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/fc/e47698c2e2e8fa69eb59eefe06dd34/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/b2103a28e0704b2806bc92b3739726/1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/e47698c2e2e8fa69eb59eefe06dd34/.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/80/b2103a28e0704b2806bc92b3739726/1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 1.3s, est remaining 24.1s, peak mem 1621MB, user 25.9s, sys 3.0s, output queue size 146
progress 10% @chr2:70000001, elapsed 2.2s, est remaining 19.5s, peak mem 2013MB, user 55.4s, sys 4.5s, output queue size 118
progress 15% @chr3:18000001, elapsed 3.1s, est remaining 17.7s, peak mem 2568MB, user 83.2s, sys 5.3s, output queue size 203
progress 20% @chr3:158000001, elapsed 4.0s, est remaining 15.9s, peak mem 2880MB, user 106.1s, sys 5.8s, output queue size 364
progress 25% @chr4:129000001, elapsed 4.8s, est remaining 14.3s, peak mem 3025MB, user 133.3s, sys 7.2s, output queue size 302
progress 30% @chr5:107000001, elapsed 5.3s, est remaining 12.4s, peak mem 3125MB, user 150.2s, sys 7.7s, output queue size 464
progress 35% @chr6:91000001, elapsed 6.1s, est remaining 11.4s, peak mem 3203MB, user 171.1s, sys 8.3s, output queue size 625
progress 40% @chr7:48000001, elapsed 7.1s, est remaining 10.6s, peak mem 3536MB, user 193.8s, sys 9.0s, output queue size 786
progress 45% @chr6:127000001, elapsed 8.2s, est remaining 10.0s, peak mem 3545MB, user 229.8s, sys 10.0s, output queue size 948
progress 50% @chr9:42000001, elapsed 9.1s, est remaining 9.1s, peak mem 3655MB, user 256.1s, sys 10.5s, output queue size 366
progress 55% @chr9:132000001, elapsed 10.1s, est remaining 8.3s, peak mem 3672MB, user 287.7s, sys 11.0s, output queue size 527
progress 60% @chr12:2000001, elapsed 11.2s, est remaining 7.5s, peak mem 3677MB, user 314.7s, sys 11.4s, output queue size 689
progress 65% @chr13:24000001, elapsed 12.3s, est remaining 6.6s, peak mem 3749MB, user 348.9s, sys 11.9s, output queue size 672
progress 70% @chr14:79000001, elapsed 12.9s, est remaining 5.5s, peak mem 3785MB, user 368.8s, sys 12.3s, output queue size 833
progress 75% @chr16:39000001, elapsed 14.1s, est remaining 4.7s, peak mem 3857MB, user 404.3s, sys 12.9s, output queue size 995
progress 80% @chr18:25000001, elapsed 15.8s, est remaining 4.0s, peak mem 3961MB, user 444.9s, sys 13.4s, output queue size 1157
progress 85% @chr19:42000001, elapsed 17.4s, est remaining 3.1s, peak mem 4020MB, user 493.3s, sys 14.0s, output queue size 1319
progress 90% @chrX:30000001, elapsed 18.4s, est remaining 2.0s, peak mem 4020MB, user 534.9s, sys 15.0s, output queue size 947
progress 95% @chrY:50000001, elapsed 19.2s, est remaining 1.0s, peak mem 4122MB, user 560.0s, sys 15.3s, output queue size 675
progress 100% @chr15:88000001, elapsed 21.9s, est remaining 0.0s, peak mem 4156MB, user 596.1s, sys 15.9s, output queue size 4099
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 17508428407
reads: 361302612
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.550 user 0.158 sys 0.861 real
VcfLineRecordHelper::sort: 33 calls 0.751 user 0.159 sys 0.896 real
advance: 3219322 calls 375.899 user 11.232 sys 390.055 real
calc: 3219322 calls 103.367 user 1.376 sys 103.352 real
done: 1 calls 0.550 user 0.158 sys 0.861 real
execute: 1 calls 0.003 user 0.003 sys 21.979 real
fetch: 3219322 calls 99.019 user 1.245 sys 100.632 real
idle: 165 calls 0.119 user 0.002 sys 124.579 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 4358782976 mem 600.422 user 16.657 sys 24.016 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.md.score --metrics 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.md.metrics 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:174000001, elapsed 8.2s, est remaining 155.3s, peak mem 2140MB, user 210.5s, sys 3.0s, output queue size 42
progress 10% @chr2:79000001, elapsed 14.2s, est remaining 127.7s, peak mem 2948MB, user 403.9s, sys 4.7s, output queue size 48
progress 15% @chr2:237000001, elapsed 22.0s, est remaining 124.5s, peak mem 3512MB, user 618.5s, sys 6.6s, output queue size 203
progress 20% @chr3:173000001, elapsed 28.3s, est remaining 113.3s, peak mem 3585MB, user 828.5s, sys 8.5s, output queue size 141
progress 25% @chr4:103000001, elapsed 33.8s, est remaining 101.5s, peak mem 3657MB, user 1002.7s, sys 9.6s, output queue size 302
progress 30% @chr5:101000001, elapsed 38.2s, est remaining 89.1s, peak mem 3726MB, user 1136.9s, sys 10.6s, output queue size 464
progress 35% @chr6:41000001, elapsed 44.2s, est remaining 82.2s, peak mem 3844MB, user 1300.8s, sys 11.8s, output queue size 625
progress 40% @chr7:6000001, elapsed 51.6s, est remaining 77.3s, peak mem 3994MB, user 1527.5s, sys 13.3s, output queue size 195
progress 45% @chr8:72000001, elapsed 59.3s, est remaining 72.5s, peak mem 3994MB, user 1763.9s, sys 14.8s, output queue size 204
progress 50% @chr9:86000001, elapsed 65.8s, est remaining 65.8s, peak mem 3995MB, user 1945.9s, sys 16.1s, output queue size 366
progress 55% @chr10:99000001, elapsed 73.5s, est remaining 60.1s, peak mem 4035MB, user 2178.4s, sys 17.6s, output queue size 348
progress 60% @chr12:5000001, elapsed 81.2s, est remaining 54.1s, peak mem 4035MB, user 2411.2s, sys 18.8s, output queue size 510
progress 65% @chr13:19000001, elapsed 88.8s, est remaining 47.8s, peak mem 4037MB, user 2646.6s, sys 21.6s, output queue size 672
progress 70% @chr14:82000001, elapsed 93.7s, est remaining 40.2s, peak mem 4063MB, user 2800.8s, sys 23.4s, output queue size 833
progress 75% @chr16:38000001, elapsed 102.3s, est remaining 34.1s, peak mem 4116MB, user 3048.3s, sys 26.0s, output queue size 461
progress 80% @chr18:11000001, elapsed 114.7s, est remaining 28.7s, peak mem 4116MB, user 3416.2s, sys 29.8s, output queue size 190
progress 85% @chr19:42000001, elapsed 125.1s, est remaining 22.1s, peak mem 4116MB, user 3774.8s, sys 32.5s, output queue size 351
progress 90% @chrX:35000001, elapsed 132.6s, est remaining 14.7s, peak mem 4195MB, user 3986.2s, sys 34.0s, output queue size 513
progress 95% @chrY:50000001, elapsed 138.5s, est remaining 7.3s, peak mem 4257MB, user 4151.1s, sys 35.5s, output queue size 675
progress 100% @chrX:67000001, elapsed 145.4s, est remaining 0.0s, peak mem 4273MB, user 4315.1s, sys 37.7s, output queue size 3540
library 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1:
chimeric_paired 2861583
duped 135335808
duped_chimeric_paired 379562
duped_paired 135334613
duped_unpaired 1195
optical_dup 41098802
paired 360084560
reads 361301818
secondary_supplementary 1214142
unmapped 2352
unpaired 1558
optical dup clusters 24661384, maxdup 25, total optical dup pairs 41098802
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 17508428407
reads: 361302612
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2212289 calls 3.431 user 0.255 sys 3.779 real
MateInfoByVcf::load: 2212289 calls 1358.253 user 9.761 sys 1292.499 real
MateInfoByVcf::parse_events: 2212289 calls 1318.533 user 8.685 sys 1269.758 real
advance: 3219322 calls 356.293 user 8.884 sys 406.003 real
calc: 3219322 calls 2409.752 user 15.057 sys 2473.573 real
done: 1 calls 0.051 user 0.000 sys 0.056 real
exec_no_coor: 1 calls 0.000 user 0.009 sys 0.005 real
execute: 1 calls 0.005 user 0.003 sys 145.572 real
fetch: 3219323 calls 126.420 user 1.035 sys 121.440 real
find_pairEnds: 2212289 calls 149.125 user 0.897 sys 159.191 real
idle: 14960 calls 14.988 user 0.084 sys 153.720 real
init: 1 calls 0.009 user 0.001 sys 0.008 real
markDup: 2212289 calls 613.150 user 4.322 sys 659.046 real
vcfadvance: 2212289 calls 2.186 user 0.507 sys 2.673 real
write: 3219323 calls 1786.943 user 9.763 sys 1802.756 real
overall: 4481028096 mem 4334.943 user 43.904 sys 146.602 real