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/f7/c88f4e7cd2b5ae8937efc26a365b46/Filler-D0001215.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/12c45981c968bc418bf271f0a829ab/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/12c45981c968bc418bf271f0a829ab/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/c88f4e7cd2b5ae8937efc26a365b46/Filler-D0001215.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-D0001215.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0001215.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 5.7s, est remaining 109.2s, peak mem 2872MB, user 127.2s, sys 9.5s, output queue size 160
progress 10% @chr2:89000001, elapsed 9.3s, est remaining 84.0s, peak mem 3292MB, user 260.9s, sys 12.7s, output queue size 47
progress 15% @chr2:215000001, elapsed 13.4s, est remaining 75.7s, peak mem 5517MB, user 368.0s, sys 14.6s, output queue size 203
progress 20% @chr3:136000001, elapsed 18.0s, est remaining 72.1s, peak mem 8563MB, user 485.1s, sys 16.2s, output queue size 364
progress 25% @chr4:137000001, elapsed 21.1s, est remaining 63.2s, peak mem 10473MB, user 590.1s, sys 18.3s, output queue size 525
progress 30% @chr5:55000001, elapsed 23.3s, est remaining 54.4s, peak mem 11843MB, user 669.1s, sys 19.1s, output queue size 687
progress 35% @chr6:91000001, elapsed 27.3s, est remaining 50.6s, peak mem 14864MB, user 767.7s, sys 20.0s, output queue size 848
progress 40% @chr7:65000001, elapsed 31.0s, est remaining 46.5s, peak mem 17423MB, user 859.3s, sys 21.1s, output queue size 1009
progress 45% @chr8:71000001, elapsed 35.8s, est remaining 43.7s, peak mem 21415MB, user 1010.8s, sys 23.5s, output queue size 1171
progress 50% @chr9:84000001, elapsed 38.8s, est remaining 38.8s, peak mem 23719MB, user 1109.6s, sys 25.3s, output queue size 1333
progress 55% @chr10:98000001, elapsed 43.6s, est remaining 35.7s, peak mem 24967MB, user 1244.5s, sys 27.4s, output queue size 1494
progress 60% @chr12:5000001, elapsed 49.4s, est remaining 33.0s, peak mem 26052MB, user 1401.3s, sys 28.5s, output queue size 1656
progress 65% @chr11:1000001, elapsed 54.5s, est remaining 29.3s, peak mem 26052MB, user 1545.6s, sys 29.6s, output queue size 1818
progress 70% @chr14:72000001, elapsed 59.2s, est remaining 25.4s, peak mem 26052MB, user 1701.4s, sys 30.7s, output queue size 1979
progress 75% @chr16:42000001, elapsed 64.4s, est remaining 21.5s, peak mem 26139MB, user 1838.1s, sys 31.6s, output queue size 2141
progress 80% @chr18:9000001, elapsed 76.0s, est remaining 19.0s, peak mem 27060MB, user 2126.9s, sys 33.7s, output queue size 2303
progress 85% @chr19:40000001, elapsed 86.3s, est remaining 15.2s, peak mem 27060MB, user 2528.4s, sys 49.4s, output queue size 367
progress 90% @chrX:15000001, elapsed 96.8s, est remaining 10.8s, peak mem 31459MB, user 2810.4s, sys 51.3s, output queue size 529
progress 95% @chrY:49000001, elapsed 101.5s, est remaining 5.3s, peak mem 33974MB, user 2950.6s, sys 52.5s, output queue size 690
progress 100% @chr19:7000001, elapsed 177.0s, est remaining 0.0s, peak mem 44915MB, user 3342.7s, sys 66.3s, 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: 65809481583
reads: 2274394963
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 9.484 user 1.926 sys 13.475 real
VcfLineRecordHelper::sort: 243 calls 17.046 user 0.599 sys 17.603 real
advance: 3219322 calls 1531.130 user 50.651 sys 1585.290 real
calc: 3219322 calls 760.675 user 9.413 sys 772.090 real
done: 1 calls 9.484 user 1.926 sys 13.475 real
execute: 1 calls 0.001 user 0.002 sys 177.043 real
fetch: 3219322 calls 904.216 user 3.876 sys 907.682 real
idle: 2659 calls 0.868 user 0.017 sys 2509.692 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 47097806848 mem 3399.544 user 70.443 sys 191.897 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0001215.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0001215.md.score --metrics Filler-D0001215.md.metrics Filler-D0001215.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 30.3s, est remaining 574.8s, peak mem 3272MB, user 764.9s, sys 13.9s, output queue size 52
progress 10% @chr2:89000001, elapsed 49.8s, est remaining 447.8s, peak mem 4374MB, user 1433.7s, sys 20.2s, output queue size 47
progress 15% @chr2:201000001, elapsed 71.1s, est remaining 402.7s, peak mem 18032MB, user 2016.4s, sys 25.2s, output queue size 203
progress 20% @chr3:174000001, elapsed 94.9s, est remaining 379.6s, peak mem 27671MB, user 2659.4s, sys 32.3s, output queue size 364
progress 25% @chr4:134000001, elapsed 113.0s, est remaining 339.1s, peak mem 29947MB, user 3303.0s, sys 36.7s, output queue size 525
progress 30% @chr5:69000001, elapsed 128.0s, est remaining 298.6s, peak mem 31480MB, user 3731.8s, sys 39.8s, output queue size 687
progress 35% @chr6:86000001, elapsed 150.8s, est remaining 280.1s, peak mem 34155MB, user 4313.8s, sys 44.0s, output queue size 848
progress 40% @chr7:67000001, elapsed 170.9s, est remaining 256.4s, peak mem 34398MB, user 4914.9s, sys 47.8s, output queue size 1009
progress 45% @chr8:71000001, elapsed 196.0s, est remaining 239.6s, peak mem 35682MB, user 5714.1s, sys 52.9s, output queue size 1171
progress 50% @chr9:85000001, elapsed 212.8s, est remaining 212.8s, peak mem 37081MB, user 6204.3s, sys 56.1s, output queue size 1333
progress 55% @chr10:118000001, elapsed 241.0s, est remaining 197.2s, peak mem 38962MB, user 6933.1s, sys 61.3s, output queue size 1494
progress 60% @chr11:113000001, elapsed 273.2s, est remaining 182.2s, peak mem 38962MB, user 7860.4s, sys 65.8s, output queue size 1656
progress 65% @chr12:52000001, elapsed 301.0s, est remaining 162.1s, peak mem 38962MB, user 8651.4s, sys 71.1s, output queue size 1818
progress 70% @chr13:102000001, elapsed 328.8s, est remaining 140.9s, peak mem 38962MB, user 9518.4s, sys 75.5s, output queue size 1979
progress 75% @chr16:42000001, elapsed 359.4s, est remaining 119.8s, peak mem 38962MB, user 10287.4s, sys 79.0s, output queue size 2141
progress 80% @chr18:2000001, elapsed 417.6s, est remaining 104.4s, peak mem 39041MB, user 12092.9s, sys 87.7s, output queue size 2303
progress 85% @chr20:20000001, elapsed 470.8s, est remaining 83.1s, peak mem 40880MB, user 13582.6s, sys 95.6s, output queue size 2465
progress 90% @chr22:18000001, elapsed 532.4s, est remaining 59.2s, peak mem 49275MB, user 15223.8s, sys 104.1s, output queue size 2627
progress 95% @chrY:53000001, elapsed 558.3s, est remaining 29.4s, peak mem 49275MB, user 15892.3s, sys 107.9s, output queue size 2789
progress 100% @chr19:7000001, elapsed 895.8s, est remaining 0.0s, peak mem 58974MB, user 18162.7s, sys 172.1s, output queue size 3822
library Filler-D0001215:
chimeric_paired 67886493
duped 1966387396
duped_chimeric_paired 34041266
duped_paired 1966350112
duped_unpaired 37284
optical_dup 191558386
paired 2255207240
reads 2274362965
secondary_supplementary 19077477
unmapped 71122
unpaired 39124
optical dup clusters 58500022, maxdup 617, total optical dup pairs 191558386
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: 65809481583
reads: 2274394963
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2744292 calls 106.996 user 2.016 sys 112.595 real
MateInfoByVcf::load: 2744292 calls 2016.254 user 18.927 sys 1781.915 real
MateInfoByVcf::parse_events: 2744292 calls 1685.430 user 14.420 sys 1540.721 real
advance: 3219322 calls 1432.637 user 58.285 sys 1654.161 real
calc: 3219322 calls 13135.643 user 76.888 sys 13361.368 real
done: 1 calls 0.080 user 0.000 sys 0.083 real
exec_no_coor: 1 calls 0.143 user 0.117 sys 0.290 real
execute: 1 calls 0.004 user 0.004 sys 898.935 real
fetch: 3219323 calls 1157.150 user 5.767 sys 1156.257 real
find_pairEnds: 2744292 calls 1293.199 user 4.328 sys 1382.132 real
idle: 720248 calls 239.921 user 7.053 sys 9181.812 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 2744292 calls 5200.253 user 26.798 sys 5522.488 real
vcfadvance: 2744292 calls 21.939 user 8.177 sys 29.451 real
write: 3219323 calls 7797.648 user 48.547 sys 7673.801 real
overall: 61838917632 mem 18452.315 user 205.347 sys 901.249 real