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% @chr1:163000001, elapsed 0.1s, est remaining 1.7s, peak mem 78MB, user 0.1s, sys 2.2s, output queue size 5
progress 10% @chr2:78000001, elapsed 0.2s, est remaining 1.5s, peak mem 78MB, user 0.2s, sys 4.4s, output queue size 33
progress 15% @chr2:237000001, elapsed 0.2s, est remaining 1.4s, peak mem 78MB, user 0.3s, sys 6.8s, output queue size 24
progress 20% @chr3:156000001, elapsed 0.3s, est remaining 1.3s, peak mem 78MB, user 0.5s, sys 9.1s, output queue size 8
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.2s, peak mem 78MB, user 0.6s, sys 11.3s, output queue size 3
progress 30% @chr5:85000001, elapsed 0.5s, est remaining 1.1s, peak mem 78MB, user 0.8s, sys 13.5s, output queue size 3
progress 35% @chr6:64000001, elapsed 0.6s, est remaining 1.0s, peak mem 78MB, user 0.9s, sys 15.8s, output queue size 1
progress 40% @chr7:54000001, elapsed 0.6s, est remaining 0.9s, peak mem 78MB, user 1.0s, sys 18.1s, output queue size 13
progress 45% @chr8:56000001, elapsed 0.7s, est remaining 0.9s, peak mem 78MB, user 1.1s, sys 20.4s, output queue size 4
progress 50% @chr9:70000001, elapsed 0.8s, est remaining 0.8s, peak mem 78MB, user 1.2s, sys 22.7s, output queue size 3
progress 55% @chr10:94000001, elapsed 0.9s, est remaining 0.7s, peak mem 78MB, user 1.3s, sys 25.0s, output queue size 1
progress 60% @chr11:122000001, elapsed 0.9s, est remaining 0.6s, peak mem 78MB, user 1.5s, sys 27.3s, output queue size 2
progress 65% @chr13:14000001, elapsed 1.0s, est remaining 0.6s, peak mem 78MB, user 1.6s, sys 29.6s, output queue size 1
progress 70% @chr14:60000001, elapsed 1.1s, est remaining 0.5s, peak mem 78MB, user 1.7s, sys 31.9s, output queue size 1
progress 75% @chr16:14000001, elapsed 1.2s, est remaining 0.4s, peak mem 78MB, user 1.8s, sys 34.2s, output queue size 8
progress 80% @chr17:74000001, elapsed 1.3s, est remaining 0.3s, peak mem 78MB, user 1.9s, sys 36.8s, output queue size 10
progress 85% @chr20:7000001, elapsed 1.4s, est remaining 0.3s, peak mem 78MB, user 2.1s, sys 41.1s, output queue size 15
progress 90% @chrX:42000001, elapsed 1.7s, est remaining 0.2s, peak mem 81MB, user 2.7s, sys 45.5s, output queue size 114
progress 95% @chrY:41000001, elapsed 1.8s, est remaining 0.1s, peak mem 102MB, user 3.2s, sys 49.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.2s, est remaining 0.0s, peak mem 171MB, user 4.0s, sys 57.6s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.036 user 0.000 sys 0.049 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.384 user 14.039 sys 15.132 real
calc: 3219322 calls 0.302 user 9.331 sys 8.799 real
done: 1 calls 0.036 user 0.000 sys 0.049 real
execute: 1 calls 0.004 user 0.004 sys 2.220 real
fetch: 3219322 calls 0.331 user 9.025 sys 8.817 real
idle: 80 calls 0.019 user 0.030 sys 37.476 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 214908928 mem 4.159 user 58.021 sys 3.280 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% @chr1:143000001, elapsed 0.3s, est remaining 5.2s, peak mem 159MB, user 0.5s, sys 6.6s, output queue size 18
progress 10% @chr2:99000001, elapsed 0.5s, est remaining 4.5s, peak mem 192MB, user 0.9s, sys 13.3s, output queue size 30
progress 15% @chr2:221000001, elapsed 0.7s, est remaining 4.1s, peak mem 207MB, user 1.2s, sys 19.9s, output queue size 23
progress 20% @chr3:177000001, elapsed 0.9s, est remaining 3.8s, peak mem 219MB, user 1.5s, sys 26.5s, output queue size 23
progress 25% @chr4:101000001, elapsed 1.2s, est remaining 3.5s, peak mem 225MB, user 1.8s, sys 33.1s, output queue size 31
progress 30% @chr5:71000001, elapsed 1.4s, est remaining 3.2s, peak mem 231MB, user 2.1s, sys 39.7s, output queue size 36
progress 35% @chr6:54000001, elapsed 1.6s, est remaining 3.0s, peak mem 231MB, user 2.4s, sys 46.4s, output queue size 14
progress 40% @chr7:67000001, elapsed 1.8s, est remaining 2.8s, peak mem 246MB, user 2.6s, sys 53.3s, output queue size 11
progress 45% @chr8:51000001, elapsed 2.1s, est remaining 2.5s, peak mem 255MB, user 3.0s, sys 60.3s, output queue size 8
progress 50% @chr9:80000001, elapsed 2.3s, est remaining 2.3s, peak mem 255MB, user 3.4s, sys 67.1s, output queue size 4
progress 55% @chr10:100000001, elapsed 2.5s, est remaining 2.1s, peak mem 255MB, user 3.8s, sys 74.0s, output queue size 3
progress 60% @chr11:126000001, elapsed 2.8s, est remaining 1.9s, peak mem 255MB, user 4.1s, sys 80.6s, output queue size 8
progress 65% @chr13:2000001, elapsed 3.0s, est remaining 1.6s, peak mem 255MB, user 4.3s, sys 87.5s, output queue size 13
progress 70% @chr14:51000001, elapsed 3.2s, est remaining 1.4s, peak mem 258MB, user 4.6s, sys 94.4s, output queue size 16
progress 75% @chr16:4000001, elapsed 3.5s, est remaining 1.2s, peak mem 258MB, user 5.0s, sys 101.1s, output queue size 9
progress 80% @chr17:72000001, elapsed 3.7s, est remaining 0.9s, peak mem 258MB, user 5.3s, sys 107.6s, output queue size 12
progress 85% @chr20:22000001, elapsed 3.9s, est remaining 0.7s, peak mem 258MB, user 5.6s, sys 114.2s, output queue size 3
progress 90% @chrX:22000001, elapsed 4.3s, est remaining 0.5s, peak mem 450MB, user 9.1s, sys 118.9s, output queue size 114
progress 95% @chrY:34000001, elapsed 4.5s, est remaining 0.2s, peak mem 480MB, user 11.2s, sys 125.5s, output queue size 271
progress 100% @chr21:41000001, elapsed 5.4s, est remaining 0.0s, peak mem 501MB, user 15.3s, sys 132.4s, 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: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.010 user 0.034 sys 0.069 real
MateInfoByVcf::load: 23378 calls 4.241 user 1.364 sys 4.171 real
MateInfoByVcf::parse_events: 23378 calls 4.130 user 1.176 sys 3.844 real
advance: 3219322 calls 1.192 user 18.938 sys 16.954 real
calc: 3219322 calls 4.843 user 47.504 sys 53.960 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 0.004 user 0.003 sys 5.459 real
fetch: 3219322 calls 0.324 user 18.344 sys 12.668 real
find_pairEnds: 23378 calls 0.273 user 0.076 sys 0.404 real
idle: 1070 calls 0.044 user 0.142 sys 48.941 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 23378 calls 0.905 user 0.340 sys 1.748 real
vcfadvance: 23378 calls 0.025 user 0.118 sys 0.190 real
write: 3219322 calls 2.574 user 13.082 sys 19.962 real
overall: 525492224 mem 16.020 user 133.743 sys 6.485 real