cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_BL.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:165000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.2s, sys 1.5s, output queue size 5
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.2s, sys 3.1s, output queue size 5
progress 15% @chr2:233000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.4s, sys 4.9s, output queue size 2
progress 20% @chr3:153000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.5s, sys 6.5s, output queue size 2
progress 25% @chr4:117000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.6s, sys 8.2s, output queue size 17
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.7s, sys 9.9s, output queue size 12
progress 35% @chr6:68000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 11.5s, output queue size 6
progress 40% @chr7:52000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.0s, sys 13.2s, output queue size 3
progress 45% @chr8:58000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.2s, sys 14.9s, output queue size 5
progress 50% @chr9:73000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.3s, sys 16.6s, output queue size 1
progress 55% @chr10:95000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.3s, sys 18.4s, output queue size 2
progress 60% @chr11:123000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.5s, sys 20.1s, output queue size 29
progress 65% @chr12:124000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.6s, sys 21.8s, output queue size 25
progress 70% @chr14:62000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.7s, sys 23.5s, output queue size 18
progress 75% @chr16:15000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 1.8s, sys 25.2s, output queue size 9
progress 80% @chr18:1, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 1.9s, sys 27.0s, output queue size 5
progress 85% @chr20:24000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.0s, sys 28.7s, output queue size 3
progress 90% @chrX:32000001, elapsed 1.1s, est remaining 0.1s, peak mem 111MB, user 2.5s, sys 30.4s, output queue size 114
progress 95% @chrY:31000001, elapsed 1.2s, est remaining 0.1s, peak mem 144MB, user 2.9s, sys 32.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.5s, est remaining 0.0s, peak mem 180MB, user 3.6s, sys 35.5s, output queue size 3664
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: 50411651
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.025 user 0.017 sys 0.050 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.247 user 7.000 sys 8.732 real
calc: 3219322 calls 0.369 user 6.052 sys 6.231 real
done: 1 calls 0.025 user 0.017 sys 0.050 real
execute: 1 calls 0.001 user 0.001 sys 1.483 real
fetch: 3219322 calls 0.344 user 5.411 sys 6.151 real
idle: 73 calls 0.007 user 0.010 sys 36.850 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 226471936 mem 3.793 user 36.106 sys 2.547 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_BL.md.score --metrics HCC1395_BL.md.metrics HCC1395_BL.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:150000001, elapsed 0.2s, est remaining 4.3s, peak mem 168MB, user 0.5s, sys 5.3s, output queue size 11
progress 10% @chr2:63000001, elapsed 0.4s, est remaining 3.9s, peak mem 186MB, user 0.8s, sys 11.4s, output queue size 20
progress 15% @chr2:226000001, elapsed 0.6s, est remaining 3.6s, peak mem 204MB, user 1.1s, sys 17.3s, output queue size 10
progress 20% @chr3:144000001, elapsed 0.8s, est remaining 3.3s, peak mem 219MB, user 1.5s, sys 23.2s, output queue size 34
progress 25% @chr4:134000001, elapsed 1.0s, est remaining 3.1s, peak mem 240MB, user 1.8s, sys 29.0s, output queue size 12
progress 30% @chr5:79000001, elapsed 1.2s, est remaining 2.9s, peak mem 243MB, user 2.1s, sys 35.2s, output queue size 13
progress 35% @chr6:60000001, elapsed 1.4s, est remaining 2.7s, peak mem 246MB, user 2.4s, sys 41.3s, output queue size 20
progress 40% @chr7:59000001, elapsed 1.7s, est remaining 2.5s, peak mem 249MB, user 2.7s, sys 47.6s, output queue size 16
progress 45% @chr8:60000001, elapsed 1.9s, est remaining 2.3s, peak mem 252MB, user 3.1s, sys 53.9s, output queue size 21
progress 50% @chr9:75000001, elapsed 2.1s, est remaining 2.1s, peak mem 252MB, user 3.4s, sys 60.4s, output queue size 3
progress 55% @chr10:96000001, elapsed 2.3s, est remaining 1.9s, peak mem 255MB, user 3.7s, sys 66.6s, output queue size 5
progress 60% @chr11:118000001, elapsed 2.5s, est remaining 1.7s, peak mem 255MB, user 4.0s, sys 73.2s, output queue size 20
progress 65% @chr13:8000001, elapsed 2.7s, est remaining 1.5s, peak mem 261MB, user 4.2s, sys 79.8s, output queue size 7
progress 70% @chr14:51000001, elapsed 3.0s, est remaining 1.3s, peak mem 267MB, user 4.5s, sys 86.5s, output queue size 10
progress 75% @chr16:8000001, elapsed 3.2s, est remaining 1.1s, peak mem 267MB, user 4.9s, sys 93.4s, output queue size 5
progress 80% @chr18:3000001, elapsed 3.4s, est remaining 0.9s, peak mem 270MB, user 5.2s, sys 100.3s, output queue size 6
progress 85% @chr20:32000001, elapsed 3.7s, est remaining 0.6s, peak mem 270MB, user 5.5s, sys 107.1s, output queue size 8
progress 90% @chrX:31000001, elapsed 4.0s, est remaining 0.4s, peak mem 474MB, user 8.4s, sys 111.4s, output queue size 114
progress 95% @chrY:34000001, elapsed 4.3s, est remaining 0.2s, peak mem 492MB, user 12.2s, sys 117.1s, output queue size 247
progress 100% @chr21:41000001, elapsed 5.2s, est remaining 0.0s, peak mem 513MB, user 15.3s, sys 124.0s, output queue size 3664
library HCC1395_BL:
chimeric_paired 873
duped 146553
duped_chimeric_paired 2
duped_paired 146548
duped_unpaired 5
optical_dup 4835
paired 999974
reads 1001089
secondary_supplementary 1097
unmapped 9
unpaired 9
optical dup clusters 4702, maxdup 7, total optical dup pairs 4835
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: 50411651
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.002 user 0.013 sys 0.068 real
MateInfoByVcf::load: 25531 calls 4.192 user 1.268 sys 4.562 real
MateInfoByVcf::parse_events: 25531 calls 4.130 user 1.165 sys 4.268 real
advance: 3219322 calls 1.400 user 15.742 sys 17.402 real
calc: 3219322 calls 4.822 user 45.630 sys 51.127 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.004 sys 5.295 real
fetch: 3219322 calls 0.401 user 15.006 sys 15.448 real
find_pairEnds: 25531 calls 0.222 user 0.055 sys 0.387 real
idle: 988 calls 0.054 user 0.163 sys 52.368 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 25531 calls 0.927 user 0.255 sys 1.592 real
vcfadvance: 25531 calls 0.004 user 0.146 sys 0.100 real
write: 3219322 calls 2.553 user 15.316 sys 17.660 real
overall: 538025984 mem 15.801 user 125.359 sys 6.321 real