Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/f4ab261597db89e2038fb6c4e311f2/Filler-D0000335.bam
  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/4c/b0ef85a84da5c734a943e5c7686a25/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/b0ef85a84da5c734a943e5c7686a25/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/f4ab261597db89e2038fb6c4e311f2/Filler-D0000335.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 Filler-D0000335.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0000335.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 6.1s, est remaining 116.5s, peak mem 3416MB, user 140.1s, sys 8.8s, output queue size 160
progress 10% @chr2:72000001, elapsed 10.2s, est remaining 91.7s, peak mem 4340MB, user 273.4s, sys 11.2s, output queue size 170
progress 15% @chr2:206000001, elapsed 14.2s, est remaining 80.6s, peak mem 6741MB, user 392.0s, sys 12.7s, output queue size 208
progress 20% @chr3:176000001, elapsed 18.9s, est remaining 75.5s, peak mem 9967MB, user 507.7s, sys 13.9s, output queue size 364
progress 25% @chr4:120000001, elapsed 22.1s, est remaining 66.4s, peak mem 13163MB, user 633.0s, sys 15.1s, output queue size 525
progress 30% @chr5:83000001, elapsed 24.6s, est remaining 57.4s, peak mem 14712MB, user 710.7s, sys 15.7s, output queue size 686
progress 35% @chr6:70000001, elapsed 28.6s, est remaining 53.0s, peak mem 17565MB, user 809.4s, sys 16.8s, output queue size 848
progress 40% @chr7:30000001, elapsed 32.2s, est remaining 48.3s, peak mem 19787MB, user 897.6s, sys 17.8s, output queue size 1009
progress 45% @chr8:83000001, elapsed 36.9s, est remaining 45.1s, peak mem 21682MB, user 1043.8s, sys 19.0s, output queue size 1171
progress 50% @chr9:1, elapsed 39.9s, est remaining 39.9s, peak mem 22543MB, user 1149.7s, sys 21.3s, output queue size 1333
progress 55% @chr10:118000001, elapsed 45.1s, est remaining 36.9s, peak mem 22914MB, user 1282.3s, sys 22.6s, output queue size 1494
progress 60% @chr11:130000001, elapsed 51.5s, est remaining 34.4s, peak mem 22914MB, user 1456.8s, sys 24.2s, output queue size 1656
progress 65% @chr12:56000001, elapsed 56.3s, est remaining 30.3s, peak mem 22914MB, user 1611.6s, sys 25.3s, output queue size 1818
progress 70% @chr14:86000001, elapsed 60.6s, est remaining 26.0s, peak mem 22914MB, user 1751.3s, sys 26.2s, output queue size 1979
progress 75% @chr16:41000001, elapsed 66.2s, est remaining 22.1s, peak mem 22914MB, user 1885.9s, sys 27.1s, output queue size 2141
progress 80% @chr17:7000001, elapsed 77.3s, est remaining 19.3s, peak mem 23465MB, user 2223.6s, sys 44.9s, output queue size 1232
progress 85% @chr20:2000001, elapsed 86.5s, est remaining 15.3s, peak mem 23842MB, user 2545.8s, sys 47.2s, output queue size 367
progress 90% @chr22:37000001, elapsed 96.6s, est remaining 10.7s, peak mem 27720MB, user 2826.6s, sys 48.6s, output queue size 529
progress 95% @chrY:51000001, elapsed 100.9s, est remaining 5.3s, peak mem 30144MB, user 2933.0s, sys 49.4s, output queue size 690
progress 100% @chr19:7000001, elapsed 176.8s, est remaining 0.0s, peak mem 42317MB, user 3346.1s, sys 65.2s, 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: 68370821001
reads: 2293496371
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 6.236 user 1.621 sys 8.992 real
VcfLineRecordHelper::sort: 188 calls 12.949 user 0.121 sys 13.080 real
advance: 3219322 calls 1548.440 user 46.479 sys 1596.054 real
calc: 3219322 calls 755.186 user 9.036 sys 764.845 real
done: 1 calls 6.236 user 1.621 sys 8.992 real
execute: 1 calls 0.002 user 0.002 sys 176.854 real
fetch: 3219322 calls 896.216 user 7.622 sys 906.242 real
idle: 2504 calls 0.924 user 0.009 sys 2361.981 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 44373245952 mem 3388.331 user 68.905 sys 187.185 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0000335.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0000335.md.score --metrics Filler-D0000335.md.metrics Filler-D0000335.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 33.2s, est remaining 630.7s, peak mem 4346MB, user 838.8s, sys 17.7s, output queue size 52
progress 10% @chr2:89000001, elapsed 55.2s, est remaining 497.2s, peak mem 5824MB, user 1577.6s, sys 25.2s, output queue size 94
progress 15% @chr2:201000001, elapsed 77.9s, est remaining 441.6s, peak mem 18942MB, user 2219.8s, sys 31.3s, output queue size 203
progress 20% @chr3:138000001, elapsed 105.4s, est remaining 421.7s, peak mem 24272MB, user 2969.7s, sys 36.7s, output queue size 364
progress 25% @chr4:120000001, elapsed 123.7s, est remaining 371.1s, peak mem 27534MB, user 3620.3s, sys 41.5s, output queue size 525
progress 30% @chr5:105000001, elapsed 138.4s, est remaining 322.9s, peak mem 28062MB, user 4011.0s, sys 45.5s, output queue size 686
progress 35% @chr6:44000001, elapsed 163.3s, est remaining 303.3s, peak mem 29041MB, user 4667.6s, sys 50.3s, output queue size 848
progress 40% @chr7:67000001, elapsed 185.2s, est remaining 277.8s, peak mem 29683MB, user 5284.0s, sys 54.4s, output queue size 1009
progress 45% @chr7:102000001, elapsed 213.5s, est remaining 260.9s, peak mem 31562MB, user 6205.7s, sys 60.8s, output queue size 1171
progress 50% @chr9:39000001, elapsed 231.4s, est remaining 231.4s, peak mem 31562MB, user 6702.9s, sys 64.0s, output queue size 1333
progress 55% @chr10:93000001, elapsed 263.0s, est remaining 215.2s, peak mem 31562MB, user 7559.4s, sys 68.6s, output queue size 1494
progress 60% @chr11:1, elapsed 299.5s, est remaining 199.6s, peak mem 31562MB, user 8565.4s, sys 72.9s, output queue size 1656
progress 65% @chr12:52000001, elapsed 328.4s, est remaining 176.8s, peak mem 31562MB, user 9419.0s, sys 77.2s, output queue size 1818
progress 70% @chr14:82000001, elapsed 355.7s, est remaining 152.4s, peak mem 31591MB, user 10311.0s, sys 81.4s, output queue size 1979
progress 75% @chr16:42000001, elapsed 388.3s, est remaining 129.4s, peak mem 33106MB, user 11146.7s, sys 85.6s, output queue size 2141
progress 80% @chr17:44000001, elapsed 456.1s, est remaining 114.0s, peak mem 33106MB, user 13142.1s, sys 93.7s, output queue size 2303
progress 85% @chr20:42000001, elapsed 511.5s, est remaining 90.3s, peak mem 33106MB, user 15162.5s, sys 120.6s, output queue size 367
progress 90% @chrX:36000001, elapsed 568.0s, est remaining 63.1s, peak mem 43881MB, user 16740.9s, sys 129.1s, output queue size 529
progress 95% @chrY:52000001, elapsed 591.0s, est remaining 31.1s, peak mem 43881MB, user 17360.7s, sys 132.7s, output queue size 690
progress 100% @chr19:7000001, elapsed 874.1s, est remaining 0.0s, peak mem 52553MB, user 19062.9s, sys 156.9s, output queue size 3822
library Filler-D0000335:
chimeric_paired 59947561
duped 1902149206
duped_chimeric_paired 27044426
duped_paired 1902115905
duped_unpaired 33301
optical_dup 141624196
paired 2274215092
reads 2293466179
secondary_supplementary 19181057
unmapped 65207
unpaired 35015
optical dup clusters 56708198, maxdup 464, total optical dup pairs 141624196
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: 68370821001
reads: 2293496371
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2825954 calls 92.537 user 2.076 sys 97.662 real
MateInfoByVcf::load: 2825954 calls 2091.395 user 18.704 sys 1861.405 real
MateInfoByVcf::parse_events: 2825954 calls 1776.701 user 13.908 sys 1635.369 real
advance: 3219322 calls 1495.603 user 47.571 sys 1713.626 real
calc: 3219322 calls 13732.709 user 77.633 sys 13951.360 real
done: 1 calls 0.069 user 0.048 sys 0.125 real
exec_no_coor: 1 calls 0.176 user 0.124 sys 0.309 real
execute: 1 calls 0.004 user 0.003 sys 877.757 real
fetch: 3219323 calls 1299.185 user 5.170 sys 1301.759 real
find_pairEnds: 2825954 calls 1373.094 user 4.495 sys 1467.168 real
idle: 734326 calls 239.492 user 6.003 sys 7640.702 real
init: 1 calls 0.010 user 0.000 sys 0.008 real
markDup: 2825954 calls 5454.452 user 27.716 sys 5773.217 real
vcfadvance: 2825954 calls 19.425 user 3.837 sys 22.819 real
write: 3219323 calls 8128.539 user 48.578 sys 8002.525 real
overall: 55106719744 mem 19349.885 user 194.441 sys 880.455 real