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% @chr1:159000001, elapsed 0.1s, est remaining 1.6s, peak mem 81MB, user 0.1s, sys 2.0s, output queue size 2
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 1.4s, peak mem 81MB, user 0.3s, sys 4.2s, output queue size 13
progress 15% @chr2:235000001, elapsed 0.2s, est remaining 1.3s, peak mem 81MB, user 0.5s, sys 6.3s, output queue size 4
progress 20% @chr3:152000001, elapsed 0.3s, est remaining 1.2s, peak mem 81MB, user 0.6s, sys 8.4s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.4s, est remaining 1.1s, peak mem 81MB, user 0.8s, sys 10.6s, output queue size 1
progress 30% @chr5:82000001, elapsed 0.5s, est remaining 1.1s, peak mem 81MB, user 0.9s, sys 12.8s, output queue size 7
progress 35% @chr6:64000001, elapsed 0.5s, est remaining 1.0s, peak mem 81MB, user 1.1s, sys 15.0s, output queue size 1
progress 40% @chr7:54000001, elapsed 0.6s, est remaining 0.9s, peak mem 81MB, user 1.4s, sys 17.0s, output queue size 1
progress 45% @chr8:47000001, elapsed 0.7s, est remaining 0.9s, peak mem 81MB, user 1.6s, sys 19.7s, output queue size 10
progress 50% @chr9:61000001, elapsed 0.9s, est remaining 0.9s, peak mem 81MB, user 1.9s, sys 24.5s, output queue size 23
progress 55% @chr10:118000001, elapsed 1.1s, est remaining 0.9s, peak mem 81MB, user 2.1s, sys 29.9s, output queue size 11
progress 60% @chr11:95000001, elapsed 1.3s, est remaining 0.8s, peak mem 81MB, user 2.3s, sys 35.5s, output queue size 28
progress 65% @chr13:7000001, elapsed 1.4s, est remaining 0.8s, peak mem 81MB, user 2.5s, sys 41.3s, output queue size 9
progress 70% @chr14:55000001, elapsed 1.6s, est remaining 0.7s, peak mem 81MB, user 2.8s, sys 47.1s, output queue size 6
progress 75% @chr16:23000001, elapsed 1.8s, est remaining 0.6s, peak mem 81MB, user 2.9s, sys 52.8s, output queue size 6
progress 80% @chr17:78000001, elapsed 2.0s, est remaining 0.5s, peak mem 81MB, user 3.1s, sys 58.5s, output queue size 11
progress 85% @chr20:19000001, elapsed 2.2s, est remaining 0.4s, peak mem 81MB, user 3.3s, sys 64.1s, output queue size 3
progress 90% @chrX:19000001, elapsed 2.4s, est remaining 0.3s, peak mem 105MB, user 4.0s, sys 68.8s, output queue size 114
progress 95% @chrY:50000001, elapsed 2.7s, est remaining 0.1s, peak mem 138MB, user 4.3s, sys 74.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.0s, est remaining 0.0s, peak mem 171MB, user 5.1s, sys 83.4s, 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: 50411660
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.034 user 0.013 sys 0.053 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.387 user 17.410 sys 18.573 real
calc: 3219322 calls 0.435 user 13.536 sys 13.772 real
done: 1 calls 0.034 user 0.013 sys 0.053 real
execute: 1 calls 0.000 user 0.001 sys 3.009 real
fetch: 3219322 calls 0.423 user 13.121 sys 13.780 real
idle: 78 calls 0.011 user 0.012 sys 34.860 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 229740544 mem 5.285 user 84.041 sys 4.074 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% @chr1:167000001, elapsed 0.3s, est remaining 6.3s, peak mem 171MB, user 0.5s, sys 8.6s, output queue size 10
progress 10% @chr2:72000001, elapsed 0.6s, est remaining 5.4s, peak mem 189MB, user 0.8s, sys 16.7s, output queue size 2
progress 15% @chr2:230000001, elapsed 0.9s, est remaining 5.0s, peak mem 219MB, user 1.2s, sys 24.7s, output queue size 5
progress 20% @chr3:159000001, elapsed 1.1s, est remaining 4.6s, peak mem 243MB, user 1.5s, sys 32.7s, output queue size 14
progress 25% @chr4:123000001, elapsed 1.4s, est remaining 4.2s, peak mem 246MB, user 1.8s, sys 40.6s, output queue size 7
progress 30% @chr5:87000001, elapsed 1.7s, est remaining 3.9s, peak mem 252MB, user 2.2s, sys 48.6s, output queue size 12
progress 35% @chr6:69000001, elapsed 2.0s, est remaining 3.6s, peak mem 252MB, user 2.5s, sys 56.7s, output queue size 7
progress 40% @chr7:53000001, elapsed 2.2s, est remaining 3.4s, peak mem 255MB, user 2.9s, sys 65.4s, output queue size 2
progress 45% @chr8:55000001, elapsed 2.5s, est remaining 3.1s, peak mem 258MB, user 3.3s, sys 73.9s, output queue size 7
progress 50% @chr9:74000001, elapsed 2.8s, est remaining 2.8s, peak mem 261MB, user 3.6s, sys 82.3s, output queue size 2
progress 55% @chr10:93000001, elapsed 3.1s, est remaining 2.5s, peak mem 261MB, user 3.9s, sys 90.7s, output queue size 4
progress 60% @chr11:123000001, elapsed 3.4s, est remaining 2.3s, peak mem 261MB, user 4.2s, sys 99.3s, output queue size 4
progress 65% @chr13:9000001, elapsed 3.7s, est remaining 2.0s, peak mem 264MB, user 4.5s, sys 108.1s, output queue size 6
progress 70% @chr14:52000001, elapsed 4.0s, est remaining 1.7s, peak mem 264MB, user 4.9s, sys 116.8s, output queue size 9
progress 75% @chr16:15000001, elapsed 4.3s, est remaining 1.4s, peak mem 267MB, user 5.1s, sys 125.6s, output queue size 9
progress 80% @chr18:4000001, elapsed 4.5s, est remaining 1.1s, peak mem 270MB, user 5.5s, sys 134.3s, output queue size 5
progress 85% @chr20:17000001, elapsed 4.8s, est remaining 0.9s, peak mem 273MB, user 5.8s, sys 142.9s, output queue size 5
progress 90% @chrX:35000001, elapsed 5.3s, est remaining 0.6s, peak mem 495MB, user 9.4s, sys 148.9s, output queue size 114
progress 95% @chrY:22000001, elapsed 5.6s, est remaining 0.3s, peak mem 516MB, user 12.9s, sys 156.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 6.6s, est remaining 0.0s, peak mem 528MB, user 16.2s, sys 165.0s, 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: 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: 50411660
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.006 user 0.031 sys 0.082 real
MateInfoByVcf::load: 25531 calls 4.461 user 1.529 sys 4.894 real
MateInfoByVcf::parse_events: 25531 calls 4.343 user 1.380 sys 4.486 real
advance: 3219322 calls 1.331 user 21.886 sys 22.994 real
calc: 3219322 calls 5.133 user 62.619 sys 68.306 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.002 sys 6.652 real
fetch: 3219322 calls 0.539 user 21.228 sys 15.937 real
find_pairEnds: 25531 calls 0.201 user 0.050 sys 0.428 real
idle: 980 calls 0.049 user 0.199 sys 51.929 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 25531 calls 0.898 user 0.317 sys 1.867 real
vcfadvance: 25531 calls 0.021 user 0.192 sys 0.205 real
write: 3219322 calls 2.767 user 21.750 sys 22.996 real
overall: 553746432 mem 16.680 user 166.362 sys 7.671 real