, sys 42.3s, output queue size 513
progress 95% @chrY:55000001, elapsed 250.8s, est remaining 13.2s, peak mem 7377MB, user 7554.0s, sys 43.6s, output queue size 675
progress 100% @chr22:23000001, elapsed 271.3s, est remaining 0.0s, peak mem 7385MB, user 7860.4s, sys 45.0s, output queue size 3635
library 1136_3WJ-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 14063077
duped 408602885
duped_chimeric_paired 3018598
duped_paired 408599875
duped_unpaired 3010
optical_dup 49013337
paired 746403978
reads 753546503
secondary_supplementary 7135483
unmapped 6731
unpaired 3521
optical dup clusters 27750764, maxdup 49, total optical dup pairs 49013337
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: 39230677996
reads: 753549713
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2551356 calls 4.567 user 0.243 sys 5.294 real
MateInfoByVcf::load: 2551356 calls 1756.533 user 9.542 sys 1683.047 real
MateInfoByVcf::parse_events: 2551356 calls 1693.659 user 8.104 sys 1648.159 real
advance: 3219322 calls 612.229 user 12.516 sys 687.236 real
calc: 3219322 calls 5109.696 user 19.426 sys 5187.667 real
done: 1 calls 0.058 user 0.000 sys 0.066 real
exec_no_coor: 1 calls 0.000 user 0.010 sys 0.011 real
execute: 1 calls 0.004 user 0.003 sys 271.756 real
fetch: 3219323 calls 273.477 user 1.023 sys 260.006 real
find_pairEnds: 2551356 calls 310.539 user 0.601 sys 319.824 real
idle: 24933 calls 6.984 user 0.235 sys 512.027 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 2551356 calls 1224.030 user 4.388 sys 1289.438 real
vcfadvance: 2551356 calls 3.142 user 0.401 sys 3.176 real
write: 3219323 calls 3860.154 user 13.946 sys 3868.155 real
overall: 7743975424 mem 7872.319 user 57.404 sys 273.033 real