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% @chr1:131000001, elapsed 0.1s, est remaining 1.9s, peak mem 79MB, user 0.2s, sys 2.5s, output queue size 30
progress 10% @chr2:77000001, elapsed 0.2s, est remaining 1.7s, peak mem 79MB, user 0.5s, sys 4.9s, output queue size 22
progress 15% @chr3:1, elapsed 0.3s, est remaining 1.6s, peak mem 79MB, user 0.8s, sys 7.2s, output queue size 14
progress 20% @chr3:162000001, elapsed 0.4s, est remaining 1.5s, peak mem 79MB, user 1.0s, sys 9.8s, output queue size 23
progress 25% @chr4:116000001, elapsed 0.5s, est remaining 1.4s, peak mem 79MB, user 1.3s, sys 12.3s, output queue size 20
progress 30% @chr5:92000001, elapsed 0.5s, est remaining 1.3s, peak mem 79MB, user 1.5s, sys 14.9s, output queue size 19
progress 35% @chr6:72000001, elapsed 0.6s, est remaining 1.2s, peak mem 79MB, user 1.8s, sys 17.6s, output queue size 4
progress 40% @chr7:59000001, elapsed 0.7s, est remaining 1.1s, peak mem 79MB, user 2.0s, sys 20.4s, output queue size 12
progress 45% @chr8:65000001, elapsed 0.8s, est remaining 1.0s, peak mem 79MB, user 2.3s, sys 23.0s, output queue size 16
progress 50% @chr9:79000001, elapsed 0.9s, est remaining 0.9s, peak mem 79MB, user 2.5s, sys 25.7s, output queue size 17
progress 55% @chr10:74000001, elapsed 1.0s, est remaining 0.8s, peak mem 79MB, user 2.8s, sys 28.3s, output queue size 21
progress 60% @chr11:129000001, elapsed 1.1s, est remaining 0.7s, peak mem 79MB, user 3.0s, sys 30.9s, output queue size 21
progress 65% @chr13:17000001, elapsed 1.2s, est remaining 0.7s, peak mem 79MB, user 3.3s, sys 33.5s, output queue size 18
progress 70% @chr14:68000001, elapsed 1.3s, est remaining 0.6s, peak mem 79MB, user 3.5s, sys 36.0s, output queue size 18
progress 75% @chr16:19000001, elapsed 1.4s, est remaining 0.5s, peak mem 79MB, user 3.7s, sys 38.7s, output queue size 20
progress 80% @chr18:1000001, elapsed 1.5s, est remaining 0.4s, peak mem 79MB, user 4.1s, sys 41.2s, output queue size 11
progress 85% @chr20:26000001, elapsed 1.6s, est remaining 0.3s, peak mem 79MB, user 4.3s, sys 44.0s, output queue size 22
progress 90% @chrX:32000001, elapsed 1.7s, est remaining 0.2s, peak mem 114MB, user 4.8s, sys 46.5s, output queue size 114
progress 95% @chrY:29000001, elapsed 1.8s, est remaining 0.1s, peak mem 141MB, user 5.3s, sys 49.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.1s, est remaining 0.0s, peak mem 180MB, user 6.1s, sys 54.2s, 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: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.032 user 0.006 sys 0.046 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.576 user 10.377 sys 12.847 real
calc: 3219322 calls 0.368 user 8.436 sys 9.644 real
done: 1 calls 0.032 user 0.006 sys 0.046 real
execute: 1 calls 0.001 user 0.001 sys 2.127 real
fetch: 3219322 calls 0.346 user 8.284 sys 9.663 real
idle: 72 calls 0.003 user 0.012 sys 35.819 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 227430400 mem 6.252 user 54.716 sys 3.190 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% @chr1:167000001, elapsed 0.1s, est remaining 2.2s, peak mem 187MB, user 0.4s, sys 2.5s, output queue size 17
progress 10% @chr2:79000001, elapsed 0.2s, est remaining 1.8s, peak mem 209MB, user 0.8s, sys 4.9s, output queue size 14
progress 15% @chr2:239000001, elapsed 0.3s, est remaining 1.7s, peak mem 235MB, user 1.2s, sys 7.2s, output queue size 13
progress 20% @chr3:159000001, elapsed 0.4s, est remaining 1.5s, peak mem 244MB, user 1.5s, sys 9.5s, output queue size 17
progress 25% @chr4:120000001, elapsed 0.5s, est remaining 1.4s, peak mem 247MB, user 1.8s, sys 11.9s, output queue size 11
progress 30% @chr5:93000001, elapsed 0.6s, est remaining 1.3s, peak mem 254MB, user 2.1s, sys 14.2s, output queue size 16
progress 35% @chr6:70000001, elapsed 0.6s, est remaining 1.2s, peak mem 259MB, user 2.4s, sys 16.5s, output queue size 23
progress 40% @chr7:59000001, elapsed 0.7s, est remaining 1.1s, peak mem 263MB, user 2.9s, sys 18.8s, output queue size 16
progress 45% @chr8:56000001, elapsed 0.8s, est remaining 1.0s, peak mem 272MB, user 3.3s, sys 21.1s, output queue size 15
progress 50% @chr9:77000001, elapsed 0.9s, est remaining 0.9s, peak mem 281MB, user 3.6s, sys 23.5s, output queue size 26
progress 55% @chr10:102000001, elapsed 1.0s, est remaining 0.8s, peak mem 284MB, user 4.0s, sys 25.7s, output queue size 14
progress 60% @chr11:132000001, elapsed 1.1s, est remaining 0.7s, peak mem 286MB, user 4.4s, sys 27.9s, output queue size 26
progress 65% @chr12:126000001, elapsed 1.2s, est remaining 0.6s, peak mem 287MB, user 4.7s, sys 30.3s, output queue size 23
progress 70% @chr14:66000001, elapsed 1.2s, est remaining 0.5s, peak mem 290MB, user 5.0s, sys 32.6s, output queue size 20
progress 75% @chr16:7000001, elapsed 1.3s, est remaining 0.4s, peak mem 290MB, user 5.3s, sys 35.6s, output queue size 24
progress 80% @chr18:5000001, elapsed 1.4s, est remaining 0.4s, peak mem 292MB, user 5.6s, sys 38.2s, output queue size 18
progress 85% @chr20:25000001, elapsed 1.5s, est remaining 0.3s, peak mem 296MB, user 5.8s, sys 40.5s, output queue size 37
progress 90% @chrX:38000001, elapsed 1.7s, est remaining 0.2s, peak mem 512MB, user 8.1s, sys 41.9s, output queue size 114
progress 95% @chrY:36000001, elapsed 1.8s, est remaining 0.1s, peak mem 533MB, user 9.7s, sys 43.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 566MB, user 14.8s, sys 45.0s, 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: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.001 user 0.011 sys 0.021 real
MateInfoByVcf::load: 23378 calls 3.872 user 0.709 sys 3.603 real
MateInfoByVcf::parse_events: 23378 calls 3.798 user 0.663 sys 3.500 real
advance: 3219322 calls 1.123 user 5.367 sys 7.443 real
calc: 3219322 calls 4.961 user 15.597 sys 21.692 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 0.002 user 0.001 sys 2.862 real
fetch: 3219322 calls 0.435 user 5.369 sys 6.361 real
find_pairEnds: 23378 calls 0.212 user 0.004 sys 0.341 real
idle: 2166 calls 0.212 user 0.175 sys 56.454 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.893 user 0.062 sys 1.321 real
vcfadvance: 23378 calls 0.016 user 0.038 sys 0.034 real
write: 3219322 calls 2.357 user 5.509 sys 7.680 real
overall: 594042880 mem 15.837 user 46.185 sys 3.879 real