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% @chr1:162000001, elapsed 0.1s, est remaining 1.8s, peak mem 81MB, user 0.2s, sys 2.2s, output queue size 11
progress 10% @chr2:71000001, elapsed 0.2s, est remaining 1.6s, peak mem 81MB, user 0.5s, sys 4.5s, output queue size 2
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.5s, peak mem 81MB, user 0.7s, sys 6.8s, output queue size 4
progress 20% @chr3:141000001, elapsed 0.3s, est remaining 1.4s, peak mem 81MB, user 0.9s, sys 9.2s, output queue size 12
progress 25% @chr4:114000001, elapsed 0.4s, est remaining 1.3s, peak mem 81MB, user 1.2s, sys 11.4s, output queue size 1
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.2s, peak mem 81MB, user 1.4s, sys 13.8s, output queue size 7
progress 35% @chr6:53000001, elapsed 0.6s, est remaining 1.1s, peak mem 81MB, user 1.6s, sys 16.2s, output queue size 12
progress 40% @chr7:55000001, elapsed 0.7s, est remaining 1.0s, peak mem 81MB, user 1.8s, sys 18.6s, output queue size 3
progress 45% @chr8:54000001, elapsed 0.8s, est remaining 0.9s, peak mem 81MB, user 1.9s, sys 21.0s, output queue size 9
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 81MB, user 2.1s, sys 23.4s, output queue size 1
progress 55% @chr10:95000001, elapsed 0.9s, est remaining 0.8s, peak mem 81MB, user 2.4s, sys 25.7s, output queue size 3
progress 60% @chr11:122000001, elapsed 1.0s, est remaining 0.7s, peak mem 81MB, user 2.6s, sys 28.0s, output queue size 10
progress 65% @chr12:132000001, elapsed 1.1s, est remaining 0.6s, peak mem 81MB, user 2.9s, sys 30.3s, output queue size 17
progress 70% @chr14:62000001, elapsed 1.2s, est remaining 0.5s, peak mem 81MB, user 3.0s, sys 32.8s, output queue size 5
progress 75% @chr16:14000001, elapsed 1.3s, est remaining 0.4s, peak mem 81MB, user 3.1s, sys 35.2s, output queue size 12
progress 80% @chr18:1, elapsed 1.3s, est remaining 0.3s, peak mem 81MB, user 3.2s, sys 37.6s, output queue size 2
progress 85% @chr20:26000001, elapsed 1.4s, est remaining 0.3s, peak mem 81MB, user 3.3s, sys 39.9s, output queue size 10
progress 90% @chrX:28000001, elapsed 1.5s, est remaining 0.2s, peak mem 115MB, user 3.9s, sys 42.2s, output queue size 114
progress 95% @chrY:31000001, elapsed 1.6s, est remaining 0.1s, peak mem 144MB, user 4.1s, sys 44.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.9s, est remaining 0.0s, peak mem 193MB, user 4.9s, sys 48.6s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 50408312
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.032 user 0.005 sys 0.049 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.211 user 9.752 sys 11.061 real
calc: 3219322 calls 0.483 user 7.595 sys 8.446 real
done: 1 calls 0.032 user 0.005 sys 0.049 real
execute: 1 calls 0.000 user 0.010 sys 1.929 real
fetch: 3219322 calls 0.331 user 7.782 sys 8.464 real
idle: 74 calls 0.007 user 0.033 sys 36.475 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 241934336 mem 5.018 user 49.126 sys 2.984 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% @chr1:162000001, elapsed 0.1s, est remaining 2.0s, peak mem 191MB, user 0.4s, sys 2.3s, output queue size 29
progress 10% @chr2:72000001, elapsed 0.2s, est remaining 1.7s, peak mem 229MB, user 0.6s, sys 4.6s, output queue size 15
progress 15% @chr2:236000001, elapsed 0.3s, est remaining 1.5s, peak mem 244MB, user 0.9s, sys 6.8s, output queue size 9
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.4s, peak mem 256MB, user 1.1s, sys 9.1s, output queue size 2
progress 25% @chr4:115000001, elapsed 0.4s, est remaining 1.3s, peak mem 260MB, user 1.3s, sys 11.4s, output queue size 12
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.2s, peak mem 265MB, user 1.4s, sys 13.7s, output queue size 4
progress 35% @chr6:66000001, elapsed 0.6s, est remaining 1.1s, peak mem 272MB, user 1.6s, sys 16.0s, output queue size 10
progress 40% @chr7:55000001, elapsed 0.7s, est remaining 1.0s, peak mem 275MB, user 1.8s, sys 18.3s, output queue size 18
progress 45% @chr8:56000001, elapsed 0.7s, est remaining 0.9s, peak mem 281MB, user 2.1s, sys 20.5s, output queue size 1
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 287MB, user 2.2s, sys 22.8s, output queue size 15
progress 55% @chr10:94000001, elapsed 0.9s, est remaining 0.7s, peak mem 289MB, user 2.4s, sys 25.1s, output queue size 1
progress 60% @chr11:121000001, elapsed 1.0s, est remaining 0.7s, peak mem 290MB, user 2.6s, sys 27.5s, output queue size 2
progress 65% @chr13:16000001, elapsed 1.1s, est remaining 0.6s, peak mem 292MB, user 2.8s, sys 29.9s, output queue size 6
progress 70% @chr14:55000001, elapsed 1.2s, est remaining 0.5s, peak mem 293MB, user 3.0s, sys 32.3s, output queue size 11
progress 75% @chr16:1, elapsed 1.2s, est remaining 0.4s, peak mem 293MB, user 3.2s, sys 34.6s, output queue size 20
progress 80% @chr18:1, elapsed 1.3s, est remaining 0.3s, peak mem 293MB, user 3.4s, sys 36.9s, output queue size 2
progress 85% @chr20:21000001, elapsed 1.4s, est remaining 0.2s, peak mem 299MB, user 3.7s, sys 39.2s, output queue size 1
progress 90% @chrX:41000001, elapsed 1.6s, est remaining 0.2s, peak mem 527MB, user 5.6s, sys 40.4s, output queue size 114
progress 95% @chrY:40000001, elapsed 1.7s, est remaining 0.1s, peak mem 545MB, user 7.1s, sys 41.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 574MB, user 12.8s, sys 42.7s, 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: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 50408312
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.008 user 0.002 sys 0.020 real
MateInfoByVcf::load: 25531 calls 4.260 user 0.613 sys 3.776 real
MateInfoByVcf::parse_events: 25531 calls 4.176 user 0.594 sys 3.680 real
advance: 3219322 calls 1.123 user 5.096 sys 6.801 real
calc: 3219322 calls 4.104 user 15.447 sys 20.166 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.005 sys 2.833 real
fetch: 3219322 calls 0.414 user 5.037 sys 5.677 real
find_pairEnds: 25531 calls 0.181 user 0.013 sys 0.326 real
idle: 1794 calls 0.167 user 0.091 sys 60.027 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 25531 calls 0.754 user 0.029 sys 1.252 real
vcfadvance: 25531 calls 0.005 user 0.086 sys 0.024 real
write: 3219322 calls 2.188 user 5.283 sys 7.430 real
overall: 602275840 mem 13.780 user 43.706 sys 3.854 real