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/c5/1c0b5298cb21dd31eee7485d0ab36e/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/5187111309415267074d2fd576e349/Filler-D0002564.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/1c0b5298cb21dd31eee7485d0ab36e/.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/3c/5187111309415267074d2fd576e349/Filler-D0002564.bam
==> STAGING COMPLETE (6 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0002564.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0002564.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:176000001, elapsed 4.2s, est remaining 79.8s, peak mem 2537MB, user 99.2s, sys 6.7s, output queue size 118
progress 10% @chr1:155000001, elapsed 7.0s, est remaining 62.7s, peak mem 3332MB, user 190.9s, sys 9.0s, output queue size 170
progress 15% @chr3:21000001, elapsed 10.1s, est remaining 57.0s, peak mem 4978MB, user 274.1s, sys 13.6s, output queue size 203
progress 20% @chr3:150000001, elapsed 13.3s, est remaining 53.0s, peak mem 6844MB, user 358.2s, sys 15.9s, output queue size 364
progress 25% @chr4:110000001, elapsed 15.2s, est remaining 45.7s, peak mem 8602MB, user 433.6s, sys 18.0s, output queue size 525
progress 30% @chr5:76000001, elapsed 17.0s, est remaining 39.6s, peak mem 9644MB, user 481.2s, sys 18.8s, output queue size 687
progress 35% @chr6:91000001, elapsed 19.7s, est remaining 36.7s, peak mem 11645MB, user 551.4s, sys 19.8s, output queue size 848
progress 40% @chr7:56000001, elapsed 22.5s, est remaining 33.8s, peak mem 13305MB, user 630.4s, sys 21.1s, output queue size 1009
progress 45% @chr7:151000001, elapsed 25.7s, est remaining 31.4s, peak mem 15796MB, user 721.6s, sys 23.2s, output queue size 1171
progress 50% @chr9:102000001, elapsed 27.8s, est remaining 27.8s, peak mem 17384MB, user 777.5s, sys 24.9s, output queue size 1333
progress 55% @chr10:98000001, elapsed 31.5s, est remaining 25.8s, peak mem 20183MB, user 876.1s, sys 27.2s, output queue size 1494
progress 60% @chr12:1000001, elapsed 35.6s, est remaining 23.8s, peak mem 22607MB, user 1004.4s, sys 29.5s, output queue size 1656
progress 65% @chr12:120000001, elapsed 38.9s, est remaining 21.0s, peak mem 24629MB, user 1100.6s, sys 30.9s, output queue size 1818
progress 70% @chr14:84000001, elapsed 42.2s, est remaining 18.1s, peak mem 26339MB, user 1206.6s, sys 31.8s, output queue size 1979
progress 75% @chr16:42000001, elapsed 46.1s, est remaining 15.4s, peak mem 27270MB, user 1302.3s, sys 32.9s, output queue size 2141
progress 80% @chr17:44000001, elapsed 53.3s, est remaining 13.3s, peak mem 29050MB, user 1495.6s, sys 34.7s, output queue size 2303
progress 85% @chr20:42000001, elapsed 60.2s, est remaining 10.6s, peak mem 29632MB, user 1715.0s, sys 36.9s, output queue size 2465
progress 90% @chrX:39000001, elapsed 68.1s, est remaining 7.6s, peak mem 32498MB, user 1918.5s, sys 39.1s, output queue size 2627
progress 95% @chrY:52000001, elapsed 71.1s, est remaining 3.7s, peak mem 33588MB, user 1993.4s, sys 40.4s, output queue size 2788
progress 100% @chr19:7000001, elapsed 141.3s, est remaining 0.0s, peak mem 47841MB, user 2354.1s, sys 87.5s, 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: 51370344938
reads: 1758817594
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 7.559 user 2.368 sys 15.732 real
VcfLineRecordHelper::sort: 285 calls 17.678 user 1.242 sys 18.979 real
advance: 3219322 calls 1145.482 user 63.144 sys 1216.134 real
calc: 3219322 calls 552.846 user 13.806 sys 565.950 real
done: 1 calls 7.559 user 2.368 sys 15.732 real
execute: 1 calls 0.001 user 0.000 sys 141.351 real
fetch: 3219322 calls 556.822 user 7.928 sys 562.284 real
idle: 2552 calls 0.796 user 0.009 sys 2437.677 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 50177978368 mem 2410.085 user 92.875 sys 158.283 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0002564.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0002564.md.score --metrics Filler-D0002564.md.metrics Filler-D0002564.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 23.0s, est remaining 437.1s, peak mem 3118MB, user 575.9s, sys 11.8s, output queue size 52
progress 10% @chr2:68000001, elapsed 38.3s, est remaining 344.3s, peak mem 4018MB, user 1102.2s, sys 18.0s, output queue size 47
progress 15% @chr3:3000001, elapsed 54.7s, est remaining 310.2s, peak mem 14325MB, user 1557.4s, sys 22.0s, output queue size 203
progress 20% @chr3:156000001, elapsed 74.2s, est remaining 296.6s, peak mem 24018MB, user 2081.6s, sys 26.9s, output queue size 364
progress 25% @chr4:136000001, elapsed 87.7s, est remaining 263.0s, peak mem 30764MB, user 2549.7s, sys 33.6s, output queue size 525
progress 30% @chr5:72000001, elapsed 98.6s, est remaining 230.1s, peak mem 31789MB, user 2869.1s, sys 37.1s, output queue size 687
progress 35% @chr6:86000001, elapsed 116.5s, est remaining 216.3s, peak mem 33361MB, user 3326.5s, sys 41.4s, output queue size 848
progress 40% @chr7:64000001, elapsed 132.6s, est remaining 199.0s, peak mem 35480MB, user 3778.7s, sys 45.8s, output queue size 1009
progress 45% @chr8:75000001, elapsed 152.3s, est remaining 186.1s, peak mem 38093MB, user 4345.7s, sys 50.5s, output queue size 1171
progress 50% @chr9:86000001, elapsed 166.0s, est remaining 166.0s, peak mem 38893MB, user 4699.5s, sys 54.4s, output queue size 1333
progress 55% @chr10:118000001, elapsed 187.1s, est remaining 153.1s, peak mem 39571MB, user 5388.5s, sys 62.3s, output queue size 1494
progress 60% @chr11:126000001, elapsed 212.4s, est remaining 141.6s, peak mem 40222MB, user 6058.2s, sys 68.4s, output queue size 1656
progress 65% @chr12:120000001, elapsed 233.8s, est remaining 125.9s, peak mem 42490MB, user 6678.1s, sys 72.1s, output queue size 1818
progress 70% @chr14:84000001, elapsed 254.3s, est remaining 109.0s, peak mem 42490MB, user 7350.7s, sys 76.3s, output queue size 1979
progress 75% @chr16:42000001, elapsed 277.8s, est remaining 92.6s, peak mem 42490MB, user 7975.8s, sys 79.4s, output queue size 2141
progress 80% @chr18:3000001, elapsed 323.7s, est remaining 80.9s, peak mem 42490MB, user 9133.5s, sys 85.1s, output queue size 2303
progress 85% @chr20:20000001, elapsed 365.2s, est remaining 64.4s, peak mem 42490MB, user 10514.7s, sys 91.6s, output queue size 2465
progress 90% @chrX:22000001, elapsed 412.3s, est remaining 45.8s, peak mem 52938MB, user 11778.8s, sys 97.1s, output queue size 2627
progress 95% @chrY:52000001, elapsed 432.0s, est remaining 22.7s, peak mem 53125MB, user 12264.0s, sys 99.5s, output queue size 2788
progress 100% @chr19:7000001, elapsed 713.3s, est remaining 0.0s, peak mem 64969MB, user 14238.5s, sys 151.6s, output queue size 3822
library Filler-D0002564:
chimeric_paired 67291782
duped 1499622554
duped_chimeric_paired 32565446
duped_paired 1499586281
duped_unpaired 36273
optical_dup 215600877
paired 1741029860
reads 1758787294
secondary_supplementary 17681960
unmapped 68037
unpaired 37737
optical dup clusters 55687854, maxdup 773, total optical dup pairs 215600877
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: 51370344938
reads: 1758817594
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2677478 calls 118.234 user 2.725 sys 125.598 real
MateInfoByVcf::load: 2677478 calls 1924.340 user 20.602 sys 1683.916 real
MateInfoByVcf::parse_events: 2677478 calls 1581.390 user 14.610 sys 1429.958 real
advance: 3219322 calls 1090.489 user 40.550 sys 1296.878 real
calc: 3219322 calls 10018.008 user 70.375 sys 10239.904 real
done: 1 calls 0.078 user 0.010 sys 0.091 real
exec_no_coor: 1 calls 0.159 user 0.111 sys 0.285 real
execute: 1 calls 0.001 user 0.001 sys 715.331 real
fetch: 3219323 calls 879.971 user 10.784 sys 877.601 real
find_pairEnds: 2677478 calls 981.949 user 3.866 sys 1075.052 real
idle: 781763 calls 347.123 user 7.356 sys 7317.158 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 2677478 calls 3945.425 user 26.184 sys 4284.600 real
vcfadvance: 2677478 calls 19.389 user 4.483 sys 23.323 real
write: 3219323 calls 5971.694 user 42.949 sys 5831.780 real
overall: 68125872128 mem 14658.889 user 179.873 sys 717.863 real