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% @chr1:167000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.1s, sys 1.5s, output queue size 26
progress 10% @chr2:78000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.3s, sys 3.2s, output queue size 19
progress 15% @chr2:209000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 5.0s, output queue size 26
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.6s, sys 6.8s, output queue size 6
progress 25% @chr4:116000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.7s, sys 8.6s, output queue size 12
progress 30% @chr5:81000001, elapsed 0.4s, est remaining 1.0s, peak mem 81MB, user 0.9s, sys 11.6s, output queue size 22
progress 35% @chr6:63000001, elapsed 0.5s, est remaining 1.0s, peak mem 81MB, user 1.2s, sys 15.1s, output queue size 10
progress 40% @chr7:21000001, elapsed 0.7s, est remaining 1.0s, peak mem 81MB, user 1.3s, sys 18.7s, output queue size 34
progress 45% @chr8:54000001, elapsed 0.8s, est remaining 1.0s, peak mem 81MB, user 1.5s, sys 22.2s, output queue size 22
progress 50% @chr9:70000001, elapsed 0.9s, est remaining 0.9s, peak mem 81MB, user 1.6s, sys 25.8s, output queue size 8
progress 55% @chr10:93000001, elapsed 1.0s, est remaining 0.8s, peak mem 81MB, user 1.9s, sys 29.3s, output queue size 14
progress 60% @chr11:112000001, elapsed 1.2s, est remaining 0.8s, peak mem 81MB, user 2.0s, sys 33.4s, output queue size 28
progress 65% @chr12:111000001, elapsed 1.3s, est remaining 0.7s, peak mem 81MB, user 2.2s, sys 38.3s, output queue size 38
progress 70% @chr14:80000001, elapsed 1.5s, est remaining 0.6s, peak mem 81MB, user 2.4s, sys 43.1s, output queue size 15
progress 75% @chr16:5000001, elapsed 1.7s, est remaining 0.6s, peak mem 81MB, user 2.6s, sys 47.9s, output queue size 35
progress 80% @chr18:17000001, elapsed 1.8s, est remaining 0.5s, peak mem 81MB, user 2.8s, sys 52.8s, output queue size 12
progress 85% @chr20:21000001, elapsed 2.0s, est remaining 0.4s, peak mem 81MB, user 3.0s, sys 57.7s, output queue size 12
progress 90% @chrX:26000001, elapsed 2.2s, est remaining 0.2s, peak mem 96MB, user 3.8s, sys 61.8s, output queue size 114
progress 95% @chrY:31000001, elapsed 2.4s, est remaining 0.1s, peak mem 129MB, user 4.1s, sys 67.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 183MB, user 4.9s, sys 74.3s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 50411650
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.028 user 0.010 sys 0.049 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.330 user 15.521 sys 17.376 real
calc: 3219322 calls 0.325 user 11.815 sys 11.928 real
done: 1 calls 0.028 user 0.010 sys 0.049 real
execute: 1 calls 0.002 user 0.002 sys 2.763 real
fetch: 3219322 calls 0.346 user 11.860 sys 11.972 real
idle: 81 calls 0.015 user 0.039 sys 36.231 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 228814848 mem 5.092 user 74.920 sys 3.837 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% @chr1:159000001, elapsed 0.1s, est remaining 2.0s, peak mem 174MB, user 0.3s, sys 2.5s, output queue size 2
progress 10% @chr2:73000001, elapsed 0.2s, est remaining 1.7s, peak mem 192MB, user 0.5s, sys 4.8s, output queue size 13
progress 15% @chr2:232000001, elapsed 0.3s, est remaining 1.5s, peak mem 225MB, user 0.8s, sys 7.1s, output queue size 3
progress 20% @chr3:150000001, elapsed 0.4s, est remaining 1.4s, peak mem 240MB, user 1.0s, sys 9.4s, output queue size 3
progress 25% @chr4:115000001, elapsed 0.6s, est remaining 1.7s, peak mem 240MB, user 1.3s, sys 15.4s, output queue size 2
progress 30% @chr5:87000001, elapsed 0.8s, est remaining 1.8s, peak mem 252MB, user 1.6s, sys 21.6s, output queue size 11
progress 35% @chr6:64000001, elapsed 1.0s, est remaining 1.8s, peak mem 252MB, user 1.9s, sys 27.9s, output queue size 4
progress 40% @chr7:53000001, elapsed 1.2s, est remaining 1.8s, peak mem 252MB, user 2.2s, sys 34.3s, output queue size 2
progress 45% @chr8:51000001, elapsed 1.4s, est remaining 1.7s, peak mem 255MB, user 2.4s, sys 40.8s, output queue size 7
progress 50% @chr9:67000001, elapsed 1.6s, est remaining 1.6s, peak mem 258MB, user 2.7s, sys 47.2s, output queue size 7
progress 55% @chr10:88000001, elapsed 1.9s, est remaining 1.5s, peak mem 258MB, user 2.9s, sys 53.6s, output queue size 7
progress 60% @chr11:116000001, elapsed 2.1s, est remaining 1.4s, peak mem 258MB, user 3.3s, sys 60.2s, output queue size 7
progress 65% @chr13:10000001, elapsed 2.3s, est remaining 1.2s, peak mem 258MB, user 3.7s, sys 66.8s, output queue size 5
progress 70% @chr14:66000001, elapsed 2.5s, est remaining 1.1s, peak mem 264MB, user 4.0s, sys 73.3s, output queue size 3
progress 75% @chr16:3000001, elapsed 2.8s, est remaining 0.9s, peak mem 267MB, user 4.3s, sys 79.9s, output queue size 10
progress 80% @chr18:5000001, elapsed 3.0s, est remaining 0.7s, peak mem 267MB, user 4.5s, sys 86.4s, output queue size 10
progress 85% @chr20:34000001, elapsed 3.2s, est remaining 0.6s, peak mem 267MB, user 4.9s, sys 93.0s, output queue size 12
progress 90% @chrX:31000001, elapsed 3.6s, est remaining 0.4s, peak mem 489MB, user 7.9s, sys 97.8s, output queue size 114
progress 95% @chrY:37000001, elapsed 3.8s, est remaining 0.2s, peak mem 498MB, user 10.9s, sys 103.0s, output queue size 271
progress 100% @chr21:41000001, elapsed 4.8s, est remaining 0.0s, peak mem 522MB, user 14.3s, sys 109.8s, 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 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 50411650
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.013 user 0.004 sys 0.067 real
MateInfoByVcf::load: 25531 calls 4.000 user 1.406 sys 4.363 real
MateInfoByVcf::parse_events: 25531 calls 3.897 user 1.272 sys 4.065 real
advance: 3219322 calls 1.393 user 14.154 sys 15.405 real
calc: 3219322 calls 4.564 user 39.485 sys 45.258 real
done: 1 calls 0.002 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.004 sys 4.890 real
fetch: 3219322 calls 0.391 user 12.877 sys 13.656 real
find_pairEnds: 25531 calls 0.263 user 0.052 sys 0.388 real
idle: 1041 calls 0.072 user 0.266 sys 54.750 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 25531 calls 0.853 user 0.235 sys 1.574 real
vcfadvance: 25531 calls 0.040 user 0.140 sys 0.127 real
write: 3219322 calls 2.416 user 12.512 sys 15.950 real
overall: 547512320 mem 14.942 user 111.135 sys 5.902 real