cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_tumor.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:131000001, elapsed 0.1s, est remaining 2.4s, peak mem 78MB, user 0.1s, sys 3.2s, output queue size 30
progress 10% @chr2:68000001, elapsed 0.3s, est remaining 2.4s, peak mem 78MB, user 0.3s, sys 7.4s, output queue size 13
progress 15% @chr2:222000001, elapsed 0.4s, est remaining 2.4s, peak mem 78MB, user 0.4s, sys 11.9s, output queue size 20
progress 20% @chr3:180000001, elapsed 0.6s, est remaining 2.3s, peak mem 78MB, user 0.6s, sys 16.3s, output queue size 41
progress 25% @chr4:102000001, elapsed 0.8s, est remaining 2.3s, peak mem 78MB, user 0.8s, sys 21.9s, output queue size 32
progress 30% @chr5:63000001, elapsed 0.9s, est remaining 2.2s, peak mem 78MB, user 1.1s, sys 27.2s, output queue size 24
progress 35% @chr6:89000001, elapsed 1.1s, est remaining 2.1s, peak mem 78MB, user 1.3s, sys 31.8s, output queue size 58
progress 40% @chr6:147000001, elapsed 1.3s, est remaining 1.9s, peak mem 78MB, user 1.5s, sys 36.6s, output queue size 79
progress 45% @chr8:81000001, elapsed 1.4s, est remaining 1.8s, peak mem 78MB, user 1.8s, sys 41.0s, output queue size 72
progress 50% @chr9:98000001, elapsed 1.6s, est remaining 1.6s, peak mem 78MB, user 2.0s, sys 45.7s, output queue size 70
progress 55% @chr10:120000001, elapsed 1.8s, est remaining 1.5s, peak mem 78MB, user 2.2s, sys 51.1s, output queue size 69
progress 60% @chr11:49000001, elapsed 2.0s, est remaining 1.3s, peak mem 78MB, user 2.3s, sys 56.3s, output queue size 74
progress 65% @chr13:37000001, elapsed 2.1s, est remaining 1.1s, peak mem 78MB, user 2.5s, sys 61.7s, output queue size 67
progress 70% @chr14:77000001, elapsed 2.3s, est remaining 1.0s, peak mem 78MB, user 2.7s, sys 67.1s, output queue size 57
progress 75% @chr16:36000001, elapsed 2.5s, est remaining 0.8s, peak mem 78MB, user 3.0s, sys 72.1s, output queue size 65
progress 80% @chr17:15000001, elapsed 2.6s, est remaining 0.7s, peak mem 78MB, user 3.2s, sys 77.1s, output queue size 70
progress 85% @chr19:13000001, elapsed 2.8s, est remaining 0.5s, peak mem 78MB, user 3.3s, sys 82.4s, output queue size 68
progress 90% @chrX:22000001, elapsed 3.0s, est remaining 0.3s, peak mem 81MB, user 3.7s, sys 86.6s, output queue size 114
progress 95% @chrY:44000001, elapsed 3.2s, est remaining 0.2s, peak mem 96MB, user 4.2s, sys 91.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.6s, est remaining 0.0s, peak mem 156MB, user 5.2s, sys 100.1s, 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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784676
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.013 user 0.021 sys 0.046 real
VcfLineRecordHelper::sort: 27 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.441 user 21.540 sys 22.855 real
calc: 3219322 calls 0.219 user 15.397 sys 15.913 real
done: 1 calls 0.013 user 0.021 sys 0.046 real
execute: 1 calls 0.002 user 0.009 sys 3.642 real
fetch: 3219322 calls 0.433 user 16.006 sys 16.175 real
idle: 81 calls 0.017 user 0.028 sys 37.625 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 208904192 mem 5.336 user 100.748 sys 4.703 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_tumor.md.score --metrics HCC1395_tumor.md.metrics HCC1395_tumor.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:164000001, elapsed 0.1s, est remaining 1.9s, peak mem 165MB, user 0.4s, sys 2.3s, output queue size 9
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 2.0s, peak mem 192MB, user 0.8s, sys 5.4s, output queue size 20
progress 15% @chr2:230000001, elapsed 0.4s, est remaining 2.3s, peak mem 204MB, user 1.2s, sys 10.3s, output queue size 17
progress 20% @chr3:150000001, elapsed 0.6s, est remaining 2.2s, peak mem 207MB, user 1.6s, sys 15.1s, output queue size 7
progress 25% @chr4:110000001, elapsed 0.7s, est remaining 2.2s, peak mem 216MB, user 1.9s, sys 19.9s, output queue size 25
progress 30% @chr5:81000001, elapsed 0.9s, est remaining 2.1s, peak mem 228MB, user 2.2s, sys 24.8s, output queue size 14
progress 35% @chr6:56000001, elapsed 1.1s, est remaining 2.0s, peak mem 237MB, user 2.4s, sys 30.0s, output queue size 16
progress 40% @chr7:79000001, elapsed 1.2s, est remaining 1.9s, peak mem 243MB, user 2.8s, sys 34.8s, output queue size 23
progress 45% @chr8:41000001, elapsed 1.4s, est remaining 1.7s, peak mem 252MB, user 3.3s, sys 39.8s, output queue size 28
progress 50% @chr9:69000001, elapsed 1.6s, est remaining 1.6s, peak mem 255MB, user 3.7s, sys 46.1s, output queue size 32
progress 55% @chr10:86000001, elapsed 1.9s, est remaining 1.5s, peak mem 264MB, user 4.0s, sys 52.7s, output queue size 31
progress 60% @chr12:6000001, elapsed 2.1s, est remaining 1.4s, peak mem 264MB, user 4.3s, sys 59.1s, output queue size 12
progress 65% @chr13:33000001, elapsed 2.3s, est remaining 1.2s, peak mem 264MB, user 4.6s, sys 65.5s, output queue size 11
progress 70% @chr14:75000001, elapsed 2.5s, est remaining 1.1s, peak mem 267MB, user 4.9s, sys 72.1s, output queue size 14
progress 75% @chr16:14000001, elapsed 2.7s, est remaining 0.9s, peak mem 270MB, user 5.2s, sys 78.8s, output queue size 11
progress 80% @chr17:79000001, elapsed 3.0s, est remaining 0.7s, peak mem 270MB, user 5.4s, sys 85.5s, output queue size 5
progress 85% @chr20:16000001, elapsed 3.2s, est remaining 0.6s, peak mem 273MB, user 5.7s, sys 92.2s, output queue size 6
progress 90% @chr21:32000001, elapsed 3.5s, est remaining 0.4s, peak mem 492MB, user 8.9s, sys 96.5s, output queue size 114
progress 95% @chrY:28000001, elapsed 3.8s, est remaining 0.2s, peak mem 516MB, user 11.3s, sys 102.2s, output queue size 271
progress 100% @chr21:41000001, elapsed 4.6s, est remaining 0.0s, peak mem 531MB, user 15.1s, sys 108.8s, output queue size 3664
library HCC1395_tumor:
chimeric_paired 1295
duped 169120
duped_chimeric_paired 30
duped_paired 169118
duped_unpaired 2
optical_dup 5868
paired 999972
reads 1001320
secondary_supplementary 1340
unmapped 4
unpaired 4
optical dup clusters 5659, maxdup 4, total optical dup pairs 5868
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 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784676
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.008 user 0.045 sys 0.062 real
MateInfoByVcf::load: 23378 calls 3.823 user 1.100 sys 4.025 real
MateInfoByVcf::parse_events: 23378 calls 3.767 user 0.936 sys 3.753 real
advance: 3219322 calls 1.456 user 13.456 sys 15.607 real
calc: 3219322 calls 5.222 user 40.068 sys 45.727 real
done: 1 calls 0.000 user 0.001 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.001 sys 4.695 real
fetch: 3219322 calls 0.597 user 13.473 sys 13.845 real
find_pairEnds: 23378 calls 0.254 user 0.035 sys 0.384 real
idle: 891 calls 0.045 user 0.090 sys 49.140 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.962 user 0.297 sys 1.626 real
vcfadvance: 23378 calls 0.021 user 0.155 sys 0.119 real
write: 3219322 calls 2.656 user 13.398 sys 15.991 real
overall: 556879872 mem 15.794 user 109.900 sys 5.724 real