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/0c/d7a21d61f5b35445e2a51d123884d5/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/7e9a8a006beae9b40e521eef1ddc92/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/7e9a8a006beae9b40e521eef1ddc92/.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/0c/d7a21d61f5b35445e2a51d123884d5/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:159000001, elapsed 2.8s, est remaining 54.0s, peak mem 3069MB, user 50.1s, sys 2.0s, output queue size 42
progress 10% @chr2:38000001, elapsed 6.6s, est remaining 59.1s, peak mem 5837MB, user 155.0s, sys 3.8s, output queue size 173
progress 15% @chr2:238000001, elapsed 9.2s, est remaining 52.1s, peak mem 7002MB, user 253.4s, sys 8.6s, output queue size 328
progress 20% @chr3:157000001, elapsed 11.1s, est remaining 44.4s, peak mem 7065MB, user 308.2s, sys 9.4s, output queue size 489
progress 25% @chr4:113000001, elapsed 12.8s, est remaining 38.3s, peak mem 7418MB, user 360.4s, sys 10.8s, output queue size 650
progress 30% @chr5:94000001, elapsed 14.0s, est remaining 32.6s, peak mem 7418MB, user 394.9s, sys 11.4s, output queue size 812
progress 35% @chr6:81000001, elapsed 16.4s, est remaining 30.5s, peak mem 7884MB, user 468.6s, sys 12.9s, output queue size 625
progress 40% @chr6:30000001, elapsed 18.9s, est remaining 28.4s, peak mem 8271MB, user 541.3s, sys 14.4s, output queue size 197
progress 45% @chr8:70000001, elapsed 21.6s, est remaining 26.4s, peak mem 8839MB, user 609.9s, sys 15.8s, output queue size 359
progress 50% @chr9:88000001, elapsed 24.3s, est remaining 24.3s, peak mem 8907MB, user 700.9s, sys 18.1s, output queue size 366
progress 55% @chr10:109000001, elapsed 27.4s, est remaining 22.4s, peak mem 10089MB, user 795.8s, sys 19.2s, output queue size 253
progress 60% @chr11:125000001, elapsed 29.5s, est remaining 19.7s, peak mem 10089MB, user 867.3s, sys 20.7s, output queue size 312
progress 65% @chr11:77000001, elapsed 32.1s, est remaining 17.3s, peak mem 10143MB, user 938.8s, sys 21.5s, output queue size 474
progress 70% @chr14:84000001, elapsed 34.0s, est remaining 14.6s, peak mem 10273MB, user 998.4s, sys 22.2s, output queue size 635
progress 75% @chr16:40000001, elapsed 36.8s, est remaining 12.3s, peak mem 10332MB, user 1085.8s, sys 23.0s, output queue size 797
progress 80% @chr18:13000001, elapsed 40.4s, est remaining 10.1s, peak mem 10473MB, user 1191.2s, sys 23.9s, output queue size 190
progress 85% @chr20:3000001, elapsed 44.1s, est remaining 7.8s, peak mem 10564MB, user 1307.7s, sys 25.0s, output queue size 351
progress 90% @chrX:34000001, elapsed 46.5s, est remaining 5.2s, peak mem 10564MB, user 1385.7s, sys 25.7s, output queue size 513
progress 95% @chrY:49000001, elapsed 48.3s, est remaining 2.5s, peak mem 10564MB, user 1433.6s, sys 26.3s, output queue size 675
progress 100% @chr22:23000001, elapsed 54.5s, est remaining 0.0s, peak mem 10582MB, user 1503.2s, sys 26.9s, 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: 48256144560
reads: 991312774
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.664 user 0.200 sys 0.886 real
VcfLineRecordHelper::sort: 32 calls 1.051 user 0.109 sys 1.144 real
advance: 3219322 calls 828.346 user 21.034 sys 851.358 real
calc: 3219322 calls 290.654 user 1.783 sys 293.727 real
done: 1 calls 0.664 user 0.200 sys 0.886 real
execute: 1 calls 0.001 user 0.004 sys 54.514 real
fetch: 3219322 calls 331.684 user 2.110 sys 331.599 real
idle: 245 calls 0.162 user 0.002 sys 211.496 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 11097047040 mem 1508.194 user 27.621 sys 56.546 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 17.9s, est remaining 340.9s, peak mem 4037MB, user 335.8s, sys 4.1s, output queue size 42
progress 10% @chr2:79000001, elapsed 39.2s, est remaining 352.4s, peak mem 7130MB, user 1054.0s, sys 10.0s, output queue size 172
progress 15% @chr3:3000001, elapsed 54.3s, est remaining 307.8s, peak mem 7904MB, user 1545.1s, sys 13.8s, output queue size 328
progress 20% @chr3:157000001, elapsed 67.2s, est remaining 268.7s, peak mem 7905MB, user 2000.8s, sys 16.8s, output queue size 141
progress 25% @chr4:118000001, elapsed 77.8s, est remaining 233.4s, peak mem 7905MB, user 2329.2s, sys 18.6s, output queue size 302
progress 30% @chr5:75000001, elapsed 85.8s, est remaining 200.2s, peak mem 7905MB, user 2567.9s, sys 20.3s, output queue size 464
progress 35% @chr6:77000001, elapsed 102.2s, est remaining 189.8s, peak mem 8760MB, user 3026.0s, sys 23.0s, output queue size 70
progress 40% @chr7:6000001, elapsed 118.0s, est remaining 177.1s, peak mem 9842MB, user 3475.0s, sys 25.4s, output queue size 197
progress 45% @chr8:77000001, elapsed 135.6s, est remaining 165.7s, peak mem 9896MB, user 3940.9s, sys 28.4s, output queue size 357
progress 50% @chr9:21000001, elapsed 152.8s, est remaining 152.8s, peak mem 10664MB, user 4563.8s, sys 31.5s, output queue size 187
progress 55% @chr10:73000001, elapsed 171.6s, est remaining 140.4s, peak mem 11401MB, user 5152.3s, sys 34.8s, output queue size 150
progress 60% @chr12:5000001, elapsed 185.8s, est remaining 123.9s, peak mem 11668MB, user 5542.7s, sys 37.0s, output queue size 312
progress 65% @chr13:30000001, elapsed 202.4s, est remaining 109.0s, peak mem 11668MB, user 6029.4s, sys 39.4s, output queue size 474
progress 70% @chr14:82000001, elapsed 215.4s, est remaining 92.3s, peak mem 11668MB, user 6490.4s, sys 41.5s, output queue size 299
progress 75% @chr16:42000001, elapsed 231.9s, est remaining 77.3s, peak mem 11722MB, user 6994.6s, sys 43.9s, output queue size 118
progress 80% @chr18:9000001, elapsed 254.3s, est remaining 63.6s, peak mem 11722MB, user 7639.9s, sys 46.6s, output queue size 190
progress 85% @chr19:47000001, elapsed 276.9s, est remaining 48.9s, peak mem 11879MB, user 8343.6s, sys 49.6s, output queue size 351
progress 90% @chrX:39000001, elapsed 293.2s, est remaining 32.6s, peak mem 11879MB, user 8833.4s, sys 51.8s, output queue size 513
progress 95% @chrY:52000001, elapsed 305.8s, est remaining 16.1s, peak mem 11918MB, user 9207.2s, sys 53.5s, output queue size 675
progress 100% @chr22:23000001, elapsed 327.7s, est remaining 0.0s, peak mem 11929MB, user 9529.1s, sys 55.1s, output queue size 3635
library 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 15036011
duped 541168062
duped_chimeric_paired 2874078
duped_paired 541163913
duped_unpaired 4149
optical_dup 49003336
paired 980322898
reads 991305988
secondary_supplementary 10973652
unmapped 11505
unpaired 4719
optical dup clusters 29931291, maxdup 57, total optical dup pairs 49003336
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: 48256144560
reads: 991312774
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2629546 calls 5.011 user 0.258 sys 5.502 real
MateInfoByVcf::load: 2629546 calls 1791.860 user 10.357 sys 1709.410 real
MateInfoByVcf::parse_events: 2629546 calls 1724.555 user 8.861 sys 1670.634 real
advance: 3219322 calls 765.938 user 15.477 sys 865.079 real
calc: 3219322 calls 6453.245 user 25.578 sys 6531.252 real
done: 1 calls 0.066 user 0.000 sys 0.069 real
exec_no_coor: 1 calls 0.016 user 0.011 sys 0.034 real
execute: 1 calls 0.001 user 0.001 sys 328.352 real
fetch: 3219323 calls 384.667 user 1.057 sys 372.874 real
find_pairEnds: 2629546 calls 423.326 user 0.652 sys 437.530 real
idle: 32110 calls 8.252 user 0.258 sys 576.490 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 2629546 calls 1667.360 user 5.514 sys 1751.352 real
vcfadvance: 2629546 calls 3.105 user 0.411 sys 3.375 real
write: 3219323 calls 4750.004 user 19.133 sys 4739.107 real
overall: 12508782592 mem 9541.873 user 70.059 sys 329.742 real