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 0.2s, est remaining 3.3s, peak mem 81MB, user 0.3s, sys 4.3s, output queue size 10
progress 10% @chr2:72000001, elapsed 0.3s, est remaining 3.1s, peak mem 81MB, user 0.5s, sys 9.1s, output queue size 1
progress 15% @chr2:232000001, elapsed 0.5s, est remaining 3.0s, peak mem 81MB, user 0.8s, sys 14.6s, output queue size 3
progress 20% @chr3:153000001, elapsed 0.7s, est remaining 3.0s, peak mem 81MB, user 1.0s, sys 20.9s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.9s, est remaining 2.8s, peak mem 81MB, user 1.3s, sys 26.7s, output queue size 1
progress 30% @chr5:86000001, elapsed 1.1s, est remaining 2.5s, peak mem 81MB, user 1.5s, sys 31.1s, output queue size 4
progress 35% @chr6:63000001, elapsed 1.2s, est remaining 2.3s, peak mem 81MB, user 1.8s, sys 35.2s, output queue size 2
progress 40% @chr7:53000001, elapsed 1.4s, est remaining 2.1s, peak mem 81MB, user 2.1s, sys 40.2s, output queue size 2
progress 45% @chr8:56000001, elapsed 1.6s, est remaining 1.9s, peak mem 81MB, user 2.4s, sys 44.9s, output queue size 1
progress 50% @chr9:75000001, elapsed 1.7s, est remaining 1.7s, peak mem 81MB, user 2.7s, sys 49.4s, output queue size 1
progress 55% @chr10:95000001, elapsed 1.9s, est remaining 1.5s, peak mem 81MB, user 3.0s, sys 54.3s, output queue size 1
progress 60% @chr11:123000001, elapsed 2.0s, est remaining 1.4s, peak mem 81MB, user 3.2s, sys 59.1s, output queue size 7
progress 65% @chr13:13000001, elapsed 2.2s, est remaining 1.2s, peak mem 81MB, user 3.4s, sys 64.2s, output queue size 2
progress 70% @chr14:61000001, elapsed 2.4s, est remaining 1.0s, peak mem 81MB, user 3.7s, sys 69.3s, output queue size 2
progress 75% @chr16:12000001, elapsed 2.6s, est remaining 0.9s, peak mem 81MB, user 3.9s, sys 74.5s, output queue size 1
progress 80% @chr17:81000001, elapsed 2.7s, est remaining 0.7s, peak mem 81MB, user 4.2s, sys 78.9s, output queue size 3
progress 85% @chr20:20000001, elapsed 2.9s, est remaining 0.5s, peak mem 81MB, user 4.4s, sys 83.9s, output queue size 2
progress 90% @chrX:31000001, elapsed 3.2s, est remaining 0.4s, peak mem 126MB, user 5.4s, sys 90.2s, output queue size 114
progress 95% @chrY:30000001, elapsed 3.5s, est remaining 0.2s, peak mem 166MB, user 5.8s, sys 98.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.9s, est remaining 0.0s, peak mem 190MB, user 7.0s, sys 107.6s, 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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784676
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.009 user 0.043 sys 0.061 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.981 user 22.058 sys 24.003 real
calc: 3219322 calls 0.568 user 16.850 sys 17.954 real
done: 1 calls 0.009 user 0.043 sys 0.061 real
execute: 1 calls 0.001 user 0.001 sys 3.864 real
fetch: 3219322 calls 0.707 user 17.442 sys 18.050 real
idle: 81 calls 0.003 user 0.013 sys 34.498 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 230776832 mem 7.149 user 108.617 sys 4.941 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% @chr1:160000001, elapsed 0.3s, est remaining 6.6s, peak mem 192MB, user 0.6s, sys 8.8s, output queue size 3
progress 10% @chr2:73000001, elapsed 0.6s, est remaining 5.2s, peak mem 224MB, user 1.0s, sys 16.0s, output queue size 1
progress 15% @chr2:232000001, elapsed 0.8s, est remaining 4.4s, peak mem 243MB, user 1.4s, sys 21.7s, output queue size 9
progress 20% @chr3:151000001, elapsed 1.0s, est remaining 4.0s, peak mem 254MB, user 1.8s, sys 28.1s, output queue size 2
progress 25% @chr4:114000001, elapsed 1.3s, est remaining 3.9s, peak mem 260MB, user 2.4s, sys 36.8s, output queue size 1
progress 30% @chr5:83000001, elapsed 1.6s, est remaining 3.7s, peak mem 269MB, user 2.7s, sys 44.5s, output queue size 3
progress 35% @chr6:55000001, elapsed 1.8s, est remaining 3.3s, peak mem 275MB, user 3.1s, sys 50.5s, output queue size 10
progress 40% @chr7:57000001, elapsed 2.0s, est remaining 2.9s, peak mem 278MB, user 3.4s, sys 56.3s, output queue size 7
progress 45% @chr8:57000001, elapsed 2.2s, est remaining 2.7s, peak mem 284MB, user 3.8s, sys 62.5s, output queue size 3
progress 50% @chr9:71000001, elapsed 2.4s, est remaining 2.4s, peak mem 291MB, user 4.1s, sys 68.6s, output queue size 2
progress 55% @chr10:94000001, elapsed 2.6s, est remaining 2.1s, peak mem 294MB, user 4.6s, sys 74.9s, output queue size 1
progress 60% @chr11:121000001, elapsed 2.8s, est remaining 1.9s, peak mem 299MB, user 5.0s, sys 80.7s, output queue size 2
progress 65% @chr13:13000001, elapsed 3.1s, est remaining 1.7s, peak mem 303MB, user 5.4s, sys 88.3s, output queue size 2
progress 70% @chr14:60000001, elapsed 3.3s, est remaining 1.4s, peak mem 306MB, user 5.8s, sys 96.2s, output queue size 1
progress 75% @chr16:10000001, elapsed 3.6s, est remaining 1.2s, peak mem 312MB, user 6.1s, sys 103.6s, output queue size 7
progress 80% @chr18:1, elapsed 3.8s, est remaining 1.0s, peak mem 312MB, user 6.5s, sys 111.2s, output queue size 2
progress 85% @chr20:25000001, elapsed 4.1s, est remaining 0.7s, peak mem 320MB, user 6.8s, sys 118.4s, output queue size 6
progress 90% @chrX:36000001, elapsed 4.5s, est remaining 0.5s, peak mem 522MB, user 10.4s, sys 123.6s, output queue size 114
progress 95% @chrY:27000001, elapsed 4.8s, est remaining 0.3s, peak mem 548MB, user 14.1s, sys 128.8s, output queue size 271
progress 100% @chr21:41000001, elapsed 5.5s, est remaining 0.0s, peak mem 567MB, user 18.6s, sys 134.6s, 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: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784676
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.012 user 0.035 sys 0.076 real
MateInfoByVcf::load: 23378 calls 4.965 user 1.779 sys 5.452 real
MateInfoByVcf::parse_events: 23378 calls 4.880 user 1.629 sys 5.089 real
advance: 3219322 calls 1.658 user 16.334 sys 19.427 real
calc: 3219322 calls 6.052 user 48.953 sys 55.846 real
done: 1 calls 0.002 user 0.000 sys 0.005 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.002 sys 5.535 real
fetch: 3219322 calls 0.621 user 16.174 sys 17.017 real
find_pairEnds: 23378 calls 0.357 user 0.039 sys 0.511 real
idle: 1104 calls 0.299 user 0.502 sys 43.577 real
init: 1 calls 0.010 user 0.000 sys 0.008 real
markDup: 23378 calls 1.264 user 0.317 sys 2.216 real
vcfadvance: 23378 calls 0.023 user 0.155 sys 0.167 real
write: 3219322 calls 2.838 user 16.239 sys 19.189 real
overall: 595234816 mem 19.639 user 136.818 sys 6.554 real