cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_tissue.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Sig_18_tissue.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.1s, est remaining 1.3s, peak mem 78MB, user 0.2s, sys 1.5s, output queue size 3
progress 10% @chr2:76000001, elapsed 0.1s, est remaining 1.2s, peak mem 78MB, user 0.4s, sys 3.4s, output queue size 11
progress 15% @chr2:234000001, elapsed 0.2s, est remaining 1.1s, peak mem 78MB, user 0.5s, sys 5.3s, output queue size 3
progress 20% @chr3:134000001, elapsed 0.3s, est remaining 1.0s, peak mem 78MB, user 0.6s, sys 7.1s, output queue size 19
progress 25% @chr4:117000001, elapsed 0.3s, est remaining 1.0s, peak mem 78MB, user 0.7s, sys 9.0s, output queue size 14
progress 30% @chr5:69000001, elapsed 0.4s, est remaining 0.9s, peak mem 78MB, user 0.8s, sys 10.8s, output queue size 17
progress 35% @chr6:70000001, elapsed 0.5s, est remaining 0.8s, peak mem 78MB, user 0.9s, sys 12.7s, output queue size 25
progress 40% @chr7:59000001, elapsed 0.5s, est remaining 0.8s, peak mem 78MB, user 1.1s, sys 14.6s, output queue size 27
progress 45% @chr8:60000001, elapsed 0.6s, est remaining 0.7s, peak mem 78MB, user 1.4s, sys 16.3s, output queue size 35
progress 50% @chr9:77000001, elapsed 0.7s, est remaining 0.7s, peak mem 78MB, user 1.6s, sys 18.3s, output queue size 16
progress 55% @chr10:97000001, elapsed 0.7s, est remaining 0.6s, peak mem 78MB, user 1.7s, sys 20.2s, output queue size 37
progress 60% @chr11:125000001, elapsed 0.8s, est remaining 0.5s, peak mem 78MB, user 1.9s, sys 22.1s, output queue size 33
progress 65% @chr13:19000001, elapsed 0.9s, est remaining 0.5s, peak mem 78MB, user 2.1s, sys 23.9s, output queue size 27
progress 70% @chr14:66000001, elapsed 0.9s, est remaining 0.4s, peak mem 78MB, user 2.3s, sys 25.8s, output queue size 31
progress 75% @chr16:15000001, elapsed 1.0s, est remaining 0.3s, peak mem 78MB, user 2.4s, sys 27.7s, output queue size 34
progress 80% @chr18:4000001, elapsed 1.1s, est remaining 0.3s, peak mem 78MB, user 2.6s, sys 29.8s, output queue size 16
progress 85% @chr20:15000001, elapsed 1.1s, est remaining 0.2s, peak mem 78MB, user 2.8s, sys 31.6s, output queue size 24
progress 90% @chrX:16000001, elapsed 1.2s, est remaining 0.1s, peak mem 111MB, user 3.5s, sys 33.4s, output queue size 114
progress 95% @chrY:33000001, elapsed 1.3s, est remaining 0.1s, peak mem 147MB, user 4.0s, sys 36.1s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 159MB, user 4.9s, sys 39.4s, 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: 49121348
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.025 user 0.016 sys 0.048 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.501 user 7.238 sys 9.364 real
calc: 3219322 calls 0.307 user 6.191 sys 6.927 real
done: 1 calls 0.025 user 0.016 sys 0.048 real
execute: 1 calls 0.003 user 0.003 sys 1.589 real
fetch: 3219322 calls 0.369 user 6.550 sys 6.869 real
idle: 81 calls 0.003 user 0.010 sys 35.209 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 220356608 mem 5.009 user 39.939 sys 2.652 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_tissue.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Sig_18_tissue.md.score --metrics Sig_18_tissue.md.metrics Sig_18_tissue.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:166000001, elapsed 0.1s, est remaining 2.8s, peak mem 168MB, user 0.3s, sys 3.5s, output queue size 18
progress 10% @chr2:75000001, elapsed 0.3s, est remaining 2.3s, peak mem 204MB, user 0.5s, sys 7.0s, output queue size 4
progress 15% @chr2:236000001, elapsed 0.4s, est remaining 2.1s, peak mem 231MB, user 0.7s, sys 10.2s, output queue size 15
progress 20% @chr3:152000001, elapsed 0.5s, est remaining 2.0s, peak mem 243MB, user 0.9s, sys 13.6s, output queue size 2
progress 25% @chr4:118000001, elapsed 0.6s, est remaining 1.8s, peak mem 261MB, user 1.2s, sys 16.9s, output queue size 11
progress 30% @chr5:88000001, elapsed 0.7s, est remaining 1.7s, peak mem 261MB, user 1.3s, sys 20.2s, output queue size 3
progress 35% @chr6:65000001, elapsed 0.8s, est remaining 1.5s, peak mem 273MB, user 1.6s, sys 23.4s, output queue size 8
progress 40% @chr7:46000001, elapsed 1.0s, est remaining 1.5s, peak mem 276MB, user 1.9s, sys 27.8s, output queue size 13
progress 45% @chr8:54000001, elapsed 1.2s, est remaining 1.5s, peak mem 279MB, user 2.2s, sys 34.6s, output queue size 8
progress 50% @chr9:64000001, elapsed 1.4s, est remaining 1.4s, peak mem 279MB, user 2.4s, sys 41.0s, output queue size 11
progress 55% @chr10:121000001, elapsed 1.7s, est remaining 1.4s, peak mem 279MB, user 2.8s, sys 47.9s, output queue size 18
progress 60% @chr11:92000001, elapsed 2.0s, est remaining 1.3s, peak mem 279MB, user 3.2s, sys 56.0s, output queue size 31
progress 65% @chr13:15000001, elapsed 2.2s, est remaining 1.2s, peak mem 279MB, user 3.6s, sys 64.3s, output queue size 11
progress 70% @chr14:82000001, elapsed 2.5s, est remaining 1.1s, peak mem 282MB, user 3.8s, sys 72.6s, output queue size 15
progress 75% @chr15:101000001, elapsed 2.8s, est remaining 0.9s, peak mem 282MB, user 4.1s, sys 80.8s, output queue size 14
progress 80% @chr17:79000001, elapsed 3.1s, est remaining 0.8s, peak mem 282MB, user 4.5s, sys 88.8s, output queue size 17
progress 85% @chr20:16000001, elapsed 3.3s, est remaining 0.6s, peak mem 285MB, user 4.8s, sys 97.1s, output queue size 10
progress 90% @chrX:24000001, elapsed 3.7s, est remaining 0.4s, peak mem 495MB, user 8.3s, sys 102.7s, output queue size 109
progress 95% @chrY:45000001, elapsed 4.0s, est remaining 0.2s, peak mem 504MB, user 11.3s, sys 109.8s, output queue size 240
progress 100% @chr21:41000001, elapsed 5.0s, est remaining 0.0s, peak mem 513MB, user 13.7s, sys 118.1s, output queue size 3664
library Sig_18_tissue:
chimeric_paired 1886
duped 84376
duped_chimeric_paired 8
duped_paired 84374
duped_unpaired 2
optical_dup 3799
paired 999968
reads 1001834
secondary_supplementary 1858
unmapped 8
unpaired 4
optical dup clusters 3695, maxdup 3, total optical dup pairs 3799
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: 49121348
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.018 user 0.056 sys 0.086 real
MateInfoByVcf::load: 28282 calls 3.799 user 1.574 sys 4.200 real
MateInfoByVcf::parse_events: 28282 calls 3.739 user 1.349 sys 3.835 real
advance: 3219322 calls 1.262 user 14.596 sys 16.717 real
calc: 3219322 calls 4.535 user 42.305 sys 47.986 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.006 sys 0.003 real
execute: 1 calls 0.002 user 0.005 sys 5.005 real
fetch: 3219323 calls 0.486 user 14.088 sys 14.927 real
find_pairEnds: 28282 calls 0.217 user 0.054 sys 0.404 real
idle: 968 calls 0.011 user 0.123 sys 51.363 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 28282 calls 0.881 user 0.388 sys 1.623 real
vcfadvance: 28282 calls 0.012 user 0.123 sys 0.168 real
write: 3219323 calls 2.300 user 14.252 sys 16.428 real
overall: 538017792 mem 14.027 user 119.439 sys 6.036 real