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% @chr1:183000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.1s, sys 1.5s, output queue size 2
progress 10% @chr2:69000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.2s, sys 3.4s, output queue size 4
progress 15% @chr2:230000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.3s, sys 5.2s, output queue size 5
progress 20% @chr3:150000001, elapsed 0.3s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 7.2s, output queue size 5
progress 25% @chr4:113000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.6s, sys 9.0s, output queue size 3
progress 30% @chr5:83000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 10.8s, output queue size 3
progress 35% @chr6:61000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 12.7s, output queue size 5
progress 40% @chr7:51000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.1s, sys 14.5s, output queue size 4
progress 45% @chr8:52000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.2s, sys 16.4s, output queue size 5
progress 50% @chr9:70000001, elapsed 0.7s, est remaining 0.7s, peak mem 81MB, user 1.3s, sys 18.2s, output queue size 4
progress 55% @chr10:115000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 1.5s, sys 20.0s, output queue size 3
progress 60% @chr11:120000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 21.9s, output queue size 5
progress 65% @chr13:9000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 1.8s, sys 23.6s, output queue size 6
progress 70% @chr14:55000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 1.9s, sys 25.5s, output queue size 7
progress 75% @chr16:9000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 27.2s, output queue size 5
progress 80% @chr17:76000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 2.2s, sys 29.0s, output queue size 8
progress 85% @chr20:18000001, elapsed 1.1s, est remaining 0.2s, peak mem 81MB, user 2.3s, sys 30.7s, output queue size 4
progress 90% @chrX:31000001, elapsed 1.2s, est remaining 0.1s, peak mem 132MB, user 2.9s, sys 32.3s, output queue size 114
progress 95% @chrY:46000001, elapsed 1.3s, est remaining 0.1s, peak mem 162MB, user 3.2s, sys 34.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.5s, est remaining 0.0s, peak mem 183MB, user 3.9s, sys 36.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000c06f2
features: bfebfbff 7ffefbff
extended: f3bfb7ef fb417ffe
amd bits: 2c100800 00000121
brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.038 user 0.008 sys 0.051 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.365 user 6.971 sys 8.537 real
calc: 3219322 calls 0.385 user 6.077 sys 6.420 real
done: 1 calls 0.038 user 0.008 sys 0.051 real
execute: 1 calls 0.003 user 0.005 sys 1.483 real
fetch: 3219322 calls 0.339 user 6.246 sys 6.402 real
idle: 74 calls 0.004 user 0.025 sys 35.306 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 231116800 mem 4.072 user 37.276 sys 2.551 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% @chr1:156000001, elapsed 0.1s, est remaining 2.0s, peak mem 190MB, user 0.3s, sys 2.5s, output queue size 5
progress 10% @chr2:68000001, elapsed 0.2s, est remaining 1.7s, peak mem 225MB, user 0.5s, sys 4.8s, output queue size 17
progress 15% @chr2:229000001, elapsed 0.3s, est remaining 1.5s, peak mem 240MB, user 0.8s, sys 7.0s, output queue size 6
progress 20% @chr3:147000001, elapsed 0.3s, est remaining 1.4s, peak mem 241MB, user 1.0s, sys 9.3s, output queue size 7
progress 25% @chr4:135000001, elapsed 0.4s, est remaining 1.3s, peak mem 252MB, user 1.2s, sys 11.5s, output queue size 12
progress 30% @chr5:106000001, elapsed 0.5s, est remaining 1.2s, peak mem 258MB, user 1.4s, sys 13.8s, output queue size 4
progress 35% @chr6:80000001, elapsed 0.6s, est remaining 1.1s, peak mem 265MB, user 1.6s, sys 16.1s, output queue size 28
progress 40% @chr7:51000001, elapsed 0.7s, est remaining 1.0s, peak mem 268MB, user 1.8s, sys 18.4s, output queue size 5
progress 45% @chr8:51000001, elapsed 0.8s, est remaining 0.9s, peak mem 274MB, user 2.1s, sys 20.5s, output queue size 6
progress 50% @chr9:69000001, elapsed 0.8s, est remaining 0.8s, peak mem 283MB, user 2.3s, sys 22.9s, output queue size 23
progress 55% @chr10:93000001, elapsed 0.9s, est remaining 0.7s, peak mem 289MB, user 2.4s, sys 25.2s, output queue size 9
progress 60% @chr12:5000001, elapsed 1.0s, est remaining 0.7s, peak mem 291MB, user 2.6s, sys 27.4s, output queue size 35
progress 65% @chr13:32000001, elapsed 1.1s, est remaining 0.6s, peak mem 292MB, user 2.8s, sys 29.8s, output queue size 6
progress 70% @chr14:55000001, elapsed 1.2s, est remaining 0.5s, peak mem 298MB, user 3.1s, sys 32.1s, output queue size 22
progress 75% @chr16:8000001, elapsed 1.2s, est remaining 0.4s, peak mem 300MB, user 3.2s, sys 34.5s, output queue size 5
progress 80% @chr17:81000001, elapsed 1.3s, est remaining 0.3s, peak mem 301MB, user 3.5s, sys 36.7s, output queue size 20
progress 85% @chr20:15000001, elapsed 1.4s, est remaining 0.2s, peak mem 304MB, user 3.7s, sys 39.1s, output queue size 7
progress 90% @chr21:29000001, elapsed 1.6s, est remaining 0.2s, peak mem 520MB, user 5.7s, sys 40.4s, output queue size 114
progress 95% @chrY:46000001, elapsed 1.7s, est remaining 0.1s, peak mem 552MB, user 7.2s, sys 41.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 579MB, user 12.5s, sys 43.3s, 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 6.12.88
cpu vendor: GenuineIntel
signature: 000c06f2
features: bfebfbff 7ffefbff
extended: f3bfb7ef fb417ffe
amd bits: 2c100800 00000121
brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.001 user 0.016 sys 0.019 real
MateInfoByVcf::load: 23378 calls 3.864 user 0.672 sys 3.576 real
MateInfoByVcf::parse_events: 23378 calls 3.819 user 0.618 sys 3.481 real
advance: 3219322 calls 1.150 user 5.104 sys 6.865 real
calc: 3219322 calls 4.424 user 15.561 sys 20.443 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 0.005 sys 2.869 real
fetch: 3219322 calls 0.356 user 5.181 sys 5.636 real
find_pairEnds: 23378 calls 0.233 user 0.016 sys 0.359 real
idle: 2296 calls 0.128 user 0.106 sys 61.162 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 23378 calls 0.864 user 0.070 sys 1.340 real
vcfadvance: 23378 calls 0.012 user 0.043 sys 0.028 real
write: 3219322 calls 2.430 user 5.458 sys 7.615 real
overall: 607391744 mem 13.499 user 44.049 sys 3.904 real