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/4a/f820324ad1bae5a5246a8acd635f25/Filler-D0000637.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/a960e2b275ce1ecdbf754978c3d0a5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/a960e2b275ce1ecdbf754978c3d0a5/.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/4a/f820324ad1bae5a5246a8acd635f25/Filler-D0000637.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0000637.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0000637.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 5.3s, est remaining 100.5s, peak mem 2888MB, user 114.8s, sys 7.5s, output queue size 160
progress 10% @chr2:65000001, elapsed 8.6s, est remaining 77.0s, peak mem 3337MB, user 239.1s, sys 10.5s, output queue size 94
progress 15% @chr3:18000001, elapsed 12.2s, est remaining 69.0s, peak mem 5552MB, user 338.8s, sys 11.6s, output queue size 203
progress 20% @chr3:168000001, elapsed 16.4s, est remaining 65.5s, peak mem 8516MB, user 439.8s, sys 12.5s, output queue size 364
progress 25% @chr4:133000001, elapsed 19.4s, est remaining 58.1s, peak mem 10987MB, user 544.6s, sys 13.8s, output queue size 525
progress 30% @chr5:72000001, elapsed 21.4s, est remaining 49.8s, peak mem 12131MB, user 615.8s, sys 15.1s, output queue size 687
progress 35% @chr6:92000001, elapsed 24.8s, est remaining 46.1s, peak mem 14407MB, user 704.8s, sys 15.9s, output queue size 848
progress 40% @chr7:43000001, elapsed 28.0s, est remaining 42.0s, peak mem 16761MB, user 788.6s, sys 16.4s, output queue size 1009
progress 45% @chr8:83000001, elapsed 32.3s, est remaining 39.4s, peak mem 20600MB, user 899.8s, sys 17.5s, output queue size 1171
progress 50% @chr9:39000001, elapsed 34.9s, est remaining 34.9s, peak mem 22397MB, user 1004.0s, sys 19.4s, output queue size 1333
progress 55% @chr10:118000001, elapsed 39.6s, est remaining 32.4s, peak mem 24162MB, user 1126.6s, sys 20.9s, output queue size 1494
progress 60% @chr11:120000001, elapsed 45.0s, est remaining 30.0s, peak mem 24711MB, user 1280.8s, sys 21.9s, output queue size 1656
progress 65% @chr13:25000001, elapsed 49.3s, est remaining 26.5s, peak mem 24711MB, user 1398.9s, sys 22.8s, output queue size 1818
progress 70% @chr14:68000001, elapsed 53.4s, est remaining 22.9s, peak mem 24733MB, user 1537.9s, sys 23.9s, output queue size 1979
progress 75% @chr16:42000001, elapsed 58.2s, est remaining 19.4s, peak mem 24821MB, user 1662.0s, sys 24.9s, output queue size 2141
progress 80% @chr17:44000001, elapsed 68.6s, est remaining 17.1s, peak mem 26079MB, user 1955.9s, sys 27.1s, output queue size 2303
progress 85% @chr19:35000001, elapsed 77.2s, est remaining 13.6s, peak mem 26079MB, user 2273.4s, sys 40.7s, output queue size 367
progress 90% @chrX:33000001, elapsed 86.5s, est remaining 9.6s, peak mem 30131MB, user 2518.2s, sys 42.5s, output queue size 529
progress 95% @chrY:50000001, elapsed 90.1s, est remaining 4.7s, peak mem 32153MB, user 2617.8s, sys 43.6s, output queue size 690
progress 100% @chr19:7000001, elapsed 179.6s, est remaining 0.0s, peak mem 44239MB, user 2990.9s, sys 67.4s, 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: 60166281212
reads: 2072628391
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 9.392 user 1.550 sys 12.687 real
VcfLineRecordHelper::sort: 224 calls 15.002 user 0.317 sys 15.226 real
advance: 3219322 calls 1392.292 user 51.195 sys 1444.873 real
calc: 3219322 calls 676.139 user 8.732 sys 689.586 real
done: 1 calls 9.392 user 1.550 sys 12.687 real
execute: 1 calls 0.004 user 0.003 sys 179.720 real
fetch: 3219322 calls 791.190 user 5.092 sys 795.541 real
idle: 3056 calls 0.918 user 0.022 sys 2919.524 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 46388723712 mem 3044.957 user 71.228 sys 193.675 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0000637.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0000637.md.score --metrics Filler-D0000637.md.metrics Filler-D0000637.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:184000001, elapsed 28.7s, est remaining 545.7s, peak mem 3308MB, user 698.8s, sys 12.6s, output queue size 145
progress 10% @chr2:68000001, elapsed 46.4s, est remaining 417.3s, peak mem 4414MB, user 1345.9s, sys 19.1s, output queue size 47
progress 15% @chr3:3000001, elapsed 65.6s, est remaining 371.9s, peak mem 16923MB, user 1871.6s, sys 24.1s, output queue size 203
progress 20% @chr3:161000001, elapsed 87.8s, est remaining 351.1s, peak mem 25847MB, user 2501.5s, sys 30.3s, output queue size 364
progress 25% @chr4:102000001, elapsed 104.3s, est remaining 313.0s, peak mem 28101MB, user 2996.5s, sys 34.0s, output queue size 525
progress 30% @chr5:104000001, elapsed 117.2s, est remaining 273.4s, peak mem 28920MB, user 3424.9s, sys 37.3s, output queue size 687
progress 35% @chr6:86000001, elapsed 137.9s, est remaining 256.2s, peak mem 31628MB, user 3959.6s, sys 40.8s, output queue size 848
progress 40% @chr7:70000001, elapsed 156.7s, est remaining 235.0s, peak mem 32396MB, user 4467.1s, sys 44.8s, output queue size 1009
progress 45% @chr8:69000001, elapsed 179.2s, est remaining 219.1s, peak mem 33706MB, user 5209.8s, sys 50.6s, output queue size 1171
progress 50% @chr9:74000001, elapsed 193.7s, est remaining 193.7s, peak mem 34696MB, user 5652.3s, sys 53.8s, output queue size 1333
progress 55% @chr10:96000001, elapsed 220.0s, est remaining 180.0s, peak mem 35384MB, user 6329.1s, sys 58.9s, output queue size 1494
progress 60% @chr11:126000001, elapsed 249.4s, est remaining 166.3s, peak mem 37175MB, user 7163.1s, sys 63.6s, output queue size 1656
progress 65% @chr12:120000001, elapsed 274.8s, est remaining 148.0s, peak mem 37175MB, user 7881.8s, sys 67.9s, output queue size 1818
progress 70% @chr14:79000001, elapsed 297.8s, est remaining 127.6s, peak mem 37175MB, user 8613.3s, sys 72.7s, output queue size 1979
progress 75% @chr16:42000001, elapsed 325.0s, est remaining 108.3s, peak mem 37175MB, user 9340.4s, sys 76.9s, output queue size 2141
progress 80% @chr17:41000001, elapsed 382.1s, est remaining 95.5s, peak mem 37175MB, user 11004.4s, sys 85.7s, output queue size 2303
progress 85% @chr20:42000001, elapsed 431.2s, est remaining 76.1s, peak mem 37587MB, user 12424.4s, sys 92.3s, output queue size 2465
progress 90% @chrX:35000001, elapsed 485.2s, est remaining 53.9s, peak mem 48898MB, user 13840.2s, sys 99.6s, output queue size 2627
progress 95% @chrY:53000001, elapsed 507.9s, est remaining 26.7s, peak mem 48898MB, user 14408.2s, sys 102.8s, output queue size 2789
progress 100% @chr19:7000001, elapsed 783.8s, est remaining 0.0s, peak mem 56583MB, user 16502.6s, sys 160.5s, output queue size 3822
library Filler-D0000637:
chimeric_paired 63315616
duped 1737110118
duped_chimeric_paired 30083136
duped_paired 1737075606
duped_unpaired 34512
optical_dup 194518731
paired 2054323320
reads 2072600673
secondary_supplementary 18205335
unmapped 63727
unpaired 36009
optical dup clusters 62463829, maxdup 538, total optical dup pairs 194518731
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: 60166281212
reads: 2072628391
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2739596 calls 112.544 user 2.507 sys 118.172 real
MateInfoByVcf::load: 2739596 calls 1957.155 user 19.307 sys 1734.264 real
MateInfoByVcf::parse_events: 2739596 calls 1627.623 user 14.200 sys 1491.821 real
advance: 3219322 calls 1300.696 user 44.286 sys 1504.810 real
calc: 3219322 calls 11796.334 user 82.890 sys 12022.238 real
done: 1 calls 0.072 user 0.019 sys 0.096 real
exec_no_coor: 1 calls 0.197 user 0.069 sys 0.270 real
execute: 1 calls 0.010 user 0.002 sys 786.319 real
fetch: 3219323 calls 1066.349 user 5.991 sys 1059.693 real
find_pairEnds: 2739596 calls 1181.468 user 5.099 sys 1268.976 real
idle: 768862 calls 288.838 user 7.000 sys 7289.236 real
init: 1 calls 0.000 user 0.000 sys 0.007 real
markDup: 2739596 calls 4711.406 user 34.186 sys 5035.078 real
vcfadvance: 2739596 calls 19.786 user 4.165 sys 22.744 real
write: 3219323 calls 6961.766 user 47.211 sys 6840.829 real
overall: 59332620288 mem 16858.250 user 190.644 sys 788.137 real