cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_BL.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.1s, est remaining 2.2s, peak mem 78MB, user 0.2s, sys 2.8s, output queue size 1
progress 10% @chr2:71000001, elapsed 0.2s, est remaining 1.9s, peak mem 78MB, user 0.3s, sys 5.8s, output queue size 2
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.8s, peak mem 78MB, user 0.6s, sys 8.8s, output queue size 3
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.7s, peak mem 78MB, user 0.7s, sys 11.8s, output queue size 1
progress 25% @chr4:115000001, elapsed 0.5s, est remaining 1.6s, peak mem 78MB, user 1.0s, sys 14.8s, output queue size 6
progress 30% @chr5:85000001, elapsed 0.6s, est remaining 1.5s, peak mem 78MB, user 1.1s, sys 17.9s, output queue size 1
progress 35% @chr6:64000001, elapsed 0.7s, est remaining 1.4s, peak mem 78MB, user 1.3s, sys 21.2s, output queue size 4
progress 40% @chr7:41000001, elapsed 0.9s, est remaining 1.3s, peak mem 78MB, user 1.5s, sys 24.6s, output queue size 17
progress 45% @chr8:44000001, elapsed 1.1s, est remaining 1.3s, peak mem 78MB, user 1.6s, sys 30.6s, output queue size 14
progress 50% @chr9:60000001, elapsed 1.3s, est remaining 1.3s, peak mem 78MB, user 1.9s, sys 36.3s, output queue size 31
progress 55% @chr10:82000001, elapsed 1.5s, est remaining 1.2s, peak mem 78MB, user 2.1s, sys 42.1s, output queue size 13
progress 60% @chr12:7000001, elapsed 1.7s, est remaining 1.1s, peak mem 78MB, user 2.4s, sys 48.0s, output queue size 12
progress 65% @chr13:31000001, elapsed 1.9s, est remaining 1.0s, peak mem 78MB, user 2.6s, sys 53.9s, output queue size 19
progress 70% @chr14:65000001, elapsed 2.1s, est remaining 0.9s, peak mem 78MB, user 2.8s, sys 59.9s, output queue size 7
progress 75% @chr16:32000001, elapsed 2.2s, est remaining 0.7s, peak mem 78MB, user 3.0s, sys 65.5s, output queue size 10
progress 80% @chr17:67000001, elapsed 2.4s, est remaining 0.6s, peak mem 78MB, user 3.3s, sys 71.1s, output queue size 17
progress 85% @chr20:13000001, elapsed 2.6s, est remaining 0.5s, peak mem 78MB, user 3.5s, sys 76.6s, output queue size 15
progress 90% @chrX:46000001, elapsed 2.9s, est remaining 0.3s, peak mem 87MB, user 4.2s, sys 81.1s, output queue size 114
progress 95% @chrY:21000001, elapsed 3.1s, est remaining 0.2s, peak mem 111MB, user 4.5s, sys 87.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.5s, est remaining 0.0s, peak mem 174MB, user 5.3s, sys 96.2s, 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: 50411654
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.039 user 0.000 sys 0.048 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.287 user 21.241 sys 22.489 real
calc: 3219322 calls 0.355 user 15.055 sys 15.171 real
done: 1 calls 0.039 user 0.000 sys 0.048 real
execute: 1 calls 0.001 user 0.002 sys 3.514 real
fetch: 3219322 calls 0.329 user 15.182 sys 15.123 real
idle: 81 calls 0.018 user 0.028 sys 37.043 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 225681408 mem 5.497 user 96.861 sys 4.581 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_BL.md.score --metrics HCC1395_BL.md.metrics HCC1395_BL.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:166000001, elapsed 0.3s, est remaining 6.2s, peak mem 171MB, user 0.5s, sys 8.4s, output queue size 3
progress 10% @chr2:71000001, elapsed 0.6s, est remaining 5.3s, peak mem 189MB, user 0.9s, sys 16.4s, output queue size 3
progress 15% @chr2:235000001, elapsed 0.8s, est remaining 4.7s, peak mem 198MB, user 1.1s, sys 23.8s, output queue size 8
progress 20% @chr3:158000001, elapsed 1.1s, est remaining 4.3s, peak mem 213MB, user 1.4s, sys 31.1s, output queue size 7
progress 25% @chr4:112000001, elapsed 1.3s, est remaining 4.0s, peak mem 216MB, user 1.7s, sys 38.3s, output queue size 4
progress 30% @chr5:89000001, elapsed 1.6s, est remaining 3.6s, peak mem 219MB, user 2.0s, sys 45.3s, output queue size 9
progress 35% @chr6:67000001, elapsed 1.8s, est remaining 3.3s, peak mem 225MB, user 2.4s, sys 52.4s, output queue size 8
progress 40% @chr7:58000001, elapsed 2.0s, est remaining 3.1s, peak mem 231MB, user 2.7s, sys 59.4s, output queue size 12
progress 45% @chr8:70000001, elapsed 2.3s, est remaining 2.8s, peak mem 237MB, user 3.1s, sys 65.9s, output queue size 27
progress 50% @chr9:81000001, elapsed 2.5s, est remaining 2.5s, peak mem 240MB, user 3.3s, sys 72.7s, output queue size 32
progress 55% @chr10:54000001, elapsed 2.7s, est remaining 2.2s, peak mem 243MB, user 3.5s, sys 79.2s, output queue size 41
progress 60% @chr11:134000001, elapsed 2.9s, est remaining 2.0s, peak mem 243MB, user 3.9s, sys 85.9s, output queue size 34
progress 65% @chr13:27000001, elapsed 3.2s, est remaining 1.7s, peak mem 243MB, user 4.2s, sys 92.8s, output queue size 37
progress 70% @chr14:71000001, elapsed 3.4s, est remaining 1.5s, peak mem 243MB, user 4.5s, sys 99.7s, output queue size 25
progress 75% @chr15:89000001, elapsed 3.6s, est remaining 1.2s, peak mem 243MB, user 4.8s, sys 106.7s, output queue size 26
progress 80% @chr18:6000001, elapsed 3.9s, est remaining 1.0s, peak mem 246MB, user 5.0s, sys 113.9s, output queue size 23
progress 85% @chr20:32000001, elapsed 4.1s, est remaining 0.7s, peak mem 249MB, user 5.4s, sys 121.1s, output queue size 18
progress 90% @chrX:40000001, elapsed 4.5s, est remaining 0.5s, peak mem 486MB, user 8.3s, sys 126.8s, output queue size 114
progress 95% @chrY:35000001, elapsed 4.7s, est remaining 0.2s, peak mem 492MB, user 11.6s, sys 132.1s, output queue size 271
progress 100% @chr21:41000001, elapsed 5.7s, est remaining 0.0s, peak mem 504MB, user 15.0s, sys 139.4s, output queue size 3664
library HCC1395_BL:
chimeric_paired 873
duped 146553
duped_chimeric_paired 2
duped_paired 146548
duped_unpaired 5
optical_dup 4835
paired 999974
reads 1001089
secondary_supplementary 1097
unmapped 9
unpaired 9
optical dup clusters 4702, maxdup 7, total optical dup pairs 4835
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: 50411654
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.021 user 0.045 sys 0.083 real
MateInfoByVcf::load: 25531 calls 4.263 user 1.456 sys 4.630 real
MateInfoByVcf::parse_events: 25531 calls 4.162 user 1.319 sys 4.268 real
advance: 3219322 calls 1.130 user 17.432 sys 18.970 real
calc: 3219322 calls 4.927 user 49.583 sys 55.916 real
done: 1 calls 0.002 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.003 sys 5.743 real
fetch: 3219322 calls 0.379 user 17.205 sys 17.494 real
find_pairEnds: 25531 calls 0.239 user 0.072 sys 0.405 real
idle: 917 calls 0.051 user 0.194 sys 50.557 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 25531 calls 0.916 user 0.335 sys 1.630 real
vcfadvance: 25531 calls 0.015 user 0.155 sys 0.146 real
write: 3219322 calls 2.647 user 15.993 sys 19.479 real
overall: 528576512 mem 15.450 user 140.705 sys 6.757 real