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% @chr1:160000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.1s, sys 1.6s, output queue size 22
progress 10% @chr2:47000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.3s, sys 3.4s, output queue size 26
progress 15% @chr2:232000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 5.2s, output queue size 19
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.6s, sys 7.1s, output queue size 21
progress 25% @chr4:114000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 9.0s, output queue size 15
progress 30% @chr5:88000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 10.8s, output queue size 22
progress 35% @chr6:66000001, elapsed 0.5s, est remaining 0.9s, peak mem 81MB, user 1.0s, sys 12.7s, output queue size 13
progress 40% @chr7:57000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.1s, sys 14.5s, output queue size 15
progress 45% @chr8:59000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.1s, sys 16.5s, output queue size 8
progress 50% @chr9:77000001, elapsed 0.7s, est remaining 0.7s, peak mem 81MB, user 1.3s, sys 18.4s, output queue size 14
progress 55% @chr10:95000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 1.4s, sys 20.3s, output queue size 24
progress 60% @chr11:122000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 22.1s, output queue size 10
progress 65% @chr13:10000001, elapsed 0.9s, est remaining 0.5s, peak mem 81MB, user 1.7s, sys 24.0s, output queue size 26
progress 70% @chr14:86000001, elapsed 1.0s, est remaining 0.4s, peak mem 81MB, user 1.9s, sys 27.9s, output queue size 12
progress 75% @chr16:2000001, elapsed 1.1s, est remaining 0.4s, peak mem 81MB, user 2.1s, sys 31.7s, output queue size 31
progress 80% @chr18:25000001, elapsed 1.2s, est remaining 0.3s, peak mem 81MB, user 2.3s, sys 35.0s, output queue size 26
progress 85% @chr19:41000001, elapsed 1.4s, est remaining 0.2s, peak mem 81MB, user 2.5s, sys 39.2s, output queue size 40
progress 90% @chr21:45000001, elapsed 1.6s, est remaining 0.2s, peak mem 96MB, user 3.1s, sys 43.2s, output queue size 114
progress 95% @chrY:24000001, elapsed 1.8s, est remaining 0.1s, peak mem 126MB, user 3.6s, sys 48.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.1s, est remaining 0.0s, peak mem 171MB, user 4.3s, sys 55.7s, 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: 49784679
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.013 user 0.023 sys 0.048 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.341 user 12.825 sys 14.054 real
calc: 3219322 calls 0.499 user 8.558 sys 9.064 real
done: 1 calls 0.013 user 0.023 sys 0.048 real
execute: 1 calls 0.005 user 0.002 sys 2.114 real
fetch: 3219322 calls 0.347 user 8.168 sys 9.023 real
idle: 82 calls 0.004 user 0.029 sys 35.636 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 211685376 mem 4.459 user 56.293 sys 3.177 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% @chr1:165000001, elapsed 0.1s, est remaining 1.9s, peak mem 168MB, user 0.3s, sys 2.3s, output queue size 29
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 1.6s, peak mem 192MB, user 0.5s, sys 4.5s, output queue size 14
progress 15% @chr2:233000001, elapsed 0.3s, est remaining 1.5s, peak mem 225MB, user 0.8s, sys 6.7s, output queue size 2
progress 20% @chr3:152000001, elapsed 0.3s, est remaining 1.4s, peak mem 225MB, user 1.0s, sys 8.9s, output queue size 1
progress 25% @chr4:113000001, elapsed 0.4s, est remaining 1.2s, peak mem 225MB, user 1.2s, sys 11.1s, output queue size 2
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.2s, peak mem 237MB, user 1.4s, sys 13.3s, output queue size 8
progress 35% @chr6:67000001, elapsed 0.6s, est remaining 1.1s, peak mem 243MB, user 1.6s, sys 15.5s, output queue size 16
progress 40% @chr7:53000001, elapsed 0.6s, est remaining 1.0s, peak mem 249MB, user 1.8s, sys 17.7s, output queue size 4
progress 45% @chr8:58000001, elapsed 0.7s, est remaining 0.9s, peak mem 261MB, user 2.1s, sys 19.8s, output queue size 3
progress 50% @chr9:74000001, elapsed 0.8s, est remaining 0.8s, peak mem 267MB, user 2.3s, sys 21.9s, output queue size 6
progress 55% @chr10:97000001, elapsed 0.9s, est remaining 0.7s, peak mem 267MB, user 2.5s, sys 24.1s, output queue size 9
progress 60% @chr11:125000001, elapsed 1.0s, est remaining 0.6s, peak mem 270MB, user 2.8s, sys 26.2s, output queue size 11
progress 65% @chr13:17000001, elapsed 1.0s, est remaining 0.6s, peak mem 276MB, user 2.9s, sys 28.6s, output queue size 17
progress 70% @chr14:59000001, elapsed 1.1s, est remaining 0.5s, peak mem 276MB, user 3.1s, sys 31.0s, output queue size 13
progress 75% @chr16:37000001, elapsed 1.2s, est remaining 0.4s, peak mem 279MB, user 3.4s, sys 33.9s, output queue size 29
progress 80% @chr17:72000001, elapsed 1.4s, est remaining 0.3s, peak mem 282MB, user 3.8s, sys 37.7s, output queue size 21
progress 85% @chr20:11000001, elapsed 1.6s, est remaining 0.3s, peak mem 282MB, user 4.3s, sys 43.2s, output queue size 45
progress 90% @chrX:46000001, elapsed 1.8s, est remaining 0.2s, peak mem 501MB, user 7.0s, sys 46.5s, output queue size 114
progress 95% @chrY:8000001, elapsed 2.1s, est remaining 0.1s, peak mem 519MB, user 9.7s, sys 51.5s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.2s, est remaining 0.0s, peak mem 537MB, user 13.9s, sys 57.3s, 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: 49784679
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.000 user 0.000 sys 0.053 real
MateInfoByVcf::load: 23378 calls 3.885 user 0.986 sys 3.675 real
MateInfoByVcf::parse_events: 23378 calls 3.852 user 0.943 sys 3.447 real
advance: 3219322 calls 1.250 user 6.740 sys 8.898 real
calc: 3219322 calls 4.831 user 20.498 sys 26.388 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 0.007 user 0.003 sys 3.253 real
fetch: 3219322 calls 0.422 user 6.600 sys 7.650 real
find_pairEnds: 23378 calls 0.232 user 0.010 sys 0.383 real
idle: 1304 calls 0.068 user 0.211 sys 57.268 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 23378 calls 0.918 user 0.218 sys 1.582 real
vcfadvance: 23378 calls 0.002 user 0.056 sys 0.055 real
write: 3219322 calls 2.684 user 6.946 sys 9.555 real
overall: 563187712 mem 14.675 user 58.777 sys 4.274 real